all callers implemented for slurm. testing in progress

pandora-config.example.toml

@@ -227,10 +227,10 @@ clairs_output_dir = "{result_dir}/{id}/diag/ClairS"
 #######################################
 
 # Savana binary (name or full path).
-savana_bin = "savana"
+savana_bin = "/home/t_steimle/.conda/envs/savana_env/bin/savana"
 
 # Threads for Savana.
-savana_threads = 150
+savana_threads = 40
 
 # Savana output directory template.
 # {result_dir}, {id}
@@ -296,13 +296,14 @@ bcftools_threads = 30
 #######################################
 
 # Path to longphase binary.
-longphase_bin = "/data/tools/longphase_linux-x64"
+longphase_bin = "/mnt/beegfs02/scratch/t_steimle/somatic_pipe_tools/longphase_linux-x64"
 
 # Threads for longphase.
-longphase_threads = 40
+longphase_threads = 20
 
 # Threads for longphase modcall step.
-longphase_modcall_threads = 8
+# limit memory usage here
+longphase_modcall_threads = 4
 
 # Force longphase recomputation (haplotagging/phasing).
 longphase_force = false
@@ -317,10 +318,10 @@ longphase_modcall_vcf = "{result_dir}/{id}/{time}/5mC_5hmC/{id}_{time}_5mC_5hmC_
 #######################################
 
 # Path to modkit binary.
-modkit_bin = "modkit"
+modkit_bin = "/mnt/beegfs02/scratch/t_steimle/somatic_pipe_tools/modkit_latest/modkit"
 
 # Threads for `modkit summary`.
-modkit_summary_threads = 50
+modkit_summary_threads = 40
 
 # Modkit summary file template.
 # {result_dir}, {id}, {time}

slurm-2536604.out

@@ -1,833 +0,0 @@
-
-[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4 --region chr10:63341881-134758134 --sample_name DUMCO_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
-
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/split_beds
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/candidates
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/pileup_tensor_can
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/fa_tensor_can
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/vcf_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/tmp_vcf_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/vcf
-[INFO] --include_all_ctgs enabled
-[INFO] Call variants in contigs: chr10
-[INFO] Number of chunks for each contig: 27
-
-[INFO] CALLER VERSION: 0.4.4
-[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
-[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
-[INFO] THREADS: 40
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4
-[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/output.vcf.gz
-[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
-[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
-[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/region.bed
-[INFO] GENOTYPING MODE VCF FILE PATH: None
-[INFO] HYBRID MODE VCF FILE PATH: None
-[INFO] REGION FOR CALLING: chr10:63341881-134758134
-[INFO] CONTIGS FOR CALLING: None
-[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
-[INFO] SAMTOOLS BINARY PATH: samtools
-[INFO] PYTHON BINARY PATH: python3
-[INFO] PYPY BINARY PATH: pypy3
-[INFO] PARALLEL BINARY PATH: parallel
-[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] SNV MINIMUM AF: 0.05
-[INFO] SNV MINIMUM QUAL: 8
-[INFO] INDEL MINIMUM AF: 0.1
-[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
-[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
-[INFO] INDEL MINIMUM QUAL: 8
-[INFO] NORMAL VCF FILE PATH: None
-[INFO] DISABLE PHASING: False
-[INFO] ENABLE DRY RUN: False
-[INFO] ENABLE INDEL CALLING: True
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE PRINTING GERMLINE CALLS: True
-[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-
-[INFO] Call Germline Variants in Normal BAM using Clair3
-[INFO] RUN THE FOLLOWING COMMAND:
-( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output --ctg_name=chr10 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/1_CLAIR3_NORMAL.log
-
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] CLAIR3 VERSION: v1.0.8
-[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output
-[INFO] PLATFORM: ont
-[INFO] THREADS: 40
-[INFO] BED FILE PATH: EMPTY
-[INFO] VCF FILE PATH: EMPTY
-[INFO] CONTIGS: chr10
-[INFO] CONDA PREFIX: 
-[INFO] SAMTOOLS PATH: samtools
-[INFO] PYTHON PATH: python3
-[INFO] PYPY PATH: pypy3
-[INFO] PARALLEL PATH: parallel
-[INFO] WHATSHAP PATH: whatshap
-[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] FULL ALIGN PROPORTION: 0.7
-[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
-[INFO] PHASING PROPORTION: 0.7
-[INFO] MINIMUM MQ: 5
-[INFO] MINIMUM COVERAGE: 4
-[INFO] SNP AF THRESHOLD: 0.08
-[INFO] INDEL AF THRESHOLD: 0.15
-[INFO] BASE ERROR IN GVCF: 0.001
-[INFO] GQ BIN SIZE IN GVCF: 5
-[INFO] ENABLE FILEUP ONLY CALLING: False
-[INFO] ENABLE FAST MODE CALLING: False
-[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE OUTPUT GVCF: False
-[INFO] ENABLE HAPLOID PRECISE MODE: False
-[INFO] ENABLE HAPLOID SENSITIVE MODE: False
-[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
-[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
-[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
-[INFO] ENABLE LONG INDEL CALLING: False
-[INFO] ENABLE C_IMPLEMENT: True
-
-+ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr10 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] Check environment variables
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/merge_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
-[INFO] Call variant in contigs: chr10
-[INFO] Chunk number for each contig: 27
-[INFO] 1/7 Call variants using pileup model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 8/27) : 45826
-Total time elapsed: 104.02 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 13/27) : 46506
-Total time elapsed: 114.35 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 14/27) : 48034
-Total time elapsed: 115.67 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 12/27) : 48340
-Total time elapsed: 116.09 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 17/27) : 50227
-Total time elapsed: 116.94 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 22/27) : 49884
-Total time elapsed: 117.63 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 10/27) : 54843
-Total time elapsed: 119.86 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 24/27) : 53181
-Total time elapsed: 121.26 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 23/27) : 51547
-Total time elapsed: 122.53 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 4/27) : 53706
-Total time elapsed: 122.44 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 19/27) : 52944
-Total time elapsed: 124.83 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 5/27) : 56433
-Total time elapsed: 127.15 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 16/27) : 56555
-Total time elapsed: 127.94 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 18/27) : 50434
-Total time elapsed: 103.09 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 6/27) : 56922
-Total time elapsed: 131.36 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 15/27) : 60420
-Total time elapsed: 133.49 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 25/27) : 56153
-Total time elapsed: 133.36 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 1/27) : 60078
-Total time elapsed: 134.57 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 20/27) : 50606
-Total time elapsed: 108.22 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 7/27) : 52716
-Total time elapsed: 109.48 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 11/27) : 50928
-Total time elapsed: 110.13 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 27/27) : 64119
-Total time elapsed: 138.75 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 9/27) : 62446
-Total time elapsed: 139.40 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 2/27) : 56222
-Total time elapsed: 113.42 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 3/27) : 58962
-Total time elapsed: 118.98 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 21/27) : 59650
-Total time elapsed: 119.24 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 26/27) : 61242
-Total time elapsed: 120.26 s
-
-real	2m35.699s
-user	49m49.438s
-sys	5m19.265s
-
-[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
-[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 18
-[INFO] Total heterozygous SNP positions selected: chr10: 110588
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-real	0m4.020s
-user	0m3.715s
-sys	0m0.222s
-
-[INFO] 3/7 Phase VCF file using LongPhase
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-LongPhase Ver 1.7
-
---- File Parameter --- 
-SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr10.vcf
-SV  File      : 
-MOD File      : 
-REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
-Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr10
-Generate Dot  : False
-BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam 
-
---- Phasing Parameter --- 
-Seq Platform       : ONT
-Phase Indel        : False
-Distance Threshold : 300000
-Connect Adjacent   : 20
-Edge Threshold     : 0.7
-Mapping Quality    : 1
-Variant Confidence : 0.75
-ReadTag Confidence : 0.65
-
-parsing VCF ... 0s
-parsing SV VCF ... 0s
-parsing Meth VCF ... 0s
-reading reference ... 2s
-(chr10,12s)
-parsing total:  12s
-merge results ... 0s
-writeResult SNP ... 1s
-
-total process: 15s
-
-real	0m15.388s
-user	0m29.173s
-sys	0m1.943s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] 5/7 Select candidates for full-alignment calling
-[INFO] Set variants quality cutoff 21.0
-[INFO] Set reference calls quality cutoff 14.0
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Low quality reference calls to be processed in chr10: 118735
-[INFO] Low quality variants to be processed in chr10: 196574
-
-real	0m4.194s
-user	0m3.841s
-sys	0m0.267s
-
-[INFO] 6/7 Call low-quality variants using full-alignment model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 14/32) : 10000
-Total time elapsed: 103.73 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 22/32) : 10000
-Total time elapsed: 105.81 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 21/32) : 10000
-Total time elapsed: 109.43 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 25/32) : 10000
-Total time elapsed: 109.97 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 9/32) : 10000
-Total time elapsed: 110.82 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 6/32) : 10000
-Total time elapsed: 111.30 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 12/32) : 10000
-Total time elapsed: 111.57 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 20/32) : 10000
-Total time elapsed: 112.54 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 19/32) : 10000
-Total time elapsed: 112.27 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 11/32) : 10000
-Total time elapsed: 112.56 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 16/32) : 10000
-Total time elapsed: 113.47 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 18/32) : 10000
-Total time elapsed: 113.41 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 24/32) : 10000
-Total time elapsed: 114.29 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 13/32) : 10000
-Total time elapsed: 114.42 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 23/32) : 10000
-Total time elapsed: 114.13 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 8/32) : 10000
-Total time elapsed: 114.16 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 4/32) : 10000
-Total time elapsed: 114.52 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 29/32) : 10000
-Total time elapsed: 114.46 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 28/32) : 10000
-Total time elapsed: 116.02 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 26/32) : 10000
-Total time elapsed: 116.08 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 30/32) : 10000
-Total time elapsed: 115.50 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 15/32) : 10000
-Total time elapsed: 116.81 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 27/32) : 10000
-Total time elapsed: 116.33 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 7/32) : 10000
-Total time elapsed: 117.18 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 3/32) : 10000
-Total time elapsed: 117.48 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 2/32) : 10000
-Total time elapsed: 118.46 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 17/32) : 10000
-Total time elapsed: 117.81 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 5/32) : 10000
-Total time elapsed: 119.33 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 1/32) : 10000
-Total time elapsed: 119.57 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 10/32) : 10000
-Total time elapsed: 120.78 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 32/32) : 5309
-Total time elapsed: 49.62 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 31/32) : 10000
-Total time elapsed: 86.49 s
-
-real	3m19.572s
-user	57m4.441s
-sys	3m27.409s
-
-[INFO] 7/7 Merge pileup VCF and full-alignment VCF
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Pileup variants processed in chr10: 84279
-[INFO] Full-alignment variants processed in chr10: 203368
-
-real	0m5.865s
-user	0m6.249s
-sys	0m0.277s
-
-[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
-
-real	6m46.315s
-user	107m56.463s
-sys	8m51.260s
-
-[INFO] Call Germline Variant in Tumor BAM using Clair3
-[INFO] RUN THE FOLLOWING COMMAND:
-( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output --ctg_name=chr10 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/2_CLAIR3_TUMOR.log
-
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] CLAIR3 VERSION: v1.0.8
-[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output
-[INFO] PLATFORM: ont
-[INFO] THREADS: 40
-[INFO] BED FILE PATH: EMPTY
-[INFO] VCF FILE PATH: EMPTY
-[INFO] CONTIGS: chr10
-[INFO] CONDA PREFIX: 
-[INFO] SAMTOOLS PATH: samtools
-[INFO] PYTHON PATH: python3
-[INFO] PYPY PATH: pypy3
-[INFO] PARALLEL PATH: parallel
-[INFO] WHATSHAP PATH: whatshap
-[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] FULL ALIGN PROPORTION: 0.7
-[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
-[INFO] PHASING PROPORTION: 0.7
-[INFO] MINIMUM MQ: 5
-[INFO] MINIMUM COVERAGE: 4
-[INFO] SNP AF THRESHOLD: 0.08
-[INFO] INDEL AF THRESHOLD: 0.15
-[INFO] BASE ERROR IN GVCF: 0.001
-[INFO] GQ BIN SIZE IN GVCF: 5
-[INFO] ENABLE FILEUP ONLY CALLING: False
-[INFO] ENABLE FAST MODE CALLING: False
-[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE OUTPUT GVCF: False
-[INFO] ENABLE HAPLOID PRECISE MODE: False
-[INFO] ENABLE HAPLOID SENSITIVE MODE: False
-[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
-[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
-[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
-[INFO] ENABLE LONG INDEL CALLING: False
-[INFO] ENABLE C_IMPLEMENT: True
-
-+ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr10 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] Check environment variables
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
-[INFO] Call variant in contigs: chr10
-[INFO] Chunk number for each contig: 27
-[INFO] 1/7 Call variants using pileup model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 18/27) : 11051
-Total time elapsed: 105.59 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 23/27) : 11192
-Total time elapsed: 106.77 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 21/27) : 11362
-Total time elapsed: 106.82 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 17/27) : 11922
-Total time elapsed: 107.36 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 14/27) : 13677
-Total time elapsed: 110.36 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 2/27) : 15217
-Total time elapsed: 112.66 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 24/27) : 8754
-Total time elapsed: 72.39 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 15/27) : 11427
-Total time elapsed: 73.80 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 20/27) : 10846
-Total time elapsed: 74.03 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 12/27) : 12345
-Total time elapsed: 76.32 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 13/27) : 10935
-Total time elapsed: 77.12 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 22/27) : 10696
-Total time elapsed: 75.58 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 7/27) : 12351
-Total time elapsed: 75.81 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 11/27) : 13324
-Total time elapsed: 79.17 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 26/27) : 14623
-Total time elapsed: 80.54 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 25/27) : 14602
-Total time elapsed: 82.14 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 6/27) : 17479
-Total time elapsed: 84.72 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 27/27) : 17701
-Total time elapsed: 86.03 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 16/27) : 8751
-Total time elapsed: 58.17 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 4/27) : 12459
-Total time elapsed: 61.01 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 19/27) : 11053
-Total time elapsed: 65.79 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 1/27) : 16613
-Total time elapsed: 66.04 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 5/27) : 11341
-Total time elapsed: 51.41 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 10/27) : 15398
-Total time elapsed: 72.51 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 3/27) : 14619
-Total time elapsed: 50.54 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 8/27) : 21116
-Total time elapsed: 57.86 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 9/27) : 71597
-Total time elapsed: 154.81 s
-
-real	4m30.245s
-user	30m10.643s
-sys	4m30.118s
-
-[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
-[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 20
-[INFO] Total heterozygous SNP positions selected: chr10: 114549
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-real	0m1.928s
-user	0m1.668s
-sys	0m0.180s
-
-[INFO] 3/7 Phase VCF file using LongPhase
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-LongPhase Ver 1.7
-
---- File Parameter --- 
-SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr10.vcf
-SV  File      : 
-MOD File      : 
-REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
-Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr10
-Generate Dot  : False
-BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam 
-
---- Phasing Parameter --- 
-Seq Platform       : ONT
-Phase Indel        : False
-Distance Threshold : 300000
-Connect Adjacent   : 20
-Edge Threshold     : 0.7
-Mapping Quality    : 1
-Variant Confidence : 0.75
-ReadTag Confidence : 0.65
-
-parsing VCF ... 0s
-parsing SV VCF ... 0s
-parsing Meth VCF ... 0s
-reading reference ... 2s
-(chr10,54s)
-parsing total:  54s
-merge results ... 0s
-writeResult SNP ... 1s
-
-total process: 57s
-
-real	0m57.409s
-user	2m3.634s
-sys	0m8.114s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] 5/7 Select candidates for full-alignment calling
-[INFO] Set variants quality cutoff 21.0
-[INFO] Set reference calls quality cutoff 7.0
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Low quality reference calls to be processed in chr10: 12658
-[INFO] Low quality variants to be processed in chr10: 199885
-
-real	0m1.785s
-user	0m1.545s
-sys	0m0.190s
-
-[INFO] 6/7 Call low-quality variants using full-alignment model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 22/22) : 2543
-Total time elapsed: 31.87 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 7/22) : 10000
-Total time elapsed: 101.21 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 8/22) : 10000
-Total time elapsed: 109.22 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 5/22) : 10000
-Total time elapsed: 114.37 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 9/22) : 10000
-Total time elapsed: 115.27 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 2/22) : 10000
-Total time elapsed: 117.07 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 13/22) : 10000
-Total time elapsed: 117.79 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 3/22) : 10000
-Total time elapsed: 118.03 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 1/22) : 10000
-Total time elapsed: 118.85 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 11/22) : 10000
-Total time elapsed: 120.41 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 18/22) : 10000
-Total time elapsed: 122.32 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 20/22) : 10000
-Total time elapsed: 122.68 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 10/22) : 10000
-Total time elapsed: 123.28 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 19/22) : 10000
-Total time elapsed: 123.74 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 16/22) : 10000
-Total time elapsed: 124.21 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 15/22) : 10000
-Total time elapsed: 125.40 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 4/22) : 10000
-Total time elapsed: 127.23 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 12/22) : 10000
-Total time elapsed: 127.26 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 21/22) : 10000
-Total time elapsed: 128.78 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 6/22) : 10000
-Total time elapsed: 129.25 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 17/22) : 10000
-Total time elapsed: 129.52 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr10 (chunk 14/22) : 10000
-Total time elapsed: 133.03 s
-
-real	2m16.589s
-user	40m23.948s
-sys	2m13.182s
-
-[INFO] 7/7 Merge pileup VCF and full-alignment VCF
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Pileup variants processed in chr10: 85952
-[INFO] Full-alignment variants processed in chr10: 189193
-
-real	0m3.285s
-user	0m3.344s
-sys	0m0.202s
-
-[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
-
-real	8m2.537s
-user	72m53.947s
-sys	6m53.306s
-
-[INFO] Select Heterozygous SNP for Phasing
-[INFO] RUN THE FOLLOWING COMMAND:
-( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/1_select_hetero_snp_for_phasing.log
-
-[INFO] Total HET SNP calls selected: chr10: 154989, not found:991, not match:82, low_qual_count:0. Total normal:154772 Total tumor:156062, pro: 0.9931
-
-[INFO] Phase the Tumor BAM
-[INFO] RUN THE FOLLOWING COMMAND:
-( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS
-
-LongPhase Ver 1.7
-
---- File Parameter --- 
-SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/vcf/chr10.vcf
-SV  File      : 
-MOD File      : 
-REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
-Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_chr10
-Generate Dot  : False
-BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam 
-
---- Phasing Parameter --- 
-Seq Platform       : ONT
-Phase Indel        : False
-Distance Threshold : 300000
-Connect Adjacent   : 20
-Edge Threshold     : 0.7
-Mapping Quality    : 1
-Variant Confidence : 0.75
-ReadTag Confidence : 0.65
-
-parsing VCF ... 0s
-parsing SV VCF ... 0s
-parsing Meth VCF ... 0s
-reading reference ... 2s
-(chr10,78s)
-parsing total:  78s
-merge results ... 0s
-writeResult SNP ... 1s
-
-total process: 81s
-
-[INFO] Haplotag the Tumor BAM
-[INFO] RUN THE FOLLOWING COMMAND:
-( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS
-

slurm-2536605.out

@@ -1,737 +0,0 @@
-
-[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10 --region chr14:1-14158555 --sample_name DUMCO_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
-
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/split_beds
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/candidates
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/pileup_tensor_can
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/fa_tensor_can
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/vcf_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/tmp_vcf_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/vcf
-[INFO] --include_all_ctgs enabled
-[INFO] Call variants in contigs: chr14
-[INFO] Number of chunks for each contig: 21
-
-[INFO] CALLER VERSION: 0.4.4
-[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
-[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
-[INFO] THREADS: 40
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10
-[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/output.vcf.gz
-[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
-[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
-[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/region.bed
-[INFO] GENOTYPING MODE VCF FILE PATH: None
-[INFO] HYBRID MODE VCF FILE PATH: None
-[INFO] REGION FOR CALLING: chr14:1-14158555
-[INFO] CONTIGS FOR CALLING: None
-[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
-[INFO] SAMTOOLS BINARY PATH: samtools
-[INFO] PYTHON BINARY PATH: python3
-[INFO] PYPY BINARY PATH: pypy3
-[INFO] PARALLEL BINARY PATH: parallel
-[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] SNV MINIMUM AF: 0.05
-[INFO] SNV MINIMUM QUAL: 8
-[INFO] INDEL MINIMUM AF: 0.1
-[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
-[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
-[INFO] INDEL MINIMUM QUAL: 8
-[INFO] NORMAL VCF FILE PATH: None
-[INFO] DISABLE PHASING: False
-[INFO] ENABLE DRY RUN: False
-[INFO] ENABLE INDEL CALLING: True
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE PRINTING GERMLINE CALLS: True
-[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-
-[INFO] Call Germline Variants in Normal BAM using Clair3
-[INFO] RUN THE FOLLOWING COMMAND:
-( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output --ctg_name=chr14 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/1_CLAIR3_NORMAL.log
-
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] CLAIR3 VERSION: v1.0.8
-[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output
-[INFO] PLATFORM: ont
-[INFO] THREADS: 40
-[INFO] BED FILE PATH: EMPTY
-[INFO] VCF FILE PATH: EMPTY
-[INFO] CONTIGS: chr14
-[INFO] CONDA PREFIX: 
-[INFO] SAMTOOLS PATH: samtools
-[INFO] PYTHON PATH: python3
-[INFO] PYPY PATH: pypy3
-[INFO] PARALLEL PATH: parallel
-[INFO] WHATSHAP PATH: whatshap
-[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] FULL ALIGN PROPORTION: 0.7
-[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
-[INFO] PHASING PROPORTION: 0.7
-[INFO] MINIMUM MQ: 5
-[INFO] MINIMUM COVERAGE: 4
-[INFO] SNP AF THRESHOLD: 0.08
-[INFO] INDEL AF THRESHOLD: 0.15
-[INFO] BASE ERROR IN GVCF: 0.001
-[INFO] GQ BIN SIZE IN GVCF: 5
-[INFO] ENABLE FILEUP ONLY CALLING: False
-[INFO] ENABLE FAST MODE CALLING: False
-[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE OUTPUT GVCF: False
-[INFO] ENABLE HAPLOID PRECISE MODE: False
-[INFO] ENABLE HAPLOID SENSITIVE MODE: False
-[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
-[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
-[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
-[INFO] ENABLE LONG INDEL CALLING: False
-[INFO] ENABLE C_IMPLEMENT: True
-
-+ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr14 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] Check environment variables
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/merge_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
-[INFO] Call variant in contigs: chr14
-[INFO] Chunk number for each contig: 21
-[INFO] 1/7 Call variants using pileup model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 3/21) : 27087
-Total time elapsed: 67.49 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 17/21) : 45594
-Total time elapsed: 100.19 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 8/21) : 44012
-Total time elapsed: 100.23 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 9/21) : 45077
-Total time elapsed: 103.05 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 6/21) : 46771
-Total time elapsed: 106.08 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 13/21) : 48523
-Total time elapsed: 107.31 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 10/21) : 48629
-Total time elapsed: 107.79 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 7/21) : 46998
-Total time elapsed: 110.66 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 5/21) : 46930
-Total time elapsed: 111.19 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 12/21) : 48751
-Total time elapsed: 112.04 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 11/21) : 49628
-Total time elapsed: 112.84 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 16/21) : 48404
-Total time elapsed: 113.65 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 14/21) : 52138
-Total time elapsed: 114.64 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 18/21) : 51792
-Total time elapsed: 116.28 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 19/21) : 52771
-Total time elapsed: 117.06 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 4/21) : 55960
-Total time elapsed: 119.54 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 15/21) : 58588
-Total time elapsed: 120.64 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 20/21) : 56358
-Total time elapsed: 124.53 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 2/21) : 71708
-Total time elapsed: 137.35 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 21/21) : 74382
-Total time elapsed: 139.88 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 1/21) : 75522
-Total time elapsed: 148.63 s
-
-real	2m36.411s
-user	36m19.108s
-sys	3m11.518s
-
-[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
-[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 17
-[INFO] Total heterozygous SNP positions selected: chr14: 98793
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-real	0m3.189s
-user	0m3.007s
-sys	0m0.160s
-
-[INFO] 3/7 Phase VCF file using LongPhase
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-LongPhase Ver 1.7
-
---- File Parameter --- 
-SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr14.vcf
-SV  File      : 
-MOD File      : 
-REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
-Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr14
-Generate Dot  : False
-BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam 
-
---- Phasing Parameter --- 
-Seq Platform       : ONT
-Phase Indel        : False
-Distance Threshold : 300000
-Connect Adjacent   : 20
-Edge Threshold     : 0.7
-Mapping Quality    : 1
-Variant Confidence : 0.75
-ReadTag Confidence : 0.65
-
-parsing VCF ... 0s
-parsing SV VCF ... 0s
-parsing Meth VCF ... 0s
-reading reference ... 2s
-(chr14,11s)
-parsing total:  11s
-merge results ... 0s
-writeResult SNP ... 1s
-
-total process: 14s
-
-real	0m14.363s
-user	0m28.692s
-sys	0m2.098s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] 5/7 Select candidates for full-alignment calling
-[INFO] Set variants quality cutoff 21.0
-[INFO] Set reference calls quality cutoff 14.0
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Low quality reference calls to be processed in chr14: 87036
-[INFO] Low quality variants to be processed in chr14: 156699
-
-real	0m3.580s
-user	0m3.267s
-sys	0m0.249s
-
-[INFO] 6/7 Call low-quality variants using full-alignment model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 25/25) : 3735
-Total time elapsed: 40.53 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 3/25) : 10000
-Total time elapsed: 91.52 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 5/25) : 10000
-Total time elapsed: 93.21 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 6/25) : 10000
-Total time elapsed: 95.77 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 1/25) : 10000
-Total time elapsed: 99.10 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 19/25) : 10000
-Total time elapsed: 102.41 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 2/25) : 10000
-Total time elapsed: 103.49 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 22/25) : 10000
-Total time elapsed: 103.63 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 7/25) : 10000
-Total time elapsed: 104.57 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 14/25) : 10000
-Total time elapsed: 105.63 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 4/25) : 10000
-Total time elapsed: 105.90 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 23/25) : 10000
-Total time elapsed: 105.80 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 15/25) : 10000
-Total time elapsed: 106.78 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 8/25) : 10000
-Total time elapsed: 108.01 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 21/25) : 10000
-Total time elapsed: 108.26 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 18/25) : 10000
-Total time elapsed: 108.66 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 12/25) : 10000
-Total time elapsed: 109.06 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 17/25) : 10000
-Total time elapsed: 109.26 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 10/25) : 10000
-Total time elapsed: 110.99 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 20/25) : 10000
-Total time elapsed: 112.31 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 9/25) : 10000
-Total time elapsed: 113.59 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 11/25) : 10000
-Total time elapsed: 113.18 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 24/25) : 10000
-Total time elapsed: 113.74 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 13/25) : 10000
-Total time elapsed: 114.75 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 16/25) : 10000
-Total time elapsed: 117.89 s
-
-real	2m2.215s
-user	41m45.362s
-sys	2m39.606s
-
-[INFO] 7/7 Merge pileup VCF and full-alignment VCF
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Pileup variants processed in chr14: 67189
-[INFO] Full-alignment variants processed in chr14: 152188
-
-real	0m4.735s
-user	0m4.953s
-sys	0m0.275s
-
-[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
-
-real	5m21.522s
-user	78m59.878s
-sys	5m55.410s
-
-[INFO] Call Germline Variant in Tumor BAM using Clair3
-[INFO] RUN THE FOLLOWING COMMAND:
-( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output --ctg_name=chr14 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/2_CLAIR3_TUMOR.log
-
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] CLAIR3 VERSION: v1.0.8
-[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output
-[INFO] PLATFORM: ont
-[INFO] THREADS: 40
-[INFO] BED FILE PATH: EMPTY
-[INFO] VCF FILE PATH: EMPTY
-[INFO] CONTIGS: chr14
-[INFO] CONDA PREFIX: 
-[INFO] SAMTOOLS PATH: samtools
-[INFO] PYTHON PATH: python3
-[INFO] PYPY PATH: pypy3
-[INFO] PARALLEL PATH: parallel
-[INFO] WHATSHAP PATH: whatshap
-[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] FULL ALIGN PROPORTION: 0.7
-[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
-[INFO] PHASING PROPORTION: 0.7
-[INFO] MINIMUM MQ: 5
-[INFO] MINIMUM COVERAGE: 4
-[INFO] SNP AF THRESHOLD: 0.08
-[INFO] INDEL AF THRESHOLD: 0.15
-[INFO] BASE ERROR IN GVCF: 0.001
-[INFO] GQ BIN SIZE IN GVCF: 5
-[INFO] ENABLE FILEUP ONLY CALLING: False
-[INFO] ENABLE FAST MODE CALLING: False
-[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE OUTPUT GVCF: False
-[INFO] ENABLE HAPLOID PRECISE MODE: False
-[INFO] ENABLE HAPLOID SENSITIVE MODE: False
-[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
-[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
-[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
-[INFO] ENABLE LONG INDEL CALLING: False
-[INFO] ENABLE C_IMPLEMENT: True
-
-+ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr14 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] Check environment variables
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
-[INFO] Call variant in contigs: chr14
-[INFO] Chunk number for each contig: 21
-[INFO] 1/7 Call variants using pileup model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 13/21) : 9272
-Total time elapsed: 83.25 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 16/21) : 10505
-Total time elapsed: 83.09 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 9/21) : 9874
-Total time elapsed: 83.84 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 12/21) : 10329
-Total time elapsed: 84.85 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 10/21) : 10784
-Total time elapsed: 84.83 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 11/21) : 10970
-Total time elapsed: 85.64 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 8/21) : 11132
-Total time elapsed: 85.34 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 5/21) : 10500
-Total time elapsed: 86.17 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 7/21) : 11262
-Total time elapsed: 86.28 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 15/21) : 11428
-Total time elapsed: 88.28 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 3/21) : 24051
-Total time elapsed: 107.75 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 14/21) : 9848
-Total time elapsed: 54.85 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 20/21) : 10535
-Total time elapsed: 56.16 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 18/21) : 10561
-Total time elapsed: 56.64 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 6/21) : 11505
-Total time elapsed: 57.66 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 17/21) : 10878
-Total time elapsed: 59.43 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 19/21) : 10682
-Total time elapsed: 59.99 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 4/21) : 13820
-Total time elapsed: 60.94 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 21/21) : 21301
-Total time elapsed: 70.54 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 2/21) : 49177
-Total time elapsed: 151.29 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 1/21) : 56135
-Total time elapsed: 123.51 s
-
-real	3m36.782s
-user	21m31.870s
-sys	2m35.445s
-
-[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
-[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19
-[INFO] Total heterozygous SNP positions selected: chr14: 92503
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-real	0m1.739s
-user	0m1.463s
-sys	0m0.206s
-
-[INFO] 3/7 Phase VCF file using LongPhase
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-LongPhase Ver 1.7
-
---- File Parameter --- 
-SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr14.vcf
-SV  File      : 
-MOD File      : 
-REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
-Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr14
-Generate Dot  : False
-BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam 
-
---- Phasing Parameter --- 
-Seq Platform       : ONT
-Phase Indel        : False
-Distance Threshold : 300000
-Connect Adjacent   : 20
-Edge Threshold     : 0.7
-Mapping Quality    : 1
-Variant Confidence : 0.75
-ReadTag Confidence : 0.65
-
-parsing VCF ... 0s
-parsing SV VCF ... 0s
-parsing Meth VCF ... 0s
-reading reference ... 2s
-(chr14,46s)
-parsing total:  46s
-merge results ... 0s
-writeResult SNP ... 1s
-
-total process: 49s
-
-real	0m49.025s
-user	1m52.723s
-sys	0m7.403s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] 5/7 Select candidates for full-alignment calling
-[INFO] Set variants quality cutoff 21.0
-[INFO] Set reference calls quality cutoff 8.0
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Low quality reference calls to be processed in chr14: 12071
-[INFO] Low quality variants to be processed in chr14: 149419
-
-real	0m1.560s
-user	0m1.344s
-sys	0m0.181s
-
-[INFO] 6/7 Call low-quality variants using full-alignment model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 17/17) : 1490
-Total time elapsed: 17.69 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 2/17) : 10000
-Total time elapsed: 77.45 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 3/17) : 10000
-Total time elapsed: 85.49 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 4/17) : 10000
-Total time elapsed: 108.69 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 16/17) : 10000
-Total time elapsed: 111.72 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 5/17) : 10000
-Total time elapsed: 111.92 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 6/17) : 10000
-Total time elapsed: 113.19 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 1/17) : 10000
-Total time elapsed: 116.51 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 7/17) : 10000
-Total time elapsed: 118.51 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 9/17) : 10000
-Total time elapsed: 120.23 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 8/17) : 10000
-Total time elapsed: 120.33 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 15/17) : 10000
-Total time elapsed: 120.91 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 12/17) : 10000
-Total time elapsed: 121.70 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 10/17) : 10000
-Total time elapsed: 125.60 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 11/17) : 10000
-Total time elapsed: 132.71 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 13/17) : 10000
-Total time elapsed: 133.62 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr14 (chunk 14/17) : 10000
-Total time elapsed: 137.02 s
-
-real	2m20.809s
-user	29m25.734s
-sys	1m36.544s
-
-[INFO] 7/7 Merge pileup VCF and full-alignment VCF
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Pileup variants processed in chr14: 64294
-[INFO] Full-alignment variants processed in chr14: 125164
-
-real	0m2.550s
-user	0m2.580s
-sys	0m0.179s
-
-[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
-
-real	7m1.826s
-user	53m3.431s
-sys	4m21.166s
-
-[INFO] Select Heterozygous SNP for Phasing
-[INFO] RUN THE FOLLOWING COMMAND:
-( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/1_select_hetero_snp_for_phasing.log
-
-[INFO] Total HET SNP calls selected: chr14: 109551, not found:498, not match:37, low_qual_count:0. Total normal:129319 Total tumor:110086, pro: 0.9951
-
-[INFO] Phase the Tumor BAM
-[INFO] RUN THE FOLLOWING COMMAND:
-( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS
-
-LongPhase Ver 1.7
-
---- File Parameter --- 
-SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/vcf/chr14.vcf
-SV  File      : 
-MOD File      : 
-REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
-Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_chr14
-Generate Dot  : False
-BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam 
-
---- Phasing Parameter --- 
-Seq Platform       : ONT
-Phase Indel        : False
-Distance Threshold : 300000
-Connect Adjacent   : 20
-Edge Threshold     : 0.7
-Mapping Quality    : 1
-Variant Confidence : 0.75
-ReadTag Confidence : 0.65
-
-parsing VCF ... 1s
-parsing SV VCF ... 0s
-parsing Meth VCF ... 0s
-reading reference ... 1s
-(chr14,62s)
-parsing total:  62s
-merge results ... 0s
-writeResult SNP ... 1s
-
-total process: 65s
-
-[INFO] Haplotag the Tumor BAM
-[INFO] RUN THE FOLLOWING COMMAND:
-( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS
-

slurm-2536606.out

@@ -1,418 +0,0 @@
-
-[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15 --region chr17:1-28642702 --sample_name DUMCO_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
-
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/logs
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/split_beds
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/candidates
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/pileup_tensor_can
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/fa_tensor_can
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/vcf_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/tmp_vcf_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/logs/clair3_log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/phased_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/vcf
-[INFO] --include_all_ctgs enabled
-[INFO] Call variants in contigs: chr17
-[INFO] Number of chunks for each contig: 17
-
-[INFO] CALLER VERSION: 0.4.4
-[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
-[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
-[INFO] THREADS: 40
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15
-[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/output.vcf.gz
-[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
-[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
-[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/region.bed
-[INFO] GENOTYPING MODE VCF FILE PATH: None
-[INFO] HYBRID MODE VCF FILE PATH: None
-[INFO] REGION FOR CALLING: chr17:1-28642702
-[INFO] CONTIGS FOR CALLING: None
-[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
-[INFO] SAMTOOLS BINARY PATH: samtools
-[INFO] PYTHON BINARY PATH: python3
-[INFO] PYPY BINARY PATH: pypy3
-[INFO] PARALLEL BINARY PATH: parallel
-[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] SNV MINIMUM AF: 0.05
-[INFO] SNV MINIMUM QUAL: 8
-[INFO] INDEL MINIMUM AF: 0.1
-[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
-[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
-[INFO] INDEL MINIMUM QUAL: 8
-[INFO] NORMAL VCF FILE PATH: None
-[INFO] DISABLE PHASING: False
-[INFO] ENABLE DRY RUN: False
-[INFO] ENABLE INDEL CALLING: True
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE PRINTING GERMLINE CALLS: True
-[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-
-[INFO] Call Germline Variants in Normal BAM using Clair3
-[INFO] RUN THE FOLLOWING COMMAND:
-( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output --ctg_name=chr17 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/logs/clair3_log/1_CLAIR3_NORMAL.log
-
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] CLAIR3 VERSION: v1.0.8
-[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output
-[INFO] PLATFORM: ont
-[INFO] THREADS: 40
-[INFO] BED FILE PATH: EMPTY
-[INFO] VCF FILE PATH: EMPTY
-[INFO] CONTIGS: chr17
-[INFO] CONDA PREFIX: 
-[INFO] SAMTOOLS PATH: samtools
-[INFO] PYTHON PATH: python3
-[INFO] PYPY PATH: pypy3
-[INFO] PARALLEL PATH: parallel
-[INFO] WHATSHAP PATH: whatshap
-[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] FULL ALIGN PROPORTION: 0.7
-[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
-[INFO] PHASING PROPORTION: 0.7
-[INFO] MINIMUM MQ: 5
-[INFO] MINIMUM COVERAGE: 4
-[INFO] SNP AF THRESHOLD: 0.08
-[INFO] INDEL AF THRESHOLD: 0.15
-[INFO] BASE ERROR IN GVCF: 0.001
-[INFO] GQ BIN SIZE IN GVCF: 5
-[INFO] ENABLE FILEUP ONLY CALLING: False
-[INFO] ENABLE FAST MODE CALLING: False
-[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE OUTPUT GVCF: False
-[INFO] ENABLE HAPLOID PRECISE MODE: False
-[INFO] ENABLE HAPLOID SENSITIVE MODE: False
-[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
-[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
-[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
-[INFO] ENABLE LONG INDEL CALLING: False
-[INFO] ENABLE C_IMPLEMENT: True
-
-+ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr17 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] Check environment variables
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/merge_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
-[INFO] Call variant in contigs: chr17
-[INFO] Chunk number for each contig: 17
-[INFO] 1/7 Call variants using pileup model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 6/17) : 27914
-Total time elapsed: 56.65 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 13/17) : 50335
-Total time elapsed: 84.56 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 15/17) : 51403
-Total time elapsed: 90.68 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 5/17) : 55409
-Total time elapsed: 96.01 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 4/17) : 58603
-Total time elapsed: 98.13 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 7/17) : 54606
-Total time elapsed: 98.11 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 8/17) : 59803
-Total time elapsed: 98.55 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 14/17) : 55106
-Total time elapsed: 100.54 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 3/17) : 57778
-Total time elapsed: 100.70 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 11/17) : 57487
-Total time elapsed: 102.90 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 12/17) : 57337
-Total time elapsed: 103.47 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 10/17) : 57826
-Total time elapsed: 104.26 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 2/17) : 59536
-Total time elapsed: 105.58 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 16/17) : 65379
-Total time elapsed: 111.75 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 1/17) : 66124
-Total time elapsed: 112.58 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 9/17) : 65558
-Total time elapsed: 114.98 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 17/17) : 74166
-Total time elapsed: 122.34 s
-
-real	2m9.004s
-user	26m3.068s
-sys	2m5.460s
-
-[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
-[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 18
-[INFO] Total heterozygous SNP positions selected: chr17: 61710
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-real	0m2.565s
-user	0m2.421s
-sys	0m0.123s
-
-[INFO] 3/7 Phase VCF file using LongPhase
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-LongPhase Ver 1.7
-
---- File Parameter --- 
-SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr17.vcf
-SV  File      : 
-MOD File      : 
-REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
-Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr17
-Generate Dot  : False
-BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam 
-
---- Phasing Parameter --- 
-Seq Platform       : ONT
-Phase Indel        : False
-Distance Threshold : 300000
-Connect Adjacent   : 20
-Edge Threshold     : 0.7
-Mapping Quality    : 1
-Variant Confidence : 0.75
-ReadTag Confidence : 0.65
-
-parsing VCF ... 0s
-parsing SV VCF ... 0s
-parsing Meth VCF ... 0s
-reading reference ... 1s
-(chr17,7s)
-parsing total:  7s
-merge results ... 0s
-writeResult SNP ... 0s
-
-total process: 8s
-
-real	0m8.670s
-user	0m18.510s
-sys	0m1.250s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] 5/7 Select candidates for full-alignment calling
-[INFO] Set variants quality cutoff 21.0
-[INFO] Set reference calls quality cutoff 14.0
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Low quality reference calls to be processed in chr17: 80349
-[INFO] Low quality variants to be processed in chr17: 119468
-
-real	0m2.724s
-user	0m2.475s
-sys	0m0.198s
-
-[INFO] 6/7 Call low-quality variants using full-alignment model
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 10/20) : 10000
-Total time elapsed: 82.58 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 13/20) : 10000
-Total time elapsed: 82.82 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 11/20) : 10000
-Total time elapsed: 82.94 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 7/20) : 10000
-Total time elapsed: 84.01 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 5/20) : 10000
-Total time elapsed: 84.06 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 14/20) : 10000
-Total time elapsed: 84.91 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 12/20) : 10000
-Total time elapsed: 85.09 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 8/20) : 10000
-Total time elapsed: 85.29 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 2/20) : 10000
-Total time elapsed: 86.07 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 6/20) : 10000
-Total time elapsed: 86.76 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 15/20) : 10000
-Total time elapsed: 87.23 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 18/20) : 10000
-Total time elapsed: 87.28 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 3/20) : 10000
-Total time elapsed: 87.72 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 4/20) : 10000
-Total time elapsed: 87.77 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 17/20) : 10000
-Total time elapsed: 87.96 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 9/20) : 10000
-Total time elapsed: 88.04 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 16/20) : 10000
-Total time elapsed: 88.27 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 19/20) : 10000
-Total time elapsed: 90.27 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 1/20) : 10000
-Total time elapsed: 90.39 s
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-Calling variants ...
-Total processed positions in chr17 (chunk 20/20) : 9817
-Total time elapsed: 93.15 s
-
-real	1m36.429s
-user	27m51.849s
-sys	1m41.958s
-
-[INFO] 7/7 Merge pileup VCF and full-alignment VCF
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] Pileup variants processed in chr17: 51317
-[INFO] Full-alignment variants processed in chr17: 125849
-
-real	0m3.646s
-user	0m3.834s
-sys	0m0.179s
-
-[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
-
-real	4m17.319s
-user	54m35.144s
-sys	3m50.375s
-
-[INFO] Call Germline Variant in Tumor BAM using Clair3
-[INFO] RUN THE FOLLOWING COMMAND:
-( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output --ctg_name=chr17 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/logs/clair3_log/2_CLAIR3_TUMOR.log
-
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-[INFO] CLAIR3 VERSION: v1.0.8
-[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam
-[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
-[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output
-[INFO] PLATFORM: ont
-[INFO] THREADS: 40
-[INFO] BED FILE PATH: EMPTY
-[INFO] VCF FILE PATH: EMPTY
-[INFO] CONTIGS: chr17
-[INFO] CONDA PREFIX: 
-[INFO] SAMTOOLS PATH: samtools
-[INFO] PYTHON PATH: python3
-[INFO] PYPY PATH: pypy3
-[INFO] PARALLEL PATH: parallel
-[INFO] WHATSHAP PATH: whatshap
-[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
-[INFO] CHUNK SIZE: 5000000
-[INFO] FULL ALIGN PROPORTION: 0.7
-[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
-[INFO] PHASING PROPORTION: 0.7
-[INFO] MINIMUM MQ: 5
-[INFO] MINIMUM COVERAGE: 4
-[INFO] SNP AF THRESHOLD: 0.08
-[INFO] INDEL AF THRESHOLD: 0.15
-[INFO] BASE ERROR IN GVCF: 0.001
-[INFO] GQ BIN SIZE IN GVCF: 5
-[INFO] ENABLE FILEUP ONLY CALLING: False
-[INFO] ENABLE FAST MODE CALLING: False
-[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
-[INFO] ENABLE PRINTING REFERENCE CALLS: False
-[INFO] ENABLE OUTPUT GVCF: False
-[INFO] ENABLE HAPLOID PRECISE MODE: False
-[INFO] ENABLE HAPLOID SENSITIVE MODE: False
-[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
-[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
-[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
-[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
-[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
-[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
-[INFO] ENABLE LONG INDEL CALLING: False
-[INFO] ENABLE C_IMPLEMENT: True
-
-+ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr17 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
-
-[INFO] Check environment variables
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
-[INFO] Call variant in contigs: chr17
-[INFO] Chunk number for each contig: 17
-[INFO] 1/7 Call variants using pileup model

slurm-2556285.out

@@ -0,0 +1,1120 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7 --region chr12:1-105185185 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr12
+[INFO] Number of chunks for each contig: 27
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr12:1-105185185
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output --ctg_name=chr12 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr12
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr12 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr12
+[INFO] Chunk number for each contig: 27
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr12 (chunk 8/27) : 46499
+Total time elapsed: 102.32 s
+Calling variants ...
+Total processed positions in chr12 (chunk 18/27) : 68095
+Total time elapsed: 127.61 s
+Calling variants ...
+Total processed positions in chr12 (chunk 17/27) : 76214
+Total time elapsed: 134.51 s
+Calling variants ...
+Total processed positions in chr12 (chunk 23/27) : 77100
+Total time elapsed: 148.21 s
+Calling variants ...
+Total processed positions in chr12 (chunk 14/27) : 80772
+Total time elapsed: 150.77 s
+Calling variants ...
+Total processed positions in chr12 (chunk 5/27) : 78381
+Total time elapsed: 150.98 s
+Calling variants ...
+Total processed positions in chr12 (chunk 4/27) : 80255
+Total time elapsed: 152.98 s
+Calling variants ...
+Total processed positions in chr12 (chunk 16/27) : 77789
+Total time elapsed: 154.39 s
+Calling variants ...
+Total processed positions in chr12 (chunk 15/27) : 75894
+Total time elapsed: 155.07 s
+Calling variants ...
+Total processed positions in chr12 (chunk 13/27) : 82126
+Total time elapsed: 155.02 s
+Calling variants ...
+Total processed positions in chr12 (chunk 19/27) : 79762
+Total time elapsed: 155.26 s
+Calling variants ...
+Total processed positions in chr12 (chunk 7/27) : 78143
+Total time elapsed: 155.50 s
+Calling variants ...
+Total processed positions in chr12 (chunk 10/27) : 80443
+Total time elapsed: 157.43 s
+Calling variants ...
+Total processed positions in chr12 (chunk 25/27) : 84367
+Total time elapsed: 159.08 s
+Calling variants ...
+Total processed positions in chr12 (chunk 22/27) : 88103
+Total time elapsed: 159.42 s
+Calling variants ...
+Total processed positions in chr12 (chunk 2/27) : 83654
+Total time elapsed: 159.98 s
+Calling variants ...
+Total processed positions in chr12 (chunk 9/27) : 82193
+Total time elapsed: 162.06 s
+Calling variants ...
+Total processed positions in chr12 (chunk 21/27) : 77458
+Total time elapsed: 139.98 s
+Calling variants ...
+Total processed positions in chr12 (chunk 1/27) : 91053
+Total time elapsed: 164.99 s
+Calling variants ...
+Total processed positions in chr12 (chunk 24/27) : 86005
+Total time elapsed: 143.36 s
+Calling variants ...
+Total processed positions in chr12 (chunk 20/27) : 79950
+Total time elapsed: 145.10 s
+Calling variants ...
+Total processed positions in chr12 (chunk 11/27) : 91029
+Total time elapsed: 169.43 s
+Calling variants ...
+Total processed positions in chr12 (chunk 12/27) : 85366
+Total time elapsed: 147.01 s
+Calling variants ...
+Total processed positions in chr12 (chunk 3/27) : 81325
+Total time elapsed: 147.64 s
+Calling variants ...
+Total processed positions in chr12 (chunk 26/27) : 88022
+Total time elapsed: 151.21 s
+Calling variants ...
+Total processed positions in chr12 (chunk 6/27) : 84846
+Total time elapsed: 154.47 s
+Calling variants ...
+Total processed positions in chr12 (chunk 27/27) : 95023
+Total time elapsed: 162.69 s
+
+real	3m12.806s
+user	65m23.912s
+sys	3m50.478s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16
+[INFO] Total heterozygous SNP positions selected: chr12: 89219
+
+real	0m5.088s
+user	0m4.817s
+sys	0m0.191s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr12.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr12
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr12,9s)
+parsing total:  9s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 11s
+
+real	0m11.585s
+user	0m23.044s
+sys	0m1.534s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 20.0
+[INFO] Set reference calls quality cutoff 14.0
+[INFO] Low quality reference calls to be processed in chr12: 193804
+[INFO] Low quality variants to be processed in chr12: 167735
+
+real	0m5.470s
+user	0m5.099s
+sys	0m0.282s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr12 (chunk 5/37) : 10000
+Total time elapsed: 94.51 s
+Calling variants ...
+Total processed positions in chr12 (chunk 17/37) : 10000
+Total time elapsed: 95.71 s
+Calling variants ...
+Total processed positions in chr12 (chunk 13/37) : 10000
+Total time elapsed: 96.94 s
+Calling variants ...
+Total processed positions in chr12 (chunk 15/37) : 10000
+Total time elapsed: 97.12 s
+Calling variants ...
+Total processed positions in chr12 (chunk 21/37) : 10000
+Total time elapsed: 97.34 s
+Calling variants ...
+Total processed positions in chr12 (chunk 2/37) : 10000
+Total time elapsed: 98.12 s
+Calling variants ...
+Total processed positions in chr12 (chunk 3/37) : 10000
+Total time elapsed: 99.36 s
+Calling variants ...
+Total processed positions in chr12 (chunk 22/37) : 10000
+Total time elapsed: 99.18 s
+Calling variants ...
+Total processed positions in chr12 (chunk 9/37) : 10000
+Total time elapsed: 99.50 s
+Calling variants ...
+Total processed positions in chr12 (chunk 20/37) : 10000
+Total time elapsed: 99.61 s
+Calling variants ...
+Total processed positions in chr12 (chunk 25/37) : 10000
+Total time elapsed: 100.05 s
+Calling variants ...
+Total processed positions in chr12 (chunk 1/37) : 10000
+Total time elapsed: 100.19 s
+Calling variants ...
+Total processed positions in chr12 (chunk 27/37) : 10000
+Total time elapsed: 100.61 s
+Calling variants ...
+Total processed positions in chr12 (chunk 29/37) : 10000
+Total time elapsed: 100.96 s
+Calling variants ...
+Total processed positions in chr12 (chunk 14/37) : 10000
+Total time elapsed: 101.32 s
+Calling variants ...
+Total processed positions in chr12 (chunk 7/37) : 10000
+Total time elapsed: 101.88 s
+Calling variants ...
+Total processed positions in chr12 (chunk 10/37) : 10000
+Total time elapsed: 103.02 s
+Calling variants ...
+Total processed positions in chr12 (chunk 4/37) : 10000
+Total time elapsed: 103.09 s
+Calling variants ...
+Total processed positions in chr12 (chunk 30/37) : 10000
+Total time elapsed: 103.11 s
+Calling variants ...
+Total processed positions in chr12 (chunk 23/37) : 10000
+Total time elapsed: 103.22 s
+Calling variants ...
+Total processed positions in chr12 (chunk 26/37) : 10000
+Total time elapsed: 104.15 s
+Calling variants ...
+Total processed positions in chr12 (chunk 28/37) : 10000
+Total time elapsed: 104.66 s
+Calling variants ...
+Total processed positions in chr12 (chunk 16/37) : 10000
+Total time elapsed: 104.87 s
+Calling variants ...
+Total processed positions in chr12 (chunk 8/37) : 10000
+Total time elapsed: 104.94 s
+Calling variants ...
+Total processed positions in chr12 (chunk 19/37) : 10000
+Total time elapsed: 105.31 s
+Calling variants ...
+Total processed positions in chr12 (chunk 24/37) : 10000
+Total time elapsed: 105.52 s
+Calling variants ...
+Total processed positions in chr12 (chunk 6/37) : 10000
+Total time elapsed: 105.43 s
+Calling variants ...
+Total processed positions in chr12 (chunk 11/37) : 10000
+Total time elapsed: 105.95 s
+Calling variants ...
+Total processed positions in chr12 (chunk 18/37) : 10000
+Total time elapsed: 105.83 s
+Calling variants ...
+Total processed positions in chr12 (chunk 12/37) : 10000
+Total time elapsed: 106.54 s
+Calling variants ...
+Total processed positions in chr12 (chunk 37/37) : 1539
+Total time elapsed: 14.12 s
+Calling variants ...
+Total processed positions in chr12 (chunk 32/37) : 10000
+Total time elapsed: 71.42 s
+Calling variants ...
+Total processed positions in chr12 (chunk 31/37) : 10000
+Total time elapsed: 73.05 s
+Calling variants ...
+Total processed positions in chr12 (chunk 33/37) : 10000
+Total time elapsed: 73.38 s
+Calling variants ...
+Total processed positions in chr12 (chunk 35/37) : 10000
+Total time elapsed: 75.49 s
+Calling variants ...
+Total processed positions in chr12 (chunk 34/37) : 10000
+Total time elapsed: 75.46 s
+Calling variants ...
+Total processed positions in chr12 (chunk 36/37) : 10000
+Total time elapsed: 79.45 s
+
+real	3m5.066s
+user	56m29.138s
+sys	3m33.101s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr12: 71993
+[INFO] Full-alignment variants processed in chr12: 173431
+
+real	0m6.791s
+user	0m7.403s
+sys	0m0.313s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	7m14.030s
+user	122m58.840s
+sys	7m27.983s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output --ctg_name=chr12 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr12
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr12 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr12
+[INFO] Chunk number for each contig: 27
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr12 (chunk 21/27) : 9223
+Total time elapsed: 82.61 s
+Calling variants ...
+Total processed positions in chr12 (chunk 16/27) : 9706
+Total time elapsed: 86.50 s
+Calling variants ...
+Total processed positions in chr12 (chunk 14/27) : 9976
+Total time elapsed: 86.89 s
+Calling variants ...
+Total processed positions in chr12 (chunk 10/27) : 11358
+Total time elapsed: 87.25 s
+Calling variants ...
+Total processed positions in chr12 (chunk 5/27) : 11025
+Total time elapsed: 88.34 s
+Calling variants ...
+Total processed positions in chr12 (chunk 20/27) : 11648
+Total time elapsed: 88.30 s
+Calling variants ...
+Total processed positions in chr12 (chunk 9/27) : 12539
+Total time elapsed: 88.93 s
+Calling variants ...
+Total processed positions in chr12 (chunk 12/27) : 11619
+Total time elapsed: 88.95 s
+Calling variants ...
+Total processed positions in chr12 (chunk 6/27) : 11547
+Total time elapsed: 88.97 s
+Calling variants ...
+Total processed positions in chr12 (chunk 13/27) : 12133
+Total time elapsed: 89.37 s
+Calling variants ...
+Total processed positions in chr12 (chunk 3/27) : 14660
+Total time elapsed: 92.08 s
+Calling variants ...
+Total processed positions in chr12 (chunk 26/27) : 13770
+Total time elapsed: 92.12 s
+Calling variants ...
+Total processed positions in chr12 (chunk 27/27) : 19156
+Total time elapsed: 100.86 s
+Calling variants ...
+Total processed positions in chr12 (chunk 2/27) : 12962
+Total time elapsed: 61.41 s
+Calling variants ...
+Total processed positions in chr12 (chunk 15/27) : 9489
+Total time elapsed: 56.67 s
+Calling variants ...
+Total processed positions in chr12 (chunk 17/27) : 9234
+Total time elapsed: 57.27 s
+Calling variants ...
+Total processed positions in chr12 (chunk 19/27) : 9327
+Total time elapsed: 56.49 s
+Calling variants ...
+Total processed positions in chr12 (chunk 23/27) : 9032
+Total time elapsed: 57.46 s
+Calling variants ...
+Total processed positions in chr12 (chunk 4/27) : 9289
+Total time elapsed: 57.43 s
+Calling variants ...
+Total processed positions in chr12 (chunk 22/27) : 11056
+Total time elapsed: 59.00 s
+Calling variants ...
+Total processed positions in chr12 (chunk 25/27) : 12654
+Total time elapsed: 60.01 s
+Calling variants ...
+Total processed positions in chr12 (chunk 24/27) : 11738
+Total time elapsed: 60.45 s
+Calling variants ...
+Total processed positions in chr12 (chunk 11/27) : 11555
+Total time elapsed: 60.07 s
+Calling variants ...
+Total processed positions in chr12 (chunk 7/27) : 14221
+Total time elapsed: 62.79 s
+Calling variants ...
+Total processed positions in chr12 (chunk 18/27) : 8254
+Total time elapsed: 42.19 s
+Calling variants ...
+Total processed positions in chr12 (chunk 1/27) : 14099
+Total time elapsed: 47.15 s
+Calling variants ...
+Total processed positions in chr12 (chunk 8/27) : 36309
+Total time elapsed: 86.95 s
+
+real	3m2.591s
+user	24m49.079s
+sys	4m0.775s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 20
+[INFO] Total heterozygous SNP positions selected: chr12: 93063
+
+real	0m1.611s
+user	0m1.378s
+sys	0m0.164s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr12.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr12
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr12,42s)
+parsing total:  42s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 45s
+
+real	0m44.569s
+user	1m37.014s
+sys	0m6.738s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 22.0
+[INFO] Set reference calls quality cutoff 7.0
+[INFO] Low quality reference calls to be processed in chr12: 9896
+[INFO] Low quality variants to be processed in chr12: 166782
+
+real	0m1.510s
+user	0m1.321s
+sys	0m0.156s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr12 (chunk 18/18) : 6678
+Total time elapsed: 90.63 s
+Calling variants ...
+Total processed positions in chr12 (chunk 6/18) : 10000
+Total time elapsed: 110.67 s
+Calling variants ...
+Total processed positions in chr12 (chunk 16/18) : 10000
+Total time elapsed: 113.88 s
+Calling variants ...
+Total processed positions in chr12 (chunk 7/18) : 10000
+Total time elapsed: 114.75 s
+Calling variants ...
+Total processed positions in chr12 (chunk 11/18) : 10000
+Total time elapsed: 115.95 s
+Calling variants ...
+Total processed positions in chr12 (chunk 8/18) : 10000
+Total time elapsed: 117.38 s
+Calling variants ...
+Total processed positions in chr12 (chunk 5/18) : 10000
+Total time elapsed: 117.56 s
+Calling variants ...
+Total processed positions in chr12 (chunk 1/18) : 10000
+Total time elapsed: 117.86 s
+Calling variants ...
+Total processed positions in chr12 (chunk 3/18) : 10000
+Total time elapsed: 118.30 s
+Calling variants ...
+Total processed positions in chr12 (chunk 10/18) : 10000
+Total time elapsed: 118.13 s
+Calling variants ...
+Total processed positions in chr12 (chunk 13/18) : 10000
+Total time elapsed: 119.82 s
+Calling variants ...
+Total processed positions in chr12 (chunk 4/18) : 10000
+Total time elapsed: 120.41 s
+Calling variants ...
+Total processed positions in chr12 (chunk 15/18) : 10000
+Total time elapsed: 121.87 s
+Calling variants ...
+Total processed positions in chr12 (chunk 14/18) : 10000
+Total time elapsed: 121.99 s
+Calling variants ...
+Total processed positions in chr12 (chunk 9/18) : 10000
+Total time elapsed: 122.71 s
+Calling variants ...
+Total processed positions in chr12 (chunk 2/18) : 10000
+Total time elapsed: 123.31 s
+Calling variants ...
+Total processed positions in chr12 (chunk 17/18) : 10000
+Total time elapsed: 123.09 s
+Calling variants ...
+Total processed positions in chr12 (chunk 12/18) : 10000
+Total time elapsed: 126.61 s
+
+real	2m10.378s
+user	33m30.002s
+sys	1m43.285s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr12: 71593
+[INFO] Full-alignment variants processed in chr12: 152759
+
+real	0m2.637s
+user	0m2.662s
+sys	0m0.193s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	6m12.925s
+user	60m9.139s
+sys	5m52.551s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr12: 119818, not found:473, not match:28, low_qual_count:0. Total normal:120205 Total tumor:120319, pro: 0.9958
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/vcf/chr12.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_chr12
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr12,56s)
+parsing total:  56s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 59s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_chr12.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_chr12.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr12
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 1s
+tag read start ...
+chr: chr12 ... 1123s
+tag read 1125s
+-------------------------------------------
+total process time:  1126s
+total alignment:     1449857
+total supplementary: 63961
+total secondary:     0
+total unmapped:      0
+total tag alignment: 918891
+total untagged:      530966
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr12 chunk 9/27: Total snv candidates found: 2526, total indel candidates found: 440
+[INFO] chr12 chunk 8/27: Total snv candidates found: 2811, total indel candidates found: 1113
+[INFO] chr12 chunk 0/27: Total snv candidates found: 1495, total indel candidates found: 1426
+[INFO] chr12 chunk 3/27: Total snv candidates found: 664, total indel candidates found: 1140
+[INFO] chr12 chunk 1/27: Total snv candidates found: 785, total indel candidates found: 1211
+[INFO] chr12 chunk 13/27: Total snv candidates found: 833, total indel candidates found: 1517
+[INFO] chr12 chunk 2/27: Total snv candidates found: 2279, total indel candidates found: 1237
+[INFO] chr12 chunk 16/27: Total snv candidates found: 491, total indel candidates found: 1006
+[INFO] chr12 chunk 12/27: Total snv candidates found: 804, total indel candidates found: 1380
+[INFO] chr12 chunk 14/27: Total snv candidates found: 633, total indel candidates found: 1357
+[INFO] chr12 chunk 17/27: Total snv candidates found: 600, total indel candidates found: 936
+[INFO] chr12 chunk 4/27: Total snv candidates found: 415, total indel candidates found: 859
+[INFO] chr12 chunk 6/27: Total snv candidates found: 599, total indel candidates found: 981
+[INFO] chr12 chunk 5/27: Total snv candidates found: 667, total indel candidates found: 900
+[INFO] chr12 chunk 11/27: Total snv candidates found: 480, total indel candidates found: 831
+[INFO] chr12 chunk 15/27: Total snv candidates found: 777, total indel candidates found: 729
+[INFO] chr12 chunk 7/27: Total snv candidates found: 1141, total indel candidates found: 964
+[INFO] chr12 chunk 10/27: Total snv candidates found: 712, total indel candidates found: 916
+[INFO] chr12 chunk 19/27: Total snv candidates found: 548, total indel candidates found: 788
+[INFO] chr12 chunk 22/27: Total snv candidates found: 418, total indel candidates found: 752
+[INFO] chr12 chunk 23/27: Total snv candidates found: 428, total indel candidates found: 890
+[INFO] chr12 chunk 20/27: Total snv candidates found: 395, total indel candidates found: 782
+[INFO] chr12 chunk 18/27: Total snv candidates found: 909, total indel candidates found: 816
+[INFO] chr12 chunk 26/27: Total snv candidates found: 536, total indel candidates found: 979
+[INFO] chr12 chunk 25/27: Total snv candidates found: 691, total indel candidates found: 913
+[INFO] chr12 chunk 21/27: Total snv candidates found: 425, total indel candidates found: 750
+[INFO] chr12 chunk 24/27: Total snv candidates found: 713, total indel candidates found: 1124
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/2-1_CPT.log
+
+[INFO] chr12 chunk 1-1/1 Tensors generated: 785
+[INFO] chr12 chunk 1-1/22 Tensors generated: 417
+[INFO] chr12 chunk 1-1/4 Tensors generated: 415
+[INFO] chr12 chunk 1-1/21 Tensors generated: 417
+[INFO] chr12 chunk 1-1/20 Tensors generated: 395
+[INFO] chr12 chunk 1-1/23 Tensors generated: 428
+[INFO] chr12 chunk 1-1/11 Tensors generated: 478
+[INFO] chr12 chunk 1-1/16 Tensors generated: 491
+[INFO] chr12 chunk 1-1/19 Tensors generated: 548
+[INFO] chr12 chunk 1-1/0 Tensors generated: 1488
+[INFO] chr12 chunk 1-1/26 Tensors generated: 535
+[INFO] chr12 chunk 1-1/2 Tensors generated: 2241
+[INFO] chr12 chunk 1-1/6 Tensors generated: 599
+[INFO] chr12 chunk 1-1/3 Tensors generated: 657
+[INFO] chr12 chunk 1-1/17 Tensors generated: 595
+[INFO] chr12 chunk 1-1/5 Tensors generated: 667
+[INFO] chr12 chunk 1-1/14 Tensors generated: 633
+[INFO] chr12 chunk 1-1/10 Tensors generated: 712
+[INFO] chr12 chunk 1-1/25 Tensors generated: 689
+[INFO] chr12 chunk 1-1/15 Tensors generated: 777
+[INFO] chr12 chunk 1-1/24 Tensors generated: 707
+[INFO] chr12 chunk 1-1/18 Tensors generated: 909
+[INFO] chr12 chunk 1-1/12 Tensors generated: 801
+[INFO] chr12 chunk 1-1/13 Tensors generated: 833
+[INFO] chr12 chunk 1-1/7 Tensors generated: 1134
+[INFO] chr12 chunk 1-1/8 Tensors generated: 2811
+[INFO] chr12 chunk 1-1/9 Tensors generated: 2526
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/2-2_PREDICT.log
+
+[INFO] chr12 total processed positions: 417, time elapsed: 1.3s
+[INFO] chr12 total processed positions: 415, time elapsed: 1.5s
+[INFO] chr12 total processed positions: 395, time elapsed: 1.5s
+[INFO] chr12 total processed positions: 428, time elapsed: 1.3s
+[INFO] chr12 total processed positions: 417, time elapsed: 1.2s
+[INFO] chr12 total processed positions: 478, time elapsed: 1.5s
+[INFO] chr12 total processed positions: 491, time elapsed: 1.7s
+[INFO] chr12 total processed positions: 548, time elapsed: 1.7s
+[INFO] chr12 total processed positions: 712, time elapsed: 1.9s
+[INFO] chr12 total processed positions: 595, time elapsed: 1.9s
+[INFO] chr12 total processed positions: 667, time elapsed: 1.8s
+[INFO] chr12 total processed positions: 535, time elapsed: 1.8s
+[INFO] chr12 total processed positions: 657, time elapsed: 1.8s
+[INFO] chr12 total processed positions: 689, time elapsed: 1.9s
+[INFO] chr12 total processed positions: 633, time elapsed: 1.6s
+[INFO] chr12 total processed positions: 599, time elapsed: 1.9s
+[INFO] chr12 total processed positions: 785, time elapsed: 2.1s
+[INFO] chr12 total processed positions: 707, time elapsed: 2.1s
+[INFO] chr12 total processed positions: 777, time elapsed: 2.1s
+[INFO] chr12 total processed positions: 801, time elapsed: 2.2s
+[INFO] chr12 total processed positions: 833, time elapsed: 2.2s
+[INFO] chr12 total processed positions: 909, time elapsed: 2.4s
+[INFO] chr12 total processed positions: 1134, time elapsed: 2.6s
+[INFO] chr12 total processed positions: 1488, time elapsed: 3.5s
+[INFO] chr12 total processed positions: 2241, time elapsed: 4.9s
+[INFO] chr12 total processed positions: 2526, time elapsed: 5.6s
+[INFO] chr12 total processed positions: 2811, time elapsed: 6.3s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/3-1_CPT.log
+
+[INFO] chr12 chunk 1-1/22 Tensors generated: 417
+[INFO] chr12 chunk 1-1/20 Tensors generated: 395
+[INFO] chr12 chunk 1-1/4 Tensors generated: 415
+[INFO] chr12 chunk 1-1/23 Tensors generated: 428
+[INFO] chr12 chunk 1-1/21 Tensors generated: 417
+[INFO] chr12 chunk 1-1/16 Tensors generated: 491
+[INFO] chr12 chunk 1-1/11 Tensors generated: 478
+[INFO] chr12 chunk 1-1/26 Tensors generated: 535
+[INFO] chr12 chunk 1-1/19 Tensors generated: 548
+[INFO] chr12 chunk 1-1/1 Tensors generated: 785
+[INFO] chr12 chunk 1-1/6 Tensors generated: 599
+[INFO] chr12 chunk 1-1/14 Tensors generated: 633
+[INFO] chr12 chunk 1-1/17 Tensors generated: 595
+[INFO] chr12 chunk 1-1/3 Tensors generated: 657
+[INFO] chr12 chunk 1-1/10 Tensors generated: 712
+[INFO] chr12 chunk 1-1/5 Tensors generated: 667
+[INFO] chr12 chunk 1-1/25 Tensors generated: 689
+[INFO] chr12 chunk 1-1/24 Tensors generated: 707
+[INFO] chr12 chunk 1-1/15 Tensors generated: 777
+[INFO] chr12 chunk 1-1/12 Tensors generated: 801
+[INFO] chr12 chunk 1-1/13 Tensors generated: 833
+[INFO] chr12 chunk 1-1/18 Tensors generated: 909
+[INFO] chr12 chunk 1-1/7 Tensors generated: 1134
+[INFO] chr12 chunk 1-1/0 Tensors generated: 1488
+[INFO] chr12 chunk 1-1/2 Tensors generated: 2241
+[INFO] chr12 chunk 1-1/9 Tensors generated: 2280
+[INFO] chr12 chunk 1-1/8 Tensors generated: 2778
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/3-2_PREDICT.log
+
+[INFO] chr12 total processed positions: 415, time elapsed: 48.3s
+[INFO] chr12 total processed positions: 417, time elapsed: 48.5s
+[INFO] chr12 total processed positions: 395, time elapsed: 49.5s
+[INFO] chr12 total processed positions: 428, time elapsed: 50.3s
+[INFO] chr12 total processed positions: 417, time elapsed: 54.0s
+[INFO] chr12 total processed positions: 491, time elapsed: 57.1s
+[INFO] chr12 total processed positions: 478, time elapsed: 58.8s
+[INFO] chr12 total processed positions: 548, time elapsed: 66.7s
+[INFO] chr12 total processed positions: 535, time elapsed: 69.2s
+[INFO] chr12 total processed positions: 599, time elapsed: 69.5s
+[INFO] chr12 total processed positions: 595, time elapsed: 72.0s
+[INFO] chr12 total processed positions: 633, time elapsed: 78.3s
+[INFO] chr12 total processed positions: 667, time elapsed: 79.4s
+[INFO] chr12 total processed positions: 689, time elapsed: 79.8s
+[INFO] chr12 total processed positions: 657, time elapsed: 80.2s
+[INFO] chr12 total processed positions: 707, time elapsed: 87.6s
+[INFO] chr12 total processed positions: 712, time elapsed: 88.7s
+[INFO] chr12 total processed positions: 801, time elapsed: 93.8s
+[INFO] chr12 total processed positions: 777, time elapsed: 94.4s
+[INFO] chr12 total processed positions: 833, time elapsed: 96.2s
+[INFO] chr12 total processed positions: 785, time elapsed: 97.4s
+[INFO] chr12 total processed positions: 909, time elapsed: 108.8s
+[INFO] chr12 total processed positions: 1134, time elapsed: 132.7s
+[INFO] chr12 total processed positions: 1488, time elapsed: 183.2s
+[INFO] chr12 total processed positions: 2241, time elapsed: 257.5s
+[INFO] chr12 total processed positions: 2280, time elapsed: 270.4s
+[INFO] chr12 total processed positions: 2778, time elapsed: 323.0s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --vcf_fn_prefix fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 4: Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/4_HAP_FILTER.log
+
+[INFO] Processing in chr12, total processed positions: 1000
+[INFO] Processing in chr12, total processed positions: 2000
+Total input calls: 7861, filtered by haplotype match 34
+
+[INFO] STEP 5: Merge and sort VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/output.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/5_MV.log
+
+[INFO] Full-alignment variants filtered by pileup:  818
+
+[INFO] STEP 6: Indel Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates --input_prefix INDEL_CANDIDATES_FILE_ --output_fn INDEL_CANDIDATES_FILES  && ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_6-1_create_pair_tensor_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/pileup_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/6-1_CPTI.log
+
+[INFO] chr12  Tensors generated: 1211
+[INFO] chr12  Tensors generated: 1424
+[INFO] chr12  Tensors generated: 1236
+[INFO] chr12  Tensors generated: 440
+[INFO] chr12  Tensors generated: 729
+[INFO] chr12  Tensors generated: 750
+[INFO] chr12  Tensors generated: 788
+[INFO] chr12  Tensors generated: 748
+[INFO] chr12  Tensors generated: 782
+[INFO] chr12  Tensors generated: 858
+[INFO] chr12  Tensors generated: 890
+[INFO] chr12  Tensors generated: 831
+[INFO] chr12  Tensors generated: 816
+[INFO] chr12  Tensors generated: 900
+[INFO] chr12  Tensors generated: 916
+[INFO] chr12  Tensors generated: 931
+[INFO] chr12  Tensors generated: 962
+[INFO] chr12  Tensors generated: 913
+[INFO] chr12  Tensors generated: 978
+[INFO] chr12  Tensors generated: 981
+[INFO] chr12  Tensors generated: 1006
+[INFO] chr12  Tensors generated: 1113
+[INFO] chr12  Tensors generated: 1123
+[INFO] chr12  Tensors generated: 1138
+[INFO] chr12  Tensors generated: 1357
+[INFO] chr12  Tensors generated: 1371
+[INFO] chr12  Tensors generated: 1517
+
+[INFO] Indel Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_6-2_predict_indel.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/pileup_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/6-2_PREDICT_INDEL.log
+
+[INFO] chr12 total processed positions: 440, time elapsed: 1.1s
+[INFO] chr12 total processed positions: 748, time elapsed: 1.7s
+[INFO] chr12 total processed positions: 782, time elapsed: 2.0s
+[INFO] chr12 total processed positions: 750, time elapsed: 2.0s
+[INFO] chr12 total processed positions: 729, time elapsed: 2.0s
+[INFO] chr12 total processed positions: 816, time elapsed: 2.1s
+[INFO] chr12 total processed positions: 858, time elapsed: 2.1s
+[INFO] chr12 total processed positions: 788, time elapsed: 2.0s
+[INFO] chr12 total processed positions: 890, time elapsed: 2.3s
+[INFO] chr12 total processed positions: 962, time elapsed: 2.2s
+[INFO] chr12 total processed positions: 916, time elapsed: 2.1s
+[INFO] chr12 total processed positions: 831, time elapsed: 2.0s
+[INFO] chr12 total processed positions: 931, time elapsed: 2.2s
+[INFO] chr12 total processed positions: 900, time elapsed: 2.4s
+[INFO] chr12 total processed positions: 978, time elapsed: 2.4s
+[INFO] chr12 total processed positions: 981, time elapsed: 2.4s
+[INFO] chr12 total processed positions: 1113, time elapsed: 2.4s
+[INFO] chr12 total processed positions: 1006, time elapsed: 2.7s
+[INFO] chr12 total processed positions: 913, time elapsed: 2.4s
+[INFO] chr12 total processed positions: 1138, time elapsed: 2.6s
+[INFO] chr12 total processed positions: 1123, time elapsed: 2.7s
+[INFO] chr12 total processed positions: 1357, time elapsed: 3.1s
+[INFO] chr12 total processed positions: 1236, time elapsed: 2.7s
+[INFO] chr12 total processed positions: 1211, time elapsed: 2.8s
+[INFO] chr12 total processed positions: 1517, time elapsed: 3.2s
+[INFO] chr12 total processed positions: 1371, time elapsed: 3.0s
+[INFO] chr12 total processed positions: 1424, time elapsed: 3.1s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --vcf_fn_prefix indel_p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 7: Indel Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_7-1_create_pair_tensor_fa_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/fa_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/7-1_CPTI.log
+
+[INFO] chr12  Tensors generated: 425
+[INFO] chr12  Tensors generated: 729
+[INFO] chr12  Tensors generated: 750
+[INFO] chr12  Tensors generated: 1236
+[INFO] chr12  Tensors generated: 748
+[INFO] chr12  Tensors generated: 1211
+[INFO] chr12  Tensors generated: 788
+[INFO] chr12  Tensors generated: 782
+[INFO] chr12  Tensors generated: 831
+[INFO] chr12  Tensors generated: 816
+[INFO] chr12  Tensors generated: 858
+[INFO] chr12  Tensors generated: 890
+[INFO] chr12  Tensors generated: 1424
+[INFO] chr12  Tensors generated: 900
+[INFO] chr12  Tensors generated: 916
+[INFO] chr12  Tensors generated: 931
+[INFO] chr12  Tensors generated: 913
+[INFO] chr12  Tensors generated: 1006
+[INFO] chr12  Tensors generated: 962
+[INFO] chr12  Tensors generated: 978
+[INFO] chr12  Tensors generated: 981
+[INFO] chr12  Tensors generated: 1112
+[INFO] chr12  Tensors generated: 1123
+[INFO] chr12  Tensors generated: 1138
+[INFO] chr12  Tensors generated: 1357
+[INFO] chr12  Tensors generated: 1371
+[INFO] chr12  Tensors generated: 1517
+
+[INFO] Indel Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_7-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/fa_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/7-2_PREDICT_INDEL.log
+
+[INFO] chr12 total processed positions: 425, time elapsed: 53.4s
+[INFO] chr12 total processed positions: 729, time elapsed: 83.3s
+[INFO] chr12 total processed positions: 750, time elapsed: 85.7s
+[INFO] chr12 total processed positions: 748, time elapsed: 87.5s
+[INFO] chr12 total processed positions: 788, time elapsed: 89.9s
+[INFO] chr12 total processed positions: 782, time elapsed: 95.2s
+[INFO] chr12 total processed positions: 816, time elapsed: 97.1s
+[INFO] chr12 total processed positions: 831, time elapsed: 101.4s
+[INFO] chr12 total processed positions: 916, time elapsed: 105.7s
+[INFO] chr12 total processed positions: 900, time elapsed: 106.1s
+[INFO] chr12 total processed positions: 858, time elapsed: 106.5s
+[INFO] chr12 total processed positions: 890, time elapsed: 106.7s
+[INFO] chr12 total processed positions: 931, time elapsed: 108.3s
+[INFO] chr12 total processed positions: 913, time elapsed: 110.0s
+[INFO] chr12 total processed positions: 962, time elapsed: 112.2s
+[INFO] chr12 total processed positions: 981, time elapsed: 115.5s
+[INFO] chr12 total processed positions: 978, time elapsed: 115.8s
+[INFO] chr12 total processed positions: 1006, time elapsed: 119.8s
+[INFO] chr12 total processed positions: 1123, time elapsed: 129.9s
+[INFO] chr12 total processed positions: 1112, time elapsed: 130.7s
+[INFO] chr12 total processed positions: 1138, time elapsed: 131.7s
+[INFO] chr12 total processed positions: 1211, time elapsed: 144.9s
+[INFO] chr12 total processed positions: 1236, time elapsed: 155.4s
+[INFO] chr12 total processed positions: 1357, time elapsed: 158.8s
+[INFO] chr12 total processed positions: 1371, time elapsed: 160.5s
+[INFO] chr12 total processed positions: 1517, time elapsed: 171.4s
+[INFO] chr12 total processed positions: 1424, time elapsed: 172.8s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --vcf_fn_prefix indel_fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] Indel Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 --is_indel  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/8_INDEL_HAP_FILTER.log
+
+Total input calls: 2224, filtered by haplotype match 22
+
+[INFO] STEP 8: Merge and sort Indel VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/indel.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --indel_calling  --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/8_MVI.log
+
+[INFO] Full-alignment variants filtered by pileup:  256
+
+[INFO] Total time elapsed: 47m44.00s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/output.vcf.gz
+
+[INFO] Finish calling, snv output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/snv.vcf.gz
+
+[INFO] Finish calling, indel output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/indel.vcf.gz
+
+[INFO] Finish calling, Clair3 tumor BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/clair3_tumor_germline_output.vcf.gz
+
+[INFO] Finish calling, Clair3 normal BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/clair3_normal_germline_output.vcf.gz
+
+cp /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/clair3_tumor_germline_output.vcf.gz
+slurmstepd: error: Detected 24 oom_kill events in StepId=2556285.batch. Some of the step tasks have been OOM Killed.
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556285
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n01
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 15:36:00
+Job ended at:   2025-12-08 16:23:46
+Job Wall-clock time: 00:47:46
+CPU Utilized: 07:37:54
+CPU Efficiency: 23.97% of 1-07:50:40 core-walltime
+Memory Utilized: 38.49 GB
+Memory Efficiency: 96.23% of 40.00 GB

slurm-2556286.out

@@ -0,0 +1,837 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19 --region chr19:19687872-61707364 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr19
+[INFO] Number of chunks for each contig: 13
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr19:19687872-61707364
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output --ctg_name=chr19 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr19
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr19 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr19
+[INFO] Chunk number for each contig: 13
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr19 (chunk 6/13) : 37439
+Total time elapsed: 76.50 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/13) : 71150
+Total time elapsed: 111.60 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/13) : 77159
+Total time elapsed: 123.33 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/13) : 80011
+Total time elapsed: 124.76 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/13) : 80468
+Total time elapsed: 126.74 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/13) : 77903
+Total time elapsed: 128.57 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/13) : 76878
+Total time elapsed: 134.04 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/13) : 81026
+Total time elapsed: 135.88 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/13) : 83832
+Total time elapsed: 136.52 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/13) : 82363
+Total time elapsed: 137.86 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/13) : 82264
+Total time elapsed: 137.94 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/13) : 86660
+Total time elapsed: 138.89 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/13) : 90012
+Total time elapsed: 143.08 s
+
+real	2m29.543s
+user	26m56.703s
+sys	0m54.584s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
+[INFO] Total heterozygous SNP positions selected: chr19: 52254
+
+real	0m1.699s
+user	0m1.541s
+sys	0m0.121s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr19,6s)
+parsing total:  6s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 6s
+
+real	0m6.096s
+user	0m11.240s
+sys	0m0.898s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 12.0
+[INFO] Low quality reference calls to be processed in chr19: 86848
+[INFO] Low quality variants to be processed in chr19: 96058
+
+real	0m1.960s
+user	0m1.724s
+sys	0m0.183s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr19 (chunk 19/19) : 2906
+Total time elapsed: 36.42 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/19) : 10000
+Total time elapsed: 93.49 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/19) : 10000
+Total time elapsed: 94.05 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/19) : 10000
+Total time elapsed: 93.35 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/19) : 10000
+Total time elapsed: 94.34 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/19) : 10000
+Total time elapsed: 95.86 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/19) : 10000
+Total time elapsed: 117.23 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/19) : 10000
+Total time elapsed: 120.15 s
+Calling variants ...
+Total processed positions in chr19 (chunk 17/19) : 10000
+Total time elapsed: 123.44 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/19) : 10000
+Total time elapsed: 123.86 s
+Calling variants ...
+Total processed positions in chr19 (chunk 15/19) : 10000
+Total time elapsed: 127.14 s
+Calling variants ...
+Total processed positions in chr19 (chunk 16/19) : 10000
+Total time elapsed: 126.93 s
+Calling variants ...
+Total processed positions in chr19 (chunk 18/19) : 10000
+Total time elapsed: 128.06 s
+Calling variants ...
+Total processed positions in chr19 (chunk 14/19) : 10000
+Total time elapsed: 129.98 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/19) : 10000
+Total time elapsed: 130.95 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/19) : 10000
+Total time elapsed: 130.95 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/19) : 10000
+Total time elapsed: 133.96 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/19) : 10000
+Total time elapsed: 137.57 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/19) : 10000
+Total time elapsed: 138.21 s
+
+real	2m21.463s
+user	35m16.409s
+sys	1m42.241s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr19: 41215
+[INFO] Full-alignment variants processed in chr19: 104681
+
+real	0m2.349s
+user	0m2.608s
+sys	0m0.178s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	5m13.675s
+user	62m39.427s
+sys	2m39.420s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output --ctg_name=chr19 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr19
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr19 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr19
+[INFO] Chunk number for each contig: 13
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr19 (chunk 10/13) : 10530
+Total time elapsed: 50.88 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/13) : 10757
+Total time elapsed: 52.23 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/13) : 11930
+Total time elapsed: 52.66 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/13) : 13827
+Total time elapsed: 55.87 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/13) : 13999
+Total time elapsed: 56.00 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/13) : 15863
+Total time elapsed: 56.26 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/13) : 15113
+Total time elapsed: 57.61 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/13) : 15431
+Total time elapsed: 59.04 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/13) : 19185
+Total time elapsed: 62.90 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/13) : 18004
+Total time elapsed: 62.98 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/13) : 18455
+Total time elapsed: 65.21 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/13) : 43919
+Total time elapsed: 97.41 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/13) : 53083
+Total time elapsed: 107.16 s
+
+real	1m50.498s
+user	10m58.237s
+sys	0m47.782s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 18
+[INFO] Total heterozygous SNP positions selected: chr19: 62515
+
+real	0m0.831s
+user	0m0.695s
+sys	0m0.107s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr19,20s)
+parsing total:  20s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 21s
+
+real	0m21.317s
+user	0m54.224s
+sys	0m2.968s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 7.0
+[INFO] Low quality reference calls to be processed in chr19: 10511
+[INFO] Low quality variants to be processed in chr19: 108203
+
+real	0m0.832s
+user	0m0.670s
+sys	0m0.126s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr19 (chunk 12/12) : 8714
+Total time elapsed: 93.54 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/12) : 10000
+Total time elapsed: 95.64 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/12) : 10000
+Total time elapsed: 97.47 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/12) : 10000
+Total time elapsed: 100.08 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/12) : 10000
+Total time elapsed: 101.49 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/12) : 10000
+Total time elapsed: 106.04 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/12) : 10000
+Total time elapsed: 112.68 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/12) : 10000
+Total time elapsed: 113.52 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/12) : 10000
+Total time elapsed: 114.85 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/12) : 10000
+Total time elapsed: 116.61 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/12) : 10000
+Total time elapsed: 118.10 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/12) : 10000
+Total time elapsed: 123.39 s
+
+real	2m5.940s
+user	20m24.906s
+sys	1m5.423s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr19: 46569
+[INFO] Full-alignment variants processed in chr19: 101152
+
+real	0m1.492s
+user	0m1.512s
+sys	0m0.131s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	4m26.312s
+user	32m24.642s
+sys	1m57.158s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr19: 84452, not found:765, not match:81, low_qual_count:0. Total normal:76459 Total tumor:85298, pro: 0.9901
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr19,35s)
+parsing total:  35s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 36s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_chr19.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_chr19.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr19
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 0s
+tag read start ...
+chr: chr19 ... 624s
+tag read 625s
+-------------------------------------------
+total process time:  625s
+total alignment:     734582
+total supplementary: 28447
+total secondary:     0
+total unmapped:      0
+total tag alignment: 390188
+total untagged:      344394
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr19 chunk 2/13: Total snv candidates found: 8283, total indel candidates found: 192
+[INFO] chr19 chunk 1/13: Total snv candidates found: 8305, total indel candidates found: 982
+[INFO] chr19 chunk 9/13: Total snv candidates found: 1134, total indel candidates found: 1711
+[INFO] chr19 chunk 8/13: Total snv candidates found: 724, total indel candidates found: 1286
+[INFO] chr19 chunk 6/13: Total snv candidates found: 1237, total indel candidates found: 1303
+[INFO] chr19 chunk 3/13: Total snv candidates found: 8985, total indel candidates found: 1029
+[INFO] chr19 chunk 11/13: Total snv candidates found: 1775, total indel candidates found: 1483
+[INFO] chr19 chunk 5/13: Total snv candidates found: 930, total indel candidates found: 1172
+[INFO] chr19 chunk 4/13: Total snv candidates found: 622, total indel candidates found: 1052
+[INFO] chr19 chunk 10/13: Total snv candidates found: 1091, total indel candidates found: 1615
+[INFO] chr19 chunk 12/13: Total snv candidates found: 1165, total indel candidates found: 1426
+[faidx] Truncated sequence: chr19:58474127-61708401
+[INFO] chr19 chunk 0/13: Total snv candidates found: 1028, total indel candidates found: 1065
+[INFO] chr19 chunk 7/13: Total snv candidates found: 774, total indel candidates found: 1459
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/2-1_CPT.log
+
+[INFO] chr19 chunk 1-1/4 Tensors generated: 612
+[INFO] chr19 chunk 1-1/8 Tensors generated: 721
+[INFO] chr19 chunk 1-1/5 Tensors generated: 908
+[INFO] chr19 chunk 1-1/7 Tensors generated: 772
+[INFO] chr19 chunk 1-1/0 Tensors generated: 1025
+[INFO] chr19 chunk 1-1/9 Tensors generated: 1129
+[INFO] chr19 chunk 1-1/12 Tensors generated: 1143
+[INFO] chr19 chunk 1-1/6 Tensors generated: 1221
+[INFO] chr19 chunk 1-1/10 Tensors generated: 1090
+[INFO] chr19 chunk 1-1/11 Tensors generated: 1774
+[INFO] chr19 chunk 1-1/3 Tensors generated: 8980
+[INFO] chr19 chunk 1-1/1 Tensors generated: 8202
+[INFO] chr19 chunk 1-1/2 Tensors generated: 8263
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/2-2_PREDICT.log
+
+[INFO] chr19 total processed positions: 612, time elapsed: 1.4s
+[INFO] chr19 total processed positions: 721, time elapsed: 1.6s
+[INFO] chr19 total processed positions: 772, time elapsed: 1.7s
+[INFO] chr19 total processed positions: 908, time elapsed: 1.9s
+[INFO] chr19 total processed positions: 1143, time elapsed: 2.3s
+[INFO] chr19 total processed positions: 1090, time elapsed: 2.3s
+[INFO] chr19 total processed positions: 1129, time elapsed: 2.3s
+[INFO] chr19 total processed positions: 1221, time elapsed: 2.4s
+[INFO] chr19 total processed positions: 1025, time elapsed: 2.7s
+[INFO] chr19 total processed positions: 1774, time elapsed: 4.0s
+[INFO] chr19 total processed positions: 8263, time elapsed: 13.1s
+[INFO] chr19 total processed positions: 8202, time elapsed: 13.1s
+[INFO] chr19 total processed positions: 8980, time elapsed: 14.4s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/3-1_CPT.log
+
+[INFO] chr19 chunk 1-1/4 Tensors generated: 612
+[INFO] chr19 chunk 1-1/8 Tensors generated: 721
+[INFO] chr19 chunk 1-1/7 Tensors generated: 772
+[INFO] chr19 chunk 1-1/5 Tensors generated: 908
+[INFO] chr19 chunk 1-1/0 Tensors generated: 1025
+[INFO] chr19 chunk 1-1/6 Tensors generated: 1091
+[INFO] chr19 chunk 1-1/9 Tensors generated: 1121
+[INFO] chr19 chunk 1-1/10 Tensors generated: 1089
+[INFO] chr19 chunk 1-1/12 Tensors generated: 1139
+[INFO] chr19 chunk 1-1/11 Tensors generated: 1774
+[INFO] chr19 chunk 1-1/2 Tensors generated: 6524
+[INFO] chr19 chunk 1-1/1 Tensors generated: 7891
+[INFO] chr19 chunk 1-1/3 Tensors generated: 8612
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/3-2_PREDICT.log
+
+[INFO] chr19 total processed positions: 612, time elapsed: 108.1s
+[INFO] chr19 total processed positions: 721, time elapsed: 127.1s
+[INFO] chr19 total processed positions: 772, time elapsed: 136.3s
+[INFO] chr19 total processed positions: 908, time elapsed: 160.0s
+[INFO] chr19 total processed positions: 1025, time elapsed: 180.3s
+[INFO] chr19 total processed positions: 1089, time elapsed: 191.9s
+[INFO] chr19 total processed positions: 1091, time elapsed: 192.8s
+[INFO] chr19 total processed positions: 1121, time elapsed: 198.1s
+[INFO] chr19 total processed positions: 1139, time elapsed: 201.0s
+[INFO] chr19 total processed positions: 1774, time elapsed: 312.7s
+[INFO] chr19 total processed positions: 6524, time elapsed: 1146.6s
+[INFO] chr19 total processed positions: 7891, time elapsed: 1393.6s
+[INFO] chr19 total processed positions: 8612, time elapsed: 1517.7s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --vcf_fn_prefix fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 4: Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/4_HAP_FILTER.log
+
+[INFO] Processing in chr19, total processed positions: 1000
+Total input calls: 4369, filtered by haplotype match 24
+
+[INFO] STEP 5: Merge and sort VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/output.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/5_MV.log
+
+[INFO] Full-alignment variants filtered by pileup:  400
+
+[INFO] STEP 6: Indel Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates --input_prefix INDEL_CANDIDATES_FILE_ --output_fn INDEL_CANDIDATES_FILES  && ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_6-1_create_pair_tensor_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/6-1_CPTI.log
+
+[INFO] chr19  Tensors generated: 192
+[INFO] chr19  Tensors generated: 1047
+[INFO] chr19  Tensors generated: 1063
+[INFO] chr19  Tensors generated: 976
+[INFO] chr19  Tensors generated: 1158
+[INFO] chr19  Tensors generated: 1281
+[INFO] chr19  Tensors generated: 1029
+[INFO] chr19  Tensors generated: 1299
+[INFO] chr19  Tensors generated: 1483
+[INFO] chr19  Tensors generated: 1417
+[INFO] chr19  Tensors generated: 1456
+[INFO] chr19  Tensors generated: 1707
+[INFO] chr19  Tensors generated: 1615
+
+[INFO] Indel Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_6-2_predict_indel.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/6-2_PREDICT_INDEL.log
+
+[INFO] chr19 total processed positions: 192, time elapsed: 0.5s
+[INFO] chr19 total processed positions: 976, time elapsed: 1.8s
+[INFO] chr19 total processed positions: 1047, time elapsed: 1.9s
+[INFO] chr19 total processed positions: 1063, time elapsed: 2.0s
+[INFO] chr19 total processed positions: 1158, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 1029, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 1299, time elapsed: 2.5s
+[INFO] chr19 total processed positions: 1281, time elapsed: 2.4s
+[INFO] chr19 total processed positions: 1456, time elapsed: 2.5s
+[INFO] chr19 total processed positions: 1615, time elapsed: 2.8s
+[INFO] chr19 total processed positions: 1417, time elapsed: 2.5s
+[INFO] chr19 total processed positions: 1483, time elapsed: 2.6s
+[INFO] chr19 total processed positions: 1707, time elapsed: 3.4s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --vcf_fn_prefix indel_p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 7: Indel Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_7-1_create_pair_tensor_fa_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/7-1_CPTI.log
+
+[INFO] chr19  Tensors generated: 158
+[INFO] chr19  Tensors generated: 960
+[INFO] chr19  Tensors generated: 1014
+[INFO] chr19  Tensors generated: 1047
+[INFO] chr19  Tensors generated: 1063
+[INFO] chr19  Tensors generated: 1158
+[INFO] chr19  Tensors generated: 1281
+[INFO] chr19  Tensors generated: 1293
+[INFO] chr19  Tensors generated: 1456
+[INFO] chr19  Tensors generated: 1483
+[INFO] chr19  Tensors generated: 1417
+[INFO] chr19  Tensors generated: 1702
+[INFO] chr19  Tensors generated: 1613
+
+[INFO] Indel Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_7-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/7-2_PREDICT_INDEL.log
+
+[INFO] chr19 total processed positions: 158, time elapsed: 24.8s
+[INFO] chr19 total processed positions: 960, time elapsed: 158.9s
+[INFO] chr19 total processed positions: 1014, time elapsed: 170.0s
+[INFO] chr19 total processed positions: 1047, time elapsed: 177.1s
+[INFO] chr19 total processed positions: 1063, time elapsed: 178.3s
+[INFO] chr19 total processed positions: 1158, time elapsed: 194.8s
+[INFO] chr19 total processed positions: 1281, time elapsed: 214.9s
+[INFO] chr19 total processed positions: 1293, time elapsed: 216.6s
+[INFO] chr19 total processed positions: 1417, time elapsed: 238.2s
+[INFO] chr19 total processed positions: 1456, time elapsed: 244.8s
+[INFO] chr19 total processed positions: 1483, time elapsed: 249.6s
+[INFO] chr19 total processed positions: 1613, time elapsed: 271.6s
+[INFO] chr19 total processed positions: 1702, time elapsed: 284.8s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --vcf_fn_prefix indel_fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] Indel Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 --is_indel  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/8_INDEL_HAP_FILTER.log
+
+Total input calls: 1438, filtered by haplotype match 12
+
+[INFO] STEP 8: Merge and sort Indel VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/indel.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --indel_calling  --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/8_MVI.log
+
+[INFO] Full-alignment variants filtered by pileup:  125
+
+[INFO] Total time elapsed: 54m50.00s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/output.vcf.gz
+
+[INFO] Finish calling, snv output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/snv.vcf.gz
+
+[INFO] Finish calling, indel output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/indel.vcf.gz
+
+[INFO] Finish calling, Clair3 tumor BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/clair3_tumor_germline_output.vcf.gz
+
+[INFO] Finish calling, Clair3 normal BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/clair3_normal_germline_output.vcf.gz
+
+cp /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/clair3_tumor_germline_output.vcf.gz
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556286
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n18
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 15:50:03
+Job ended at:   2025-12-08 16:44:55
+Job Wall-clock time: 00:54:52
+CPU Utilized: 05:06:15
+CPU Efficiency: 13.95% of 1-12:34:40 core-walltime
+Memory Utilized: 20.57 GB
+Memory Efficiency: 51.43% of 40.00 GB

slurm-2556287.out

@@ -0,0 +1,976 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13 --region chr15:68861668-99753195 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr15
+[INFO] Number of chunks for each contig: 20
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr15:68861668-99753195
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output --ctg_name=chr15 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr15
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr15 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr15
+[INFO] Chunk number for each contig: 20
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr15 (chunk 2/20) : 12228
+Total time elapsed: 44.06 s
+Calling variants ...
+Total processed positions in chr15 (chunk 1/20) : 17171
+Total time elapsed: 56.65 s
+Calling variants ...
+Total processed positions in chr15 (chunk 3/20) : 19201
+Total time elapsed: 57.60 s
+Calling variants ...
+Total processed positions in chr15 (chunk 9/20) : 75952
+Total time elapsed: 172.22 s
+Calling variants ...
+Total processed positions in chr15 (chunk 10/20) : 73614
+Total time elapsed: 172.93 s
+Calling variants ...
+Total processed positions in chr15 (chunk 7/20) : 78004
+Total time elapsed: 175.17 s
+Calling variants ...
+Total processed positions in chr15 (chunk 4/20) : 76273
+Total time elapsed: 182.27 s
+Calling variants ...
+Total processed positions in chr15 (chunk 15/20) : 82164
+Total time elapsed: 187.10 s
+Calling variants ...
+Total processed positions in chr15 (chunk 11/20) : 81432
+Total time elapsed: 187.39 s
+Calling variants ...
+Total processed positions in chr15 (chunk 17/20) : 87476
+Total time elapsed: 192.90 s
+Calling variants ...
+Total processed positions in chr15 (chunk 8/20) : 83225
+Total time elapsed: 193.10 s
+Calling variants ...
+Total processed positions in chr15 (chunk 5/20) : 87326
+Total time elapsed: 193.34 s
+Calling variants ...
+Total processed positions in chr15 (chunk 18/20) : 84823
+Total time elapsed: 194.61 s
+Calling variants ...
+Total processed positions in chr15 (chunk 6/20) : 80932
+Total time elapsed: 194.76 s
+Calling variants ...
+Total processed positions in chr15 (chunk 13/20) : 86377
+Total time elapsed: 196.16 s
+Calling variants ...
+Total processed positions in chr15 (chunk 16/20) : 85312
+Total time elapsed: 198.41 s
+Calling variants ...
+Total processed positions in chr15 (chunk 20/20) : 89114
+Total time elapsed: 201.11 s
+Calling variants ...
+Total processed positions in chr15 (chunk 14/20) : 81844
+Total time elapsed: 201.31 s
+Calling variants ...
+Total processed positions in chr15 (chunk 19/20) : 87661
+Total time elapsed: 211.31 s
+Calling variants ...
+Total processed positions in chr15 (chunk 12/20) : 91236
+Total time elapsed: 214.32 s
+
+real	3m42.531s
+user	55m25.930s
+sys	2m26.524s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15
+[INFO] Total heterozygous SNP positions selected: chr15: 72128
+
+real	0m2.946s
+user	0m2.713s
+sys	0m0.189s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr15.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr15
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr15,8s)
+parsing total:  8s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 11s
+
+real	0m10.891s
+user	0m33.649s
+sys	0m2.733s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 13.0
+[INFO] Low quality reference calls to be processed in chr15: 127976
+[INFO] Low quality variants to be processed in chr15: 126874
+
+real	0m3.487s
+user	0m3.038s
+sys	0m0.376s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr15 (chunk 26/26) : 4850
+Total time elapsed: 74.39 s
+Calling variants ...
+Total processed positions in chr15 (chunk 18/26) : 10000
+Total time elapsed: 116.97 s
+Calling variants ...
+Total processed positions in chr15 (chunk 13/26) : 10000
+Total time elapsed: 116.98 s
+Calling variants ...
+Total processed positions in chr15 (chunk 16/26) : 10000
+Total time elapsed: 117.15 s
+Calling variants ...
+Total processed positions in chr15 (chunk 22/26) : 10000
+Total time elapsed: 120.44 s
+Calling variants ...
+Total processed positions in chr15 (chunk 6/26) : 10000
+Total time elapsed: 119.66 s
+Calling variants ...
+Total processed positions in chr15 (chunk 1/26) : 10000
+Total time elapsed: 120.01 s
+Calling variants ...
+Total processed positions in chr15 (chunk 24/26) : 10000
+Total time elapsed: 124.22 s
+Calling variants ...
+Total processed positions in chr15 (chunk 4/26) : 10000
+Total time elapsed: 128.92 s
+Calling variants ...
+Total processed positions in chr15 (chunk 5/26) : 10000
+Total time elapsed: 131.51 s
+Calling variants ...
+Total processed positions in chr15 (chunk 23/26) : 10000
+Total time elapsed: 131.19 s
+Calling variants ...
+Total processed positions in chr15 (chunk 3/26) : 10000
+Total time elapsed: 137.09 s
+Calling variants ...
+Total processed positions in chr15 (chunk 19/26) : 10000
+Total time elapsed: 137.37 s
+Calling variants ...
+Total processed positions in chr15 (chunk 10/26) : 10000
+Total time elapsed: 136.44 s
+Calling variants ...
+Total processed positions in chr15 (chunk 15/26) : 10000
+Total time elapsed: 138.01 s
+Calling variants ...
+Total processed positions in chr15 (chunk 17/26) : 10000
+Total time elapsed: 139.18 s
+Calling variants ...
+Total processed positions in chr15 (chunk 12/26) : 10000
+Total time elapsed: 139.32 s
+Calling variants ...
+Total processed positions in chr15 (chunk 25/26) : 10000
+Total time elapsed: 140.67 s
+Calling variants ...
+Total processed positions in chr15 (chunk 11/26) : 10000
+Total time elapsed: 140.74 s
+Calling variants ...
+Total processed positions in chr15 (chunk 21/26) : 10000
+Total time elapsed: 141.21 s
+Calling variants ...
+Total processed positions in chr15 (chunk 7/26) : 10000
+Total time elapsed: 144.40 s
+Calling variants ...
+Total processed positions in chr15 (chunk 9/26) : 10000
+Total time elapsed: 144.79 s
+Calling variants ...
+Total processed positions in chr15 (chunk 20/26) : 10000
+Total time elapsed: 144.78 s
+Calling variants ...
+Total processed positions in chr15 (chunk 14/26) : 10000
+Total time elapsed: 145.40 s
+Calling variants ...
+Total processed positions in chr15 (chunk 8/26) : 10000
+Total time elapsed: 148.03 s
+Calling variants ...
+Total processed positions in chr15 (chunk 2/26) : 10000
+Total time elapsed: 149.09 s
+
+real	2m33.863s
+user	55m44.578s
+sys	2m34.887s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr15: 54400
+[INFO] Full-alignment variants processed in chr15: 132192
+
+real	0m4.082s
+user	0m5.157s
+sys	0m0.334s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	6m58.891s
+user	112m15.076s
+sys	5m7.621s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output --ctg_name=chr15 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr15
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr15 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr15
+[INFO] Chunk number for each contig: 20
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr15 (chunk 9/20) : 7491
+Total time elapsed: 86.60 s
+Calling variants ...
+Total processed positions in chr15 (chunk 10/20) : 9656
+Total time elapsed: 89.30 s
+Calling variants ...
+Total processed positions in chr15 (chunk 15/20) : 9383
+Total time elapsed: 92.48 s
+Calling variants ...
+Total processed positions in chr15 (chunk 12/20) : 11544
+Total time elapsed: 94.74 s
+Calling variants ...
+Total processed positions in chr15 (chunk 19/20) : 11914
+Total time elapsed: 95.91 s
+Calling variants ...
+Total processed positions in chr15 (chunk 18/20) : 11760
+Total time elapsed: 96.78 s
+Calling variants ...
+Total processed positions in chr15 (chunk 16/20) : 12177
+Total time elapsed: 99.46 s
+Calling variants ...
+Total processed positions in chr15 (chunk 3/20) : 18253
+Total time elapsed: 99.69 s
+Calling variants ...
+Total processed positions in chr15 (chunk 7/20) : 13907
+Total time elapsed: 100.06 s
+Calling variants ...
+Total processed positions in chr15 (chunk 20/20) : 14539
+Total time elapsed: 100.23 s
+Calling variants ...
+Total processed positions in chr15 (chunk 6/20) : 14360
+Total time elapsed: 99.88 s
+Calling variants ...
+Total processed positions in chr15 (chunk 17/20) : 14148
+Total time elapsed: 101.90 s
+Calling variants ...
+Total processed positions in chr15 (chunk 2/20) : 22300
+Total time elapsed: 112.70 s
+Calling variants ...
+Total processed positions in chr15 (chunk 5/20) : 19401
+Total time elapsed: 113.15 s
+Calling variants ...
+Total processed positions in chr15 (chunk 8/20) : 10118
+Total time elapsed: 57.97 s
+Calling variants ...
+Total processed positions in chr15 (chunk 14/20) : 9361
+Total time elapsed: 58.47 s
+Calling variants ...
+Total processed positions in chr15 (chunk 13/20) : 10162
+Total time elapsed: 58.48 s
+Calling variants ...
+Total processed positions in chr15 (chunk 11/20) : 10978
+Total time elapsed: 60.51 s
+Calling variants ...
+Total processed positions in chr15 (chunk 1/20) : 32347
+Total time elapsed: 137.86 s
+Calling variants ...
+Total processed positions in chr15 (chunk 4/20) : 60396
+Total time elapsed: 183.32 s
+
+real	3m7.851s
+user	23m54.071s
+sys	7m8.907s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19
+[INFO] Total heterozygous SNP positions selected: chr15: 76778
+
+real	0m1.598s
+user	0m1.252s
+sys	0m0.270s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr15.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr15
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr15,38s)
+parsing total:  38s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 40s
+
+real	0m40.748s
+user	2m40.352s
+sys	0m9.608s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 8.0
+[INFO] Low quality reference calls to be processed in chr15: 13159
+[INFO] Low quality variants to be processed in chr15: 134520
+
+real	0m1.547s
+user	0m1.276s
+sys	0m0.235s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr15 (chunk 15/15) : 7679
+Total time elapsed: 109.19 s
+Calling variants ...
+Total processed positions in chr15 (chunk 4/15) : 10000
+Total time elapsed: 118.51 s
+Calling variants ...
+Total processed positions in chr15 (chunk 1/15) : 10000
+Total time elapsed: 118.95 s
+Calling variants ...
+Total processed positions in chr15 (chunk 6/15) : 10000
+Total time elapsed: 131.22 s
+Calling variants ...
+Total processed positions in chr15 (chunk 5/15) : 10000
+Total time elapsed: 142.25 s
+Calling variants ...
+Total processed positions in chr15 (chunk 3/15) : 10000
+Total time elapsed: 143.55 s
+Calling variants ...
+Total processed positions in chr15 (chunk 13/15) : 10000
+Total time elapsed: 143.87 s
+Calling variants ...
+Total processed positions in chr15 (chunk 2/15) : 10000
+Total time elapsed: 144.10 s
+Calling variants ...
+Total processed positions in chr15 (chunk 14/15) : 10000
+Total time elapsed: 144.90 s
+Calling variants ...
+Total processed positions in chr15 (chunk 10/15) : 10000
+Total time elapsed: 146.37 s
+Calling variants ...
+Total processed positions in chr15 (chunk 7/15) : 10000
+Total time elapsed: 150.98 s
+Calling variants ...
+Total processed positions in chr15 (chunk 8/15) : 10000
+Total time elapsed: 152.42 s
+Calling variants ...
+Total processed positions in chr15 (chunk 12/15) : 10000
+Total time elapsed: 155.45 s
+Calling variants ...
+Total processed positions in chr15 (chunk 11/15) : 10000
+Total time elapsed: 157.94 s
+Calling variants ...
+Total processed positions in chr15 (chunk 9/15) : 10000
+Total time elapsed: 161.16 s
+
+real	2m45.139s
+user	33m43.063s
+sys	1m34.524s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr15: 58048
+[INFO] Full-alignment variants processed in chr15: 125321
+
+real	0m2.173s
+user	0m2.375s
+sys	0m0.247s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	6m50.729s
+user	60m31.927s
+sys	8m55.684s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr15: 102605, not found:921, not match:89, low_qual_count:0. Total normal:101744 Total tumor:103615, pro: 0.9903
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/vcf/chr15.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_phased_chr15
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr15,48s)
+parsing total:  48s
+merge results ... 1s
+writeResult SNP ... 0s
+
+total process: 51s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_phased_chr15.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_chr15.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr15
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 1s
+tag read start ...
+chr: chr15 ... 1180s
+tag read 1182s
+-------------------------------------------
+total process time:  1183s
+total alignment:     1464549
+total supplementary: 43357
+total secondary:     0
+total unmapped:      0
+total tag alignment: 596886
+total untagged:      867663
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr15 chunk 8/20: Total snv candidates found: 499, total indel candidates found: 486
+[INFO] chr15 chunk 4/20: Total snv candidates found: 339, total indel candidates found: 424
+[INFO] chr15 chunk 2/20: Total snv candidates found: 307, total indel candidates found: 624
+[INFO] chr15 chunk 12/20: Total snv candidates found: 444, total indel candidates found: 604
+[INFO] chr15 chunk 0/20: Total snv candidates found: 178, total indel candidates found: 439
+[INFO] chr15 chunk 3/20: Total snv candidates found: 814, total indel candidates found: 834
+[INFO] chr15 chunk 13/20: Total snv candidates found: 230, total indel candidates found: 339
+[INFO] chr15 chunk 6/20: Total snv candidates found: 211, total indel candidates found: 363
+[INFO] chr15 chunk 14/20: Total snv candidates found: 453, total indel candidates found: 415
+[INFO] chr15 chunk 1/20: Total snv candidates found: 213, total indel candidates found: 411
+[INFO] chr15 chunk 18/20: Total snv candidates found: 208, total indel candidates found: 352
+[INFO] chr15 chunk 7/20: Total snv candidates found: 366, total indel candidates found: 502
+[INFO] chr15 chunk 11/20: Total snv candidates found: 311, total indel candidates found: 452
+[INFO] chr15 chunk 10/20: Total snv candidates found: 223, total indel candidates found: 312
+[INFO] chr15 chunk 16/20: Total snv candidates found: 222, total indel candidates found: 381
+[INFO] chr15 chunk 15/20: Total snv candidates found: 213, total indel candidates found: 334
+[INFO] chr15 chunk 17/20: Total snv candidates found: 292, total indel candidates found: 419
+[INFO] chr15 chunk 5/20: Total snv candidates found: 407, total indel candidates found: 551
+[INFO] chr15 chunk 19/20: Total snv candidates found: 1333, total indel candidates found: 593
+[faidx] Truncated sequence: chr15:98207655-99754235
+[INFO] chr15 chunk 9/20: Total snv candidates found: 298, total indel candidates found: 421
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/2-1_CPT.log
+
+[INFO] chr15 chunk 1-1/6 Tensors generated: 211
+[INFO] chr15 chunk 1-1/0 Tensors generated: 178
+[INFO] chr15 chunk 1-1/16 Tensors generated: 222
+[INFO] chr15 chunk 1-1/15 Tensors generated: 213
+[INFO] chr15 chunk 1-1/18 Tensors generated: 208
+[INFO] chr15 chunk 1-1/10 Tensors generated: 223
+[INFO] chr15 chunk 1-1/13 Tensors generated: 230
+[INFO] chr15 chunk 1-1/17 Tensors generated: 292
+[INFO] chr15 chunk 1-1/4 Tensors generated: 339
+[INFO] chr15 chunk 1-1/1 Tensors generated: 212
+[INFO] chr15 chunk 1-1/9 Tensors generated: 296
+[INFO] chr15 chunk 1-1/11 Tensors generated: 311
+[INFO] chr15 chunk 1-1/2 Tensors generated: 307
+[INFO] chr15 chunk 1-1/7 Tensors generated: 366
+[INFO] chr15 chunk 1-1/5 Tensors generated: 404
+[INFO] chr15 chunk 1-1/14 Tensors generated: 453
+[INFO] chr15 chunk 1-1/12 Tensors generated: 444
+[INFO] chr15 chunk 1-1/8 Tensors generated: 498
+[INFO] chr15 chunk 1-1/3 Tensors generated: 814
+[INFO] chr15 chunk 1-1/19 Tensors generated: 1333
+[faidx] Truncated sequence: chr15:98255560-99753978
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/2-2_PREDICT.log
+
+[INFO] chr15 total processed positions: 212, time elapsed: 0.8s
+[INFO] chr15 total processed positions: 208, time elapsed: 0.7s
+[INFO] chr15 total processed positions: 211, time elapsed: 0.9s
+[INFO] chr15 total processed positions: 292, time elapsed: 0.8s
+[INFO] chr15 total processed positions: 230, time elapsed: 0.6s
+[INFO] chr15 total processed positions: 307, time elapsed: 0.9s
+[INFO] chr15 total processed positions: 178, time elapsed: 0.5s
+[INFO] chr15 total processed positions: 213, time elapsed: 0.7s
+[INFO] chr15 total processed positions: 311, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 222, time elapsed: 0.8s
+[INFO] chr15 total processed positions: 404, time elapsed: 1.1s
+[INFO] chr15 total processed positions: 223, time elapsed: 0.7s
+[INFO] chr15 total processed positions: 296, time elapsed: 0.9s
+[INFO] chr15 total processed positions: 339, time elapsed: 1.3s
+[INFO] chr15 total processed positions: 366, time elapsed: 1.4s
+[INFO] chr15 total processed positions: 453, time elapsed: 1.4s
+[INFO] chr15 total processed positions: 498, time elapsed: 1.6s
+[INFO] chr15 total processed positions: 444, time elapsed: 1.3s
+[INFO] chr15 total processed positions: 814, time elapsed: 2.4s
+[INFO] chr15 total processed positions: 1333, time elapsed: 3.9s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/3-1_CPT.log
+
+[INFO] chr15 chunk 1-1/0 Tensors generated: 178
+[INFO] chr15 chunk 1-1/15 Tensors generated: 213
+[INFO] chr15 chunk 1-1/18 Tensors generated: 208
+[INFO] chr15 chunk 1-1/1 Tensors generated: 209
+[INFO] chr15 chunk 1-1/6 Tensors generated: 211
+[INFO] chr15 chunk 1-1/16 Tensors generated: 222
+[INFO] chr15 chunk 1-1/10 Tensors generated: 223
+[INFO] chr15 chunk 1-1/13 Tensors generated: 230
+[INFO] chr15 chunk 1-1/9 Tensors generated: 296
+[INFO] chr15 chunk 1-1/17 Tensors generated: 292
+[INFO] chr15 chunk 1-1/2 Tensors generated: 307
+[INFO] chr15 chunk 1-1/11 Tensors generated: 311
+[INFO] chr15 chunk 1-1/4 Tensors generated: 339
+[INFO] chr15 chunk 1-1/7 Tensors generated: 366
+[INFO] chr15 chunk 1-1/8 Tensors generated: 474
+[INFO] chr15 chunk 1-1/5 Tensors generated: 404
+[INFO] chr15 chunk 1-1/12 Tensors generated: 444
+[INFO] chr15 chunk 1-1/14 Tensors generated: 453
+[INFO] chr15 chunk 1-1/3 Tensors generated: 814
+[INFO] chr15 chunk 1-1/19 Tensors generated: 1232
+[faidx] Truncated sequence: chr15:98255560-99753978
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/3-2_PREDICT.log
+
+[INFO] chr15 total processed positions: 178, time elapsed: 32.0s
+[INFO] chr15 total processed positions: 208, time elapsed: 37.7s
+[INFO] chr15 total processed positions: 213, time elapsed: 39.0s
+[INFO] chr15 total processed positions: 211, time elapsed: 38.8s
+[INFO] chr15 total processed positions: 223, time elapsed: 40.0s
+[INFO] chr15 total processed positions: 222, time elapsed: 40.5s
+[INFO] chr15 total processed positions: 209, time elapsed: 41.3s
+[INFO] chr15 total processed positions: 230, time elapsed: 44.8s
+[INFO] chr15 total processed positions: 292, time elapsed: 52.6s
+[INFO] chr15 total processed positions: 296, time elapsed: 53.7s
+[INFO] chr15 total processed positions: 307, time elapsed: 55.4s
+[INFO] chr15 total processed positions: 311, time elapsed: 56.6s
+[INFO] chr15 total processed positions: 339, time elapsed: 61.7s
+[INFO] chr15 total processed positions: 366, time elapsed: 67.2s
+[INFO] chr15 total processed positions: 404, time elapsed: 73.7s
+[INFO] chr15 total processed positions: 453, time elapsed: 82.2s
+[INFO] chr15 total processed positions: 444, time elapsed: 82.2s
+[INFO] chr15 total processed positions: 474, time elapsed: 86.1s
+[INFO] chr15 total processed positions: 814, time elapsed: 147.3s
+[INFO] chr15 total processed positions: 1232, time elapsed: 223.4s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output --vcf_fn_prefix fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 4: Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/4_HAP_FILTER.log
+
+Total input calls: 2571, filtered by haplotype match 6
+
+[INFO] STEP 5: Merge and sort VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/output.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/5_MV.log
+
+[INFO] Full-alignment variants filtered by pileup:  237
+
+[INFO] STEP 6: Indel Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates --input_prefix INDEL_CANDIDATES_FILE_ --output_fn INDEL_CANDIDATES_FILES  && ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_6-1_create_pair_tensor_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/pileup_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/6-1_CPTI.log
+
+[INFO] chr15  Tensors generated: 339
+[INFO] chr15  Tensors generated: 312
+[INFO] chr15  Tensors generated: 363
+[INFO] chr15  Tensors generated: 334
+[INFO] chr15  Tensors generated: 439
+[INFO] chr15  Tensors generated: 419
+[INFO] chr15  Tensors generated: 424
+[INFO] chr15  Tensors generated: 381
+[INFO] chr15  Tensors generated: 352
+[INFO] chr15  Tensors generated: 415
+[INFO] chr15  Tensors generated: 449
+[INFO] chr15  Tensors generated: 416
+[INFO] chr15  Tensors generated: 411
+[INFO] chr15  Tensors generated: 548
+[INFO] chr15  Tensors generated: 502
+[INFO] chr15  Tensors generated: 486
+[INFO] chr15  Tensors generated: 604
+[INFO] chr15  Tensors generated: 624
+[INFO] chr15  Tensors generated: 593
+[faidx] Truncated sequence: chr15:98212959-99754173
+[INFO] chr15  Tensors generated: 834
+
+[INFO] Indel Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_6-2_predict_indel.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/pileup_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/indel_p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/6-2_PREDICT_INDEL.log
+
+[INFO] chr15 total processed positions: 352, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 419, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 339, time elapsed: 0.9s
+[INFO] chr15 total processed positions: 334, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 548, time elapsed: 1.5s
+[INFO] chr15 total processed positions: 381, time elapsed: 1.1s
+[INFO] chr15 total processed positions: 439, time elapsed: 1.1s
+[INFO] chr15 total processed positions: 416, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 312, time elapsed: 0.9s
+[INFO] chr15 total processed positions: 411, time elapsed: 1.1s
+[INFO] chr15 total processed positions: 415, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 502, time elapsed: 1.2s
+[INFO] chr15 total processed positions: 424, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 449, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 624, time elapsed: 1.4s
+[INFO] chr15 total processed positions: 363, time elapsed: 0.9s
+[INFO] chr15 total processed positions: 604, time elapsed: 1.5s
+[INFO] chr15 total processed positions: 486, time elapsed: 1.0s
+[INFO] chr15 total processed positions: 593, time elapsed: 1.3s
+[INFO] chr15 total processed positions: 834, time elapsed: 1.7s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output --vcf_fn_prefix indel_p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/indel_pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 7: Indel Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_7-1_create_pair_tensor_fa_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/fa_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/7-1_CPTI.log
+
+[INFO] chr15  Tensors generated: 334
+[INFO] chr15  Tensors generated: 312
+[INFO] chr15  Tensors generated: 339
+[INFO] chr15  Tensors generated: 352
+[INFO] chr15  Tensors generated: 419
+[INFO] chr15  Tensors generated: 363
+[INFO] chr15  Tensors generated: 381
+[INFO] chr15  Tensors generated: 415
+[INFO] chr15  Tensors generated: 424
+[INFO] chr15  Tensors generated: 439
+[INFO] chr15  Tensors generated: 409
+[INFO] chr15  Tensors generated: 416
+[INFO] chr15  Tensors generated: 449
+[INFO] chr15  Tensors generated: 502
+[INFO] chr15  Tensors generated: 482
+[INFO] chr15  Tensors generated: 548
+[INFO] chr15  Tensors generated: 588
+[faidx] Truncated sequence: chr15:98212959-99754173
+[INFO] chr15  Tensors generated: 834
+[INFO] chr15  Tensors generated: 604
+[INFO] chr15  Tensors generated: 624
+
+[INFO] Indel Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/parallel_7-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/fa_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/indel_fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/7-2_PREDICT_INDEL.log
+
+[INFO] chr15 total processed positions: 312, time elapsed: 54.1s
+[INFO] chr15 total processed positions: 334, time elapsed: 57.4s
+[INFO] chr15 total processed positions: 339, time elapsed: 58.2s
+[INFO] chr15 total processed positions: 352, time elapsed: 61.2s
+[INFO] chr15 total processed positions: 363, time elapsed: 63.7s
+[INFO] chr15 total processed positions: 381, time elapsed: 66.0s
+[INFO] chr15 total processed positions: 409, time elapsed: 71.3s
+[INFO] chr15 total processed positions: 416, time elapsed: 71.9s
+[INFO] chr15 total processed positions: 415, time elapsed: 72.6s
+[INFO] chr15 total processed positions: 419, time elapsed: 73.3s
+[INFO] chr15 total processed positions: 424, time elapsed: 73.2s
+[INFO] chr15 total processed positions: 439, time elapsed: 77.7s
+[INFO] chr15 total processed positions: 449, time elapsed: 79.5s
+[INFO] chr15 total processed positions: 482, time elapsed: 82.9s
+[INFO] chr15 total processed positions: 502, time elapsed: 91.1s
+[INFO] chr15 total processed positions: 548, time elapsed: 94.2s
+[INFO] chr15 total processed positions: 588, time elapsed: 102.4s
+[INFO] chr15 total processed positions: 604, time elapsed: 104.8s
+[INFO] chr15 total processed positions: 624, time elapsed: 107.9s
+[INFO] chr15 total processed positions: 834, time elapsed: 148.8s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output --vcf_fn_prefix indel_fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/indel_full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] Indel Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/indel_pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/indel_full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 --is_indel  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/8_INDEL_HAP_FILTER.log
+
+Total input calls: 728, filtered by haplotype match 6
+
+[INFO] STEP 8: Merge and sort Indel VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/indel_pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/vcf_output/indel_full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/indel.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --indel_calling  --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/logs/8_MVI.log
+
+[INFO] Full-alignment variants filtered by pileup:  90
+
+[INFO] Total time elapsed: 43m41.00s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/output.vcf.gz
+
+[INFO] Finish calling, snv output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/snv.vcf.gz
+
+[INFO] Finish calling, indel output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/indel.vcf.gz
+
+[INFO] Finish calling, Clair3 tumor BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/clair3_tumor_germline_output.vcf.gz
+
+[INFO] Finish calling, Clair3 normal BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/clair3_normal_germline_output.vcf.gz
+
+cp /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part13/clair3_tumor_germline_output.vcf.gz
+slurmstepd: error: Detected 4 oom_kill events in StepId=2556287.batch. Some of the step tasks have been OOM Killed.
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556287
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n12
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 15:57:24
+Job ended at:   2025-12-08 16:41:08
+Job Wall-clock time: 00:43:44
+CPU Utilized: 05:11:40
+CPU Efficiency: 17.82% of 1-05:09:20 core-walltime
+Memory Utilized: 40.00 GB
+Memory Efficiency: 100.00% of 40.00 GB

slurm-2556288.out

@@ -0,0 +1,835 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18 --region chr19:1-19687871 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr19
+[INFO] Number of chunks for each contig: 13
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr19:1-19687871
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output --ctg_name=chr19 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr19
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr19 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr19
+[INFO] Chunk number for each contig: 13
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr19 (chunk 6/13) : 37439
+Total time elapsed: 89.45 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/13) : 71150
+Total time elapsed: 142.17 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/13) : 77903
+Total time elapsed: 157.90 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/13) : 82264
+Total time elapsed: 160.79 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/13) : 77159
+Total time elapsed: 161.93 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/13) : 80011
+Total time elapsed: 163.09 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/13) : 81026
+Total time elapsed: 165.24 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/13) : 76878
+Total time elapsed: 165.94 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/13) : 82363
+Total time elapsed: 166.31 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/13) : 83832
+Total time elapsed: 168.75 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/13) : 86660
+Total time elapsed: 171.00 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/13) : 80468
+Total time elapsed: 175.28 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/13) : 90012
+Total time elapsed: 179.27 s
+
+real	3m7.948s
+user	34m3.448s
+sys	1m12.228s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
+[INFO] Total heterozygous SNP positions selected: chr19: 52254
+
+real	0m2.376s
+user	0m2.156s
+sys	0m0.181s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr19,5s)
+parsing total:  5s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 7s
+
+real	0m6.950s
+user	0m20.590s
+sys	0m1.374s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 12.0
+[INFO] Low quality reference calls to be processed in chr19: 86848
+[INFO] Low quality variants to be processed in chr19: 96058
+
+real	0m2.598s
+user	0m2.315s
+sys	0m0.237s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr19 (chunk 19/19) : 2906
+Total time elapsed: 45.73 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/19) : 10000
+Total time elapsed: 121.54 s
+Calling variants ...
+Total processed positions in chr19 (chunk 14/19) : 10000
+Total time elapsed: 122.15 s
+Calling variants ...
+Total processed positions in chr19 (chunk 18/19) : 10000
+Total time elapsed: 122.53 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/19) : 10000
+Total time elapsed: 122.68 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/19) : 10000
+Total time elapsed: 122.95 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/19) : 10000
+Total time elapsed: 124.12 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/19) : 10000
+Total time elapsed: 124.04 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/19) : 10000
+Total time elapsed: 125.87 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/19) : 10000
+Total time elapsed: 125.85 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/19) : 10000
+Total time elapsed: 126.55 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/19) : 10000
+Total time elapsed: 127.93 s
+Calling variants ...
+Total processed positions in chr19 (chunk 15/19) : 10000
+Total time elapsed: 127.21 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/19) : 10000
+Total time elapsed: 129.72 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/19) : 10000
+Total time elapsed: 129.50 s
+Calling variants ...
+Total processed positions in chr19 (chunk 16/19) : 10000
+Total time elapsed: 130.44 s
+Calling variants ...
+Total processed positions in chr19 (chunk 17/19) : 10000
+Total time elapsed: 130.86 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/19) : 10000
+Total time elapsed: 134.52 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/19) : 10000
+Total time elapsed: 134.39 s
+
+real	2m18.633s
+user	37m45.730s
+sys	1m49.859s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr19: 41215
+[INFO] Full-alignment variants processed in chr19: 104681
+
+real	0m3.039s
+user	0m3.729s
+sys	0m0.287s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	5m57.040s
+user	72m32.427s
+sys	3m6.124s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output --ctg_name=chr19 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr19
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr19 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr19
+[INFO] Chunk number for each contig: 13
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr19 (chunk 10/13) : 10530
+Total time elapsed: 57.85 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/13) : 10757
+Total time elapsed: 57.86 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/13) : 11930
+Total time elapsed: 59.36 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/13) : 13827
+Total time elapsed: 64.29 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/13) : 13999
+Total time elapsed: 64.41 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/13) : 15431
+Total time elapsed: 66.90 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/13) : 15863
+Total time elapsed: 67.31 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/13) : 15113
+Total time elapsed: 70.26 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/13) : 18004
+Total time elapsed: 72.89 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/13) : 18455
+Total time elapsed: 75.61 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/13) : 19185
+Total time elapsed: 76.35 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/13) : 43919
+Total time elapsed: 114.61 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/13) : 53083
+Total time elapsed: 127.56 s
+
+real	2m11.327s
+user	13m29.567s
+sys	1m9.261s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 18
+[INFO] Total heterozygous SNP positions selected: chr19: 62515
+
+real	0m1.270s
+user	0m1.072s
+sys	0m0.169s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr19,23s)
+parsing total:  23s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 25s
+
+real	0m24.312s
+user	1m31.017s
+sys	0m5.226s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 7.0
+[INFO] Low quality reference calls to be processed in chr19: 10511
+[INFO] Low quality variants to be processed in chr19: 108203
+
+real	0m1.396s
+user	0m1.153s
+sys	0m0.203s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr19 (chunk 12/12) : 8714
+Total time elapsed: 118.40 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/12) : 10000
+Total time elapsed: 120.16 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/12) : 10000
+Total time elapsed: 120.89 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/12) : 10000
+Total time elapsed: 122.03 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/12) : 10000
+Total time elapsed: 126.72 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/12) : 10000
+Total time elapsed: 131.41 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/12) : 10000
+Total time elapsed: 138.95 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/12) : 10000
+Total time elapsed: 141.30 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/12) : 10000
+Total time elapsed: 144.17 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/12) : 10000
+Total time elapsed: 143.84 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/12) : 10000
+Total time elapsed: 145.49 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/12) : 10000
+Total time elapsed: 154.51 s
+
+real	2m37.785s
+user	25m39.050s
+sys	1m13.121s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr19: 46569
+[INFO] Full-alignment variants processed in chr19: 101152
+
+real	0m2.046s
+user	0m2.166s
+sys	0m0.224s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	5m27.660s
+user	40m52.431s
+sys	2m29.321s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr19: 84452, not found:765, not match:81, low_qual_count:0. Total normal:76459 Total tumor:85298, pro: 0.9901
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr19,41s)
+parsing total:  41s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 43s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_phased_chr19.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_chr19.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr19
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 1s
+tag read start ...
+chr: chr19 ... 627s
+tag read 628s
+-------------------------------------------
+total process time:  629s
+total alignment:     734582
+total supplementary: 28447
+total secondary:     0
+total unmapped:      0
+total tag alignment: 390188
+total untagged:      344394
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr19 chunk 10/13: Total snv candidates found: 946, total indel candidates found: 795
+[INFO] chr19 chunk 7/13: Total snv candidates found: 350, total indel candidates found: 815
+[INFO] chr19 chunk 5/13: Total snv candidates found: 831, total indel candidates found: 847
+[INFO] chr19 chunk 3/13: Total snv candidates found: 488, total indel candidates found: 773
+[INFO] chr19 chunk 1/13: Total snv candidates found: 701, total indel candidates found: 1001
+[INFO] chr19 chunk 9/13: Total snv candidates found: 542, total indel candidates found: 860
+[INFO] chr19 chunk 12/13: Total snv candidates found: 570, total indel candidates found: 891
+[INFO] chr19 chunk 2/13: Total snv candidates found: 674, total indel candidates found: 995
+[INFO] chr19 chunk 0/13: Total snv candidates found: 1711, total indel candidates found: 1191
+[INFO] chr19 chunk 8/13: Total snv candidates found: 253, total indel candidates found: 806
+[INFO] chr19 chunk 11/13: Total snv candidates found: 437, total indel candidates found: 872
+[INFO] chr19 chunk 6/13: Total snv candidates found: 349, total indel candidates found: 715
+[INFO] chr19 chunk 4/13: Total snv candidates found: 1154, total indel candidates found: 883
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/2-1_CPT.log
+
+[INFO] chr19 chunk 1-1/8 Tensors generated: 250
+[INFO] chr19 chunk 1-1/1 Tensors generated: 701
+[INFO] chr19 chunk 1-1/7 Tensors generated: 350
+[INFO] chr19 chunk 1-1/2 Tensors generated: 670
+[INFO] chr19 chunk 1-1/6 Tensors generated: 349
+[INFO] chr19 chunk 1-1/11 Tensors generated: 425
+[INFO] chr19 chunk 1-1/3 Tensors generated: 487
+[INFO] chr19 chunk 1-1/9 Tensors generated: 542
+[INFO] chr19 chunk 1-1/12 Tensors generated: 570
+[INFO] chr19 chunk 1-1/5 Tensors generated: 828
+[INFO] chr19 chunk 1-1/4 Tensors generated: 1154
+[INFO] chr19 chunk 1-1/10 Tensors generated: 946
+[INFO] chr19 chunk 1-1/0 Tensors generated: 1692
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/2-2_PREDICT.log
+
+[INFO] chr19 total processed positions: 250, time elapsed: 0.9s
+[INFO] chr19 total processed positions: 349, time elapsed: 1.1s
+[INFO] chr19 total processed positions: 350, time elapsed: 1.2s
+[INFO] chr19 total processed positions: 487, time elapsed: 1.1s
+[INFO] chr19 total processed positions: 542, time elapsed: 1.3s
+[INFO] chr19 total processed positions: 425, time elapsed: 1.5s
+[INFO] chr19 total processed positions: 570, time elapsed: 1.6s
+[INFO] chr19 total processed positions: 701, time elapsed: 1.8s
+[INFO] chr19 total processed positions: 670, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 946, time elapsed: 2.2s
+[INFO] chr19 total processed positions: 828, time elapsed: 2.4s
+[INFO] chr19 total processed positions: 1692, time elapsed: 3.6s
+[INFO] chr19 total processed positions: 1154, time elapsed: 3.5s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/3-1_CPT.log
+
+[INFO] chr19 chunk 1-1/8 Tensors generated: 250
+[INFO] chr19 chunk 1-1/7 Tensors generated: 350
+[INFO] chr19 chunk 1-1/6 Tensors generated: 349
+[INFO] chr19 chunk 1-1/11 Tensors generated: 425
+[INFO] chr19 chunk 1-1/3 Tensors generated: 487
+[INFO] chr19 chunk 1-1/9 Tensors generated: 542
+[INFO] chr19 chunk 1-1/1 Tensors generated: 701
+[INFO] chr19 chunk 1-1/12 Tensors generated: 570
+[INFO] chr19 chunk 1-1/2 Tensors generated: 670
+[INFO] chr19 chunk 1-1/5 Tensors generated: 817
+[INFO] chr19 chunk 1-1/10 Tensors generated: 946
+[INFO] chr19 chunk 1-1/0 Tensors generated: 1683
+[INFO] chr19 chunk 1-1/4 Tensors generated: 1154
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/3-2_PREDICT.log
+
+[INFO] chr19 total processed positions: 250, time elapsed: 45.0s
+[INFO] chr19 total processed positions: 349, time elapsed: 62.9s
+[INFO] chr19 total processed positions: 350, time elapsed: 63.6s
+[INFO] chr19 total processed positions: 425, time elapsed: 76.1s
+[INFO] chr19 total processed positions: 487, time elapsed: 87.2s
+[INFO] chr19 total processed positions: 542, time elapsed: 100.1s
+[INFO] chr19 total processed positions: 570, time elapsed: 102.7s
+[INFO] chr19 total processed positions: 670, time elapsed: 122.7s
+[INFO] chr19 total processed positions: 701, time elapsed: 130.2s
+[INFO] chr19 total processed positions: 817, time elapsed: 148.4s
+[INFO] chr19 total processed positions: 946, time elapsed: 170.6s
+[INFO] chr19 total processed positions: 1154, time elapsed: 218.6s
+[INFO] chr19 total processed positions: 1683, time elapsed: 305.6s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output --vcf_fn_prefix fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 4: Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/4_HAP_FILTER.log
+
+Total input calls: 2721, filtered by haplotype match 8
+
+[INFO] STEP 5: Merge and sort VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/output.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/5_MV.log
+
+[INFO] Full-alignment variants filtered by pileup:  271
+
+[INFO] STEP 6: Indel Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates --input_prefix INDEL_CANDIDATES_FILE_ --output_fn INDEL_CANDIDATES_FILES  && ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_6-1_create_pair_tensor_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/pileup_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/6-1_CPTI.log
+
+[INFO] chr19  Tensors generated: 881
+[INFO] chr19  Tensors generated: 773
+[INFO] chr19  Tensors generated: 986
+[INFO] chr19  Tensors generated: 1000
+[INFO] chr19  Tensors generated: 715
+[INFO] chr19  Tensors generated: 1183
+[INFO] chr19  Tensors generated: 795
+[INFO] chr19  Tensors generated: 801
+[INFO] chr19  Tensors generated: 860
+[INFO] chr19  Tensors generated: 868
+[INFO] chr19  Tensors generated: 815
+[INFO] chr19  Tensors generated: 891
+[INFO] chr19  Tensors generated: 846
+
+[INFO] Indel Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_6-2_predict_indel.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/pileup_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/indel_p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/6-2_PREDICT_INDEL.log
+
+[INFO] chr19 total processed positions: 715, time elapsed: 1.6s
+[INFO] chr19 total processed positions: 795, time elapsed: 1.6s
+[INFO] chr19 total processed positions: 773, time elapsed: 1.7s
+[INFO] chr19 total processed positions: 986, time elapsed: 2.2s
+[INFO] chr19 total processed positions: 801, time elapsed: 2.2s
+[INFO] chr19 total processed positions: 868, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 1000, time elapsed: 2.3s
+[INFO] chr19 total processed positions: 815, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 1183, time elapsed: 2.9s
+[INFO] chr19 total processed positions: 846, time elapsed: 2.6s
+[INFO] chr19 total processed positions: 860, time elapsed: 2.5s
+[INFO] chr19 total processed positions: 891, time elapsed: 2.7s
+[INFO] chr19 total processed positions: 881, time elapsed: 2.7s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output --vcf_fn_prefix indel_p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/indel_pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 7: Indel Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_7-1_create_pair_tensor_fa_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/fa_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/7-1_CPTI.log
+
+[INFO] chr19  Tensors generated: 715
+[INFO] chr19  Tensors generated: 773
+[INFO] chr19  Tensors generated: 801
+[INFO] chr19  Tensors generated: 795
+[INFO] chr19  Tensors generated: 986
+[INFO] chr19  Tensors generated: 815
+[INFO] chr19  Tensors generated: 860
+[INFO] chr19  Tensors generated: 845
+[INFO] chr19  Tensors generated: 1000
+[INFO] chr19  Tensors generated: 881
+[INFO] chr19  Tensors generated: 868
+[INFO] chr19  Tensors generated: 891
+[INFO] chr19  Tensors generated: 1181
+
+[INFO] Indel Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/parallel_7-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/fa_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/indel_fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/7-2_PREDICT_INDEL.log
+
+[INFO] chr19 total processed positions: 715, time elapsed: 127.0s
+[INFO] chr19 total processed positions: 773, time elapsed: 132.1s
+[INFO] chr19 total processed positions: 795, time elapsed: 136.5s
+[INFO] chr19 total processed positions: 801, time elapsed: 137.2s
+[INFO] chr19 total processed positions: 815, time elapsed: 139.3s
+[INFO] chr19 total processed positions: 868, time elapsed: 149.0s
+[INFO] chr19 total processed positions: 860, time elapsed: 149.4s
+[INFO] chr19 total processed positions: 845, time elapsed: 150.6s
+[INFO] chr19 total processed positions: 891, time elapsed: 158.6s
+[INFO] chr19 total processed positions: 881, time elapsed: 161.9s
+[INFO] chr19 total processed positions: 986, time elapsed: 170.9s
+[INFO] chr19 total processed positions: 1000, time elapsed: 171.0s
+[INFO] chr19 total processed positions: 1181, time elapsed: 205.9s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output --vcf_fn_prefix indel_fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/indel_full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] Indel Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/indel_pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/indel_full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 --is_indel  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/8_INDEL_HAP_FILTER.log
+
+Total input calls: 1032, filtered by haplotype match 12
+
+[INFO] STEP 8: Merge and sort Indel VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/indel_pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/vcf_output/indel_full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/indel.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --indel_calling  --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/logs/8_MVI.log
+
+[INFO] Full-alignment variants filtered by pileup:  100
+
+[INFO] Total time elapsed: 33m48.00s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/output.vcf.gz
+
+[INFO] Finish calling, snv output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/snv.vcf.gz
+
+[INFO] Finish calling, indel output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/indel.vcf.gz
+
+[INFO] Finish calling, Clair3 tumor BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/clair3_tumor_germline_output.vcf.gz
+
+[INFO] Finish calling, Clair3 normal BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/clair3_normal_germline_output.vcf.gz
+
+cp /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part18/clair3_tumor_germline_output.vcf.gz
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556288
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n11
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:07:06
+Job ended at:   2025-12-08 16:40:57
+Job Wall-clock time: 00:33:51
+CPU Utilized: 03:49:32
+CPU Efficiency: 16.95% of 22:34:00 core-walltime
+Memory Utilized: 23.59 GB
+Memory Efficiency: 58.98% of 40.00 GB

slurm-2556289.out

@@ -0,0 +1,846 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22 --region chr20:1-27012963 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr20
+[INFO] Number of chunks for each contig: 14
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr20:1-27012963
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output --ctg_name=chr20 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr20
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr20 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr20
+[INFO] Chunk number for each contig: 14
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr20 (chunk 6/14) : 49610
+Total time elapsed: 90.94 s
+Calling variants ...
+Total processed positions in chr20 (chunk 3/14) : 78073
+Total time elapsed: 125.83 s
+Calling variants ...
+Total processed positions in chr20 (chunk 2/14) : 76976
+Total time elapsed: 126.84 s
+Calling variants ...
+Total processed positions in chr20 (chunk 8/14) : 79273
+Total time elapsed: 129.36 s
+Calling variants ...
+Total processed positions in chr20 (chunk 4/14) : 79660
+Total time elapsed: 129.80 s
+Calling variants ...
+Total processed positions in chr20 (chunk 5/14) : 77255
+Total time elapsed: 131.21 s
+Calling variants ...
+Total processed positions in chr20 (chunk 7/14) : 75361
+Total time elapsed: 131.45 s
+Calling variants ...
+Total processed positions in chr20 (chunk 9/14) : 81579
+Total time elapsed: 133.29 s
+Calling variants ...
+Total processed positions in chr20 (chunk 11/14) : 84971
+Total time elapsed: 137.57 s
+Calling variants ...
+Total processed positions in chr20 (chunk 1/14) : 83255
+Total time elapsed: 138.84 s
+Calling variants ...
+Total processed positions in chr20 (chunk 13/14) : 85068
+Total time elapsed: 139.19 s
+Calling variants ...
+Total processed positions in chr20 (chunk 12/14) : 85050
+Total time elapsed: 141.22 s
+Calling variants ...
+Total processed positions in chr20 (chunk 10/14) : 84512
+Total time elapsed: 141.50 s
+Calling variants ...
+Total processed positions in chr20 (chunk 14/14) : 92564
+Total time elapsed: 144.24 s
+
+real	2m30.596s
+user	29m39.254s
+sys	1m19.921s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15
+[INFO] Total heterozygous SNP positions selected: chr20: 45551
+
+real	0m1.782s
+user	0m1.627s
+sys	0m0.118s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr20.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr20
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr20,4s)
+parsing total:  4s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 6s
+
+real	0m5.682s
+user	0m10.592s
+sys	0m0.850s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 13.0
+[INFO] Low quality reference calls to be processed in chr20: 99183
+[INFO] Low quality variants to be processed in chr20: 84562
+
+real	0m2.034s
+user	0m1.780s
+sys	0m0.192s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr20 (chunk 19/19) : 3745
+Total time elapsed: 41.35 s
+Calling variants ...
+Total processed positions in chr20 (chunk 14/19) : 10000
+Total time elapsed: 95.62 s
+Calling variants ...
+Total processed positions in chr20 (chunk 11/19) : 10000
+Total time elapsed: 99.19 s
+Calling variants ...
+Total processed positions in chr20 (chunk 9/19) : 10000
+Total time elapsed: 99.86 s
+Calling variants ...
+Total processed positions in chr20 (chunk 13/19) : 10000
+Total time elapsed: 101.51 s
+Calling variants ...
+Total processed positions in chr20 (chunk 4/19) : 10000
+Total time elapsed: 102.27 s
+Calling variants ...
+Total processed positions in chr20 (chunk 2/19) : 10000
+Total time elapsed: 102.14 s
+Calling variants ...
+Total processed positions in chr20 (chunk 17/19) : 10000
+Total time elapsed: 102.57 s
+Calling variants ...
+Total processed positions in chr20 (chunk 15/19) : 10000
+Total time elapsed: 102.86 s
+Calling variants ...
+Total processed positions in chr20 (chunk 10/19) : 10000
+Total time elapsed: 102.14 s
+Calling variants ...
+Total processed positions in chr20 (chunk 8/19) : 10000
+Total time elapsed: 102.25 s
+Calling variants ...
+Total processed positions in chr20 (chunk 1/19) : 10000
+Total time elapsed: 103.03 s
+Calling variants ...
+Total processed positions in chr20 (chunk 5/19) : 10000
+Total time elapsed: 104.46 s
+Calling variants ...
+Total processed positions in chr20 (chunk 6/19) : 10000
+Total time elapsed: 104.69 s
+Calling variants ...
+Total processed positions in chr20 (chunk 7/19) : 10000
+Total time elapsed: 104.23 s
+Calling variants ...
+Total processed positions in chr20 (chunk 18/19) : 10000
+Total time elapsed: 104.54 s
+Calling variants ...
+Total processed positions in chr20 (chunk 16/19) : 10000
+Total time elapsed: 105.26 s
+Calling variants ...
+Total processed positions in chr20 (chunk 12/19) : 10000
+Total time elapsed: 107.25 s
+Calling variants ...
+Total processed positions in chr20 (chunk 3/19) : 10000
+Total time elapsed: 108.64 s
+
+real	1m52.186s
+user	30m40.864s
+sys	1m38.953s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr20: 36358
+[INFO] Full-alignment variants processed in chr20: 87253
+
+real	0m2.457s
+user	0m2.727s
+sys	0m0.200s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	4m45.880s
+user	60m46.687s
+sys	3m1.485s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output --ctg_name=chr20 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr20
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr20 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr20
+[INFO] Chunk number for each contig: 14
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr20 (chunk 12/14) : 9736
+Total time elapsed: 53.63 s
+Calling variants ...
+Total processed positions in chr20 (chunk 5/14) : 8465
+Total time elapsed: 53.96 s
+Calling variants ...
+Total processed positions in chr20 (chunk 9/14) : 8456
+Total time elapsed: 54.09 s
+Calling variants ...
+Total processed positions in chr20 (chunk 3/14) : 9839
+Total time elapsed: 55.44 s
+Calling variants ...
+Total processed positions in chr20 (chunk 2/14) : 9407
+Total time elapsed: 55.96 s
+Calling variants ...
+Total processed positions in chr20 (chunk 8/14) : 9125
+Total time elapsed: 56.09 s
+Calling variants ...
+Total processed positions in chr20 (chunk 10/14) : 9956
+Total time elapsed: 56.82 s
+Calling variants ...
+Total processed positions in chr20 (chunk 13/14) : 11784
+Total time elapsed: 57.14 s
+Calling variants ...
+Total processed positions in chr20 (chunk 4/14) : 10680
+Total time elapsed: 57.59 s
+Calling variants ...
+Total processed positions in chr20 (chunk 11/14) : 12944
+Total time elapsed: 60.10 s
+Calling variants ...
+Total processed positions in chr20 (chunk 14/14) : 17216
+Total time elapsed: 66.58 s
+Calling variants ...
+Total processed positions in chr20 (chunk 1/14) : 17838
+Total time elapsed: 66.97 s
+Calling variants ...
+Total processed positions in chr20 (chunk 6/14) : 17711
+Total time elapsed: 69.12 s
+Calling variants ...
+Total processed positions in chr20 (chunk 7/14) : 53609
+Total time elapsed: 112.80 s
+
+real	1m55.654s
+user	11m9.215s
+sys	0m54.337s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19
+[INFO] Total heterozygous SNP positions selected: chr20: 45273
+
+real	0m0.721s
+user	0m0.593s
+sys	0m0.103s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr20.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr20
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr20,20s)
+parsing total:  20s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 22s
+
+real	0m21.693s
+user	0m53.644s
+sys	0m3.527s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 8.0
+[INFO] Low quality reference calls to be processed in chr20: 8756
+[INFO] Low quality variants to be processed in chr20: 83160
+
+real	0m0.744s
+user	0m0.573s
+sys	0m0.119s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr20 (chunk 10/10) : 1916
+Total time elapsed: 25.36 s
+Calling variants ...
+Total processed positions in chr20 (chunk 5/10) : 10000
+Total time elapsed: 96.98 s
+Calling variants ...
+Total processed positions in chr20 (chunk 4/10) : 10000
+Total time elapsed: 109.94 s
+Calling variants ...
+Total processed positions in chr20 (chunk 1/10) : 10000
+Total time elapsed: 113.66 s
+Calling variants ...
+Total processed positions in chr20 (chunk 7/10) : 10000
+Total time elapsed: 115.35 s
+Calling variants ...
+Total processed positions in chr20 (chunk 9/10) : 10000
+Total time elapsed: 117.39 s
+Calling variants ...
+Total processed positions in chr20 (chunk 8/10) : 10000
+Total time elapsed: 117.62 s
+Calling variants ...
+Total processed positions in chr20 (chunk 6/10) : 10000
+Total time elapsed: 120.35 s
+Calling variants ...
+Total processed positions in chr20 (chunk 3/10) : 10000
+Total time elapsed: 122.99 s
+Calling variants ...
+Total processed positions in chr20 (chunk 2/10) : 10000
+Total time elapsed: 123.58 s
+
+real	2m6.084s
+user	16m42.289s
+sys	0m51.652s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr20: 35964
+[INFO] Full-alignment variants processed in chr20: 74344
+
+real	0m1.091s
+user	0m1.090s
+sys	0m0.122s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	4m30.742s
+user	28m51.125s
+sys	1m50.480s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr20: 57143, not found:460, not match:37, low_qual_count:0. Total normal:61825 Total tumor:57640, pro: 0.9914
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/vcf/chr20.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_chr20
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr20,30s)
+parsing total:  30s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 30s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_chr20.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_chr20.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr20
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 0s
+tag read start ...
+chr: chr20 ... 666s
+tag read 667s
+-------------------------------------------
+total process time:  667s
+total alignment:     784888
+total supplementary: 30142
+total secondary:     0
+total unmapped:      0
+total tag alignment: 403864
+total untagged:      381024
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr20 chunk 13/14: Total snv candidates found: 2265, total indel candidates found: 352
+[INFO] chr20 chunk 3/14: Total snv candidates found: 201, total indel candidates found: 432
+[INFO] chr20 chunk 0/14: Total snv candidates found: 2422, total indel candidates found: 1064
+[INFO] chr20 chunk 12/14: Total snv candidates found: 317, total indel candidates found: 393
+[INFO] chr20 chunk 10/14: Total snv candidates found: 302, total indel candidates found: 412
+[INFO] chr20 chunk 2/14: Total snv candidates found: 544, total indel candidates found: 668
+[INFO] chr20 chunk 8/14: Total snv candidates found: 429, total indel candidates found: 383
+[INFO] chr20 chunk 9/14: Total snv candidates found: 328, total indel candidates found: 507
+[INFO] chr20 chunk 6/14: Total snv candidates found: 225, total indel candidates found: 366
+[INFO] chr20 chunk 11/14: Total snv candidates found: 221, total indel candidates found: 467
+[INFO] chr20 chunk 5/14: Total snv candidates found: 271, total indel candidates found: 392
+[INFO] chr20 chunk 4/14: Total snv candidates found: 166, total indel candidates found: 403
+[INFO] chr20 chunk 1/14: Total snv candidates found: 484, total indel candidates found: 710
+[INFO] chr20 chunk 7/14: Total snv candidates found: 126, total indel candidates found: 410
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/2-1_CPT.log
+
+[INFO] chr20 chunk 1-1/4 Tensors generated: 166
+[INFO] chr20 chunk 1-1/7 Tensors generated: 126
+[INFO] chr20 chunk 1-1/11 Tensors generated: 215
+[INFO] chr20 chunk 1-1/6 Tensors generated: 225
+[INFO] chr20 chunk 1-1/3 Tensors generated: 200
+[INFO] chr20 chunk 1-1/1 Tensors generated: 484
+[INFO] chr20 chunk 1-1/5 Tensors generated: 271
+[INFO] chr20 chunk 1-1/10 Tensors generated: 302
+[INFO] chr20 chunk 1-1/2 Tensors generated: 537
+[INFO] chr20 chunk 1-1/12 Tensors generated: 317
+[INFO] chr20 chunk 1-1/9 Tensors generated: 328
+[INFO] chr20 chunk 1-1/8 Tensors generated: 428
+[INFO] chr20 chunk 1-1/0 Tensors generated: 2421
+[INFO] chr20 chunk 1-1/13 Tensors generated: 2234
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/2-2_PREDICT.log
+
+[INFO] chr20 total processed positions: 126, time elapsed: 0.7s
+[INFO] chr20 total processed positions: 166, time elapsed: 0.4s
+[INFO] chr20 total processed positions: 200, time elapsed: 0.5s
+[INFO] chr20 total processed positions: 215, time elapsed: 0.4s
+[INFO] chr20 total processed positions: 225, time elapsed: 0.7s
+[INFO] chr20 total processed positions: 317, time elapsed: 0.9s
+[INFO] chr20 total processed positions: 328, time elapsed: 0.7s
+[INFO] chr20 total processed positions: 271, time elapsed: 0.5s
+[INFO] chr20 total processed positions: 428, time elapsed: 0.9s
+[INFO] chr20 total processed positions: 302, time elapsed: 0.6s
+[INFO] chr20 total processed positions: 484, time elapsed: 0.9s
+[INFO] chr20 total processed positions: 537, time elapsed: 1.2s
+[INFO] chr20 total processed positions: 2234, time elapsed: 3.6s
+[INFO] chr20 total processed positions: 2421, time elapsed: 4.1s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/3-1_CPT.log
+
+[INFO] chr20 chunk 1-1/7 Tensors generated: 126
+[INFO] chr20 chunk 1-1/4 Tensors generated: 166
+[INFO] chr20 chunk 1-1/3 Tensors generated: 200
+[INFO] chr20 chunk 1-1/6 Tensors generated: 225
+[INFO] chr20 chunk 1-1/11 Tensors generated: 215
+[INFO] chr20 chunk 1-1/10 Tensors generated: 302
+[INFO] chr20 chunk 1-1/5 Tensors generated: 271
+[INFO] chr20 chunk 1-1/9 Tensors generated: 328
+[INFO] chr20 chunk 1-1/12 Tensors generated: 317
+[INFO] chr20 chunk 1-1/1 Tensors generated: 484
+[INFO] chr20 chunk 1-1/2 Tensors generated: 537
+[INFO] chr20 chunk 1-1/8 Tensors generated: 428
+[INFO] chr20 chunk 1-1/13 Tensors generated: 2150
+[INFO] chr20 chunk 1-1/0 Tensors generated: 2421
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/3-2_PREDICT.log
+
+[INFO] chr20 total processed positions: 126, time elapsed: 23.1s
+[INFO] chr20 total processed positions: 166, time elapsed: 29.9s
+[INFO] chr20 total processed positions: 200, time elapsed: 35.6s
+[INFO] chr20 total processed positions: 215, time elapsed: 38.1s
+[INFO] chr20 total processed positions: 225, time elapsed: 39.7s
+[INFO] chr20 total processed positions: 271, time elapsed: 48.8s
+[INFO] chr20 total processed positions: 302, time elapsed: 54.7s
+[INFO] chr20 total processed positions: 317, time elapsed: 56.1s
+[INFO] chr20 total processed positions: 328, time elapsed: 58.7s
+[INFO] chr20 total processed positions: 428, time elapsed: 75.6s
+[INFO] chr20 total processed positions: 484, time elapsed: 85.6s
+[INFO] chr20 total processed positions: 537, time elapsed: 95.0s
+[INFO] chr20 total processed positions: 2150, time elapsed: 379.7s
+[INFO] chr20 total processed positions: 2421, time elapsed: 427.3s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --vcf_fn_prefix fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 4: Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/4_HAP_FILTER.log
+
+Total input calls: 1929, filtered by haplotype match 5
+
+[INFO] STEP 5: Merge and sort VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/output.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/5_MV.log
+
+[INFO] Full-alignment variants filtered by pileup:  176
+
+[INFO] STEP 6: Indel Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates --input_prefix INDEL_CANDIDATES_FILE_ --output_fn INDEL_CANDIDATES_FILES  && ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_6-1_create_pair_tensor_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/pileup_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/6-1_CPTI.log
+
+[INFO] chr20  Tensors generated: 0
+[INFO] chr20  Tensors generated: 349
+[INFO] chr20  Tensors generated: 708
+[INFO] chr20  Tensors generated: 393
+[INFO] chr20  Tensors generated: 668
+[INFO] chr20  Tensors generated: 411
+[INFO] chr20  Tensors generated: 392
+[INFO] chr20  Tensors generated: 383
+[INFO] chr20  Tensors generated: 403
+[INFO] chr20  Tensors generated: 366
+[INFO] chr20  Tensors generated: 410
+[INFO] chr20  Tensors generated: 459
+[INFO] chr20  Tensors generated: 507
+[INFO] chr20  Tensors generated: 431
+
+[INFO] Indel Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_6-2_predict_indel.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/pileup_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/6-2_PREDICT_INDEL.log
+
+[INFO] chr20 total processed positions: 0, time elapsed: 0.1s
+[INFO] No variant output for indel_p_chr20.0_0_1_indel.vcf, remove empty VCF
+[INFO] chr20 total processed positions: 383, time elapsed: 0.7s
+[INFO] chr20 total processed positions: 403, time elapsed: 0.9s
+[INFO] chr20 total processed positions: 410, time elapsed: 0.8s
+[INFO] chr20 total processed positions: 349, time elapsed: 0.7s
+[INFO] chr20 total processed positions: 431, time elapsed: 0.9s
+[INFO] chr20 total processed positions: 393, time elapsed: 0.8s
+[INFO] chr20 total processed positions: 366, time elapsed: 0.7s
+[INFO] chr20 total processed positions: 507, time elapsed: 1.0s
+[INFO] chr20 total processed positions: 392, time elapsed: 0.8s
+[INFO] chr20 total processed positions: 411, time elapsed: 0.8s
+[INFO] chr20 total processed positions: 668, time elapsed: 1.2s
+[INFO] chr20 total processed positions: 459, time elapsed: 1.0s
+[INFO] chr20 total processed positions: 708, time elapsed: 1.3s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --vcf_fn_prefix indel_p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 7: Indel Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_7-1_create_pair_tensor_fa_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/fa_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/7-1_CPTI.log
+
+[INFO] chr20  Tensors generated: 0
+[INFO] chr20  Tensors generated: 348
+[INFO] chr20  Tensors generated: 366
+[INFO] chr20  Tensors generated: 383
+[INFO] chr20  Tensors generated: 411
+[INFO] chr20  Tensors generated: 392
+[INFO] chr20  Tensors generated: 410
+[INFO] chr20  Tensors generated: 403
+[INFO] chr20  Tensors generated: 393
+[INFO] chr20  Tensors generated: 431
+[INFO] chr20  Tensors generated: 459
+[INFO] chr20  Tensors generated: 507
+[INFO] chr20  Tensors generated: 708
+[INFO] chr20  Tensors generated: 668
+
+[INFO] Indel Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/parallel_7-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/fa_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/7-2_PREDICT_INDEL.log
+
+[INFO] chr20 total processed positions: 0, time elapsed: 0.0s
+[INFO] No variant output for indel_fa_chr20.0_0_1_indel.vcf, remove empty VCF
+[INFO] chr20 total processed positions: 348, time elapsed: 59.2s
+[INFO] chr20 total processed positions: 366, time elapsed: 62.4s
+[INFO] chr20 total processed positions: 383, time elapsed: 65.0s
+[INFO] chr20 total processed positions: 392, time elapsed: 66.6s
+[INFO] chr20 total processed positions: 393, time elapsed: 66.6s
+[INFO] chr20 total processed positions: 403, time elapsed: 68.2s
+[INFO] chr20 total processed positions: 410, time elapsed: 69.7s
+[INFO] chr20 total processed positions: 411, time elapsed: 70.1s
+[INFO] chr20 total processed positions: 431, time elapsed: 74.2s
+[INFO] chr20 total processed positions: 459, time elapsed: 78.8s
+[INFO] chr20 total processed positions: 507, time elapsed: 85.5s
+[INFO] chr20 total processed positions: 668, time elapsed: 112.5s
+[INFO] chr20 total processed positions: 708, time elapsed: 118.7s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --vcf_fn_prefix indel_fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] Indel Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 --is_indel  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/8_INDEL_HAP_FILTER.log
+
+Total input calls: 486, filtered by haplotype match 3
+
+[INFO] STEP 8: Merge and sort Indel VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/indel.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --indel_calling  --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/8_MVI.log
+
+[INFO] Full-alignment variants filtered by pileup:  47
+
+[INFO] Total time elapsed: 32m19.00s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/output.vcf.gz
+
+[INFO] Finish calling, snv output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/snv.vcf.gz
+
+[INFO] Finish calling, indel output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/indel.vcf.gz
+
+[INFO] Finish calling, Clair3 tumor BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/clair3_tumor_germline_output.vcf.gz
+
+[INFO] Finish calling, Clair3 normal BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/clair3_normal_germline_output.vcf.gz
+
+cp /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/clair3_tumor_germline_output.vcf.gz
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556289
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n17
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:10:07
+Job ended at:   2025-12-08 16:42:28
+Job Wall-clock time: 00:32:21
+CPU Utilized: 02:57:02
+CPU Efficiency: 13.68% of 21:34:00 core-walltime
+Memory Utilized: 22.24 GB
+Memory Efficiency: 55.60% of 40.00 GB

slurm-2556290.out

@@ -0,0 +1,708 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23 --region chr20:27012964-66210255 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr20
+[INFO] Number of chunks for each contig: 14
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr20:27012964-66210255
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output --ctg_name=chr20 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr20
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr20 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr20
+[INFO] Chunk number for each contig: 14
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr20 (chunk 6/14) : 49610
+Total time elapsed: 84.48 s
+Calling variants ...
+Total processed positions in chr20 (chunk 3/14) : 78073
+Total time elapsed: 125.01 s
+Calling variants ...
+Total processed positions in chr20 (chunk 8/14) : 79273
+Total time elapsed: 125.47 s
+Calling variants ...
+Total processed positions in chr20 (chunk 2/14) : 76976
+Total time elapsed: 127.90 s
+Calling variants ...
+Total processed positions in chr20 (chunk 1/14) : 83255
+Total time elapsed: 128.77 s
+Calling variants ...
+Total processed positions in chr20 (chunk 7/14) : 75361
+Total time elapsed: 133.50 s
+Calling variants ...
+Total processed positions in chr20 (chunk 5/14) : 77255
+Total time elapsed: 138.58 s
+Calling variants ...
+Total processed positions in chr20 (chunk 14/14) : 92564
+Total time elapsed: 142.19 s
+Calling variants ...
+Total processed positions in chr20 (chunk 9/14) : 81579
+Total time elapsed: 141.82 s
+Calling variants ...
+Total processed positions in chr20 (chunk 12/14) : 85050
+Total time elapsed: 142.79 s
+Calling variants ...
+Total processed positions in chr20 (chunk 4/14) : 79660
+Total time elapsed: 145.64 s
+Calling variants ...
+Total processed positions in chr20 (chunk 10/14) : 84512
+Total time elapsed: 145.78 s
+Calling variants ...
+Total processed positions in chr20 (chunk 13/14) : 85068
+Total time elapsed: 146.93 s
+Calling variants ...
+Total processed positions in chr20 (chunk 11/14) : 84971
+Total time elapsed: 151.69 s
+
+real	2m38.151s
+user	30m21.785s
+sys	1m14.744s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15
+[INFO] Total heterozygous SNP positions selected: chr20: 45551
+
+real	0m1.811s
+user	0m1.647s
+sys	0m0.129s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr20.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr20
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr20,4s)
+parsing total:  4s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 6s
+
+real	0m5.455s
+user	0m10.697s
+sys	0m0.887s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 13.0
+[INFO] Low quality reference calls to be processed in chr20: 99183
+[INFO] Low quality variants to be processed in chr20: 84562
+
+real	0m2.039s
+user	0m1.790s
+sys	0m0.194s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr20 (chunk 19/19) : 3745
+Total time elapsed: 45.38 s
+Calling variants ...
+Total processed positions in chr20 (chunk 12/19) : 10000
+Total time elapsed: 97.11 s
+Calling variants ...
+Total processed positions in chr20 (chunk 8/19) : 10000
+Total time elapsed: 98.44 s
+Calling variants ...
+Total processed positions in chr20 (chunk 4/19) : 10000
+Total time elapsed: 99.77 s
+Calling variants ...
+Total processed positions in chr20 (chunk 5/19) : 10000
+Total time elapsed: 100.40 s
+Calling variants ...
+Total processed positions in chr20 (chunk 3/19) : 10000
+Total time elapsed: 99.75 s
+Calling variants ...
+Total processed positions in chr20 (chunk 10/19) : 10000
+Total time elapsed: 100.00 s
+Calling variants ...
+Total processed positions in chr20 (chunk 6/19) : 10000
+Total time elapsed: 100.45 s
+Calling variants ...
+Total processed positions in chr20 (chunk 15/19) : 10000
+Total time elapsed: 101.01 s
+Calling variants ...
+Total processed positions in chr20 (chunk 2/19) : 10000
+Total time elapsed: 100.29 s
+Calling variants ...
+Total processed positions in chr20 (chunk 17/19) : 10000
+Total time elapsed: 102.47 s
+Calling variants ...
+Total processed positions in chr20 (chunk 9/19) : 10000
+Total time elapsed: 105.90 s
+Calling variants ...
+Total processed positions in chr20 (chunk 16/19) : 10000
+Total time elapsed: 106.37 s
+Calling variants ...
+Total processed positions in chr20 (chunk 13/19) : 10000
+Total time elapsed: 107.43 s
+Calling variants ...
+Total processed positions in chr20 (chunk 1/19) : 10000
+Total time elapsed: 107.31 s
+Calling variants ...
+Total processed positions in chr20 (chunk 7/19) : 10000
+Total time elapsed: 108.56 s
+Calling variants ...
+Total processed positions in chr20 (chunk 11/19) : 10000
+Total time elapsed: 108.02 s
+Calling variants ...
+Total processed positions in chr20 (chunk 14/19) : 10000
+Total time elapsed: 113.98 s
+Calling variants ...
+Total processed positions in chr20 (chunk 18/19) : 10000
+Total time elapsed: 121.71 s
+
+real	2m5.361s
+user	31m13.765s
+sys	1m38.568s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr20: 36358
+[INFO] Full-alignment variants processed in chr20: 87253
+
+real	0m2.470s
+user	0m2.770s
+sys	0m0.178s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	5m6.452s
+user	62m2.314s
+sys	2m55.903s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output --ctg_name=chr20 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr20
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr20 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr20
+[INFO] Chunk number for each contig: 14
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr20 (chunk 5/14) : 8465
+Total time elapsed: 49.20 s
+Calling variants ...
+Total processed positions in chr20 (chunk 8/14) : 9125
+Total time elapsed: 50.86 s
+Calling variants ...
+Total processed positions in chr20 (chunk 9/14) : 8456
+Total time elapsed: 51.46 s
+Calling variants ...
+Total processed positions in chr20 (chunk 12/14) : 9736
+Total time elapsed: 52.16 s
+Calling variants ...
+Total processed positions in chr20 (chunk 2/14) : 9407
+Total time elapsed: 52.80 s
+Calling variants ...
+Total processed positions in chr20 (chunk 10/14) : 9956
+Total time elapsed: 54.30 s
+Calling variants ...
+Total processed positions in chr20 (chunk 3/14) : 9839
+Total time elapsed: 54.72 s
+Calling variants ...
+Total processed positions in chr20 (chunk 4/14) : 10680
+Total time elapsed: 55.26 s
+Calling variants ...
+Total processed positions in chr20 (chunk 13/14) : 11784
+Total time elapsed: 55.93 s
+Calling variants ...
+Total processed positions in chr20 (chunk 11/14) : 12944
+Total time elapsed: 58.61 s
+Calling variants ...
+Total processed positions in chr20 (chunk 14/14) : 17216
+Total time elapsed: 62.82 s
+Calling variants ...
+Total processed positions in chr20 (chunk 6/14) : 17711
+Total time elapsed: 64.45 s
+Calling variants ...
+Total processed positions in chr20 (chunk 1/14) : 17838
+Total time elapsed: 64.88 s
+Calling variants ...
+Total processed positions in chr20 (chunk 7/14) : 53609
+Total time elapsed: 108.72 s
+
+real	1m51.540s
+user	10m29.002s
+sys	0m52.148s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19
+[INFO] Total heterozygous SNP positions selected: chr20: 45273
+
+real	0m0.719s
+user	0m0.598s
+sys	0m0.087s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr20.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr20
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr20,15s)
+parsing total:  15s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 17s
+
+real	0m16.687s
+user	0m51.253s
+sys	0m3.133s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 8.0
+[INFO] Low quality reference calls to be processed in chr20: 8756
+[INFO] Low quality variants to be processed in chr20: 83160
+
+real	0m0.739s
+user	0m0.596s
+sys	0m0.103s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr20 (chunk 10/10) : 1916
+Total time elapsed: 25.33 s
+Calling variants ...
+Total processed positions in chr20 (chunk 5/10) : 10000
+Total time elapsed: 97.80 s
+Calling variants ...
+Total processed positions in chr20 (chunk 4/10) : 10000
+Total time elapsed: 107.36 s
+Calling variants ...
+Total processed positions in chr20 (chunk 1/10) : 10000
+Total time elapsed: 112.12 s
+Calling variants ...
+Total processed positions in chr20 (chunk 9/10) : 10000
+Total time elapsed: 114.33 s
+Calling variants ...
+Total processed positions in chr20 (chunk 7/10) : 10000
+Total time elapsed: 116.06 s
+Calling variants ...
+Total processed positions in chr20 (chunk 6/10) : 10000
+Total time elapsed: 116.78 s
+Calling variants ...
+Total processed positions in chr20 (chunk 8/10) : 10000
+Total time elapsed: 118.37 s
+Calling variants ...
+Total processed positions in chr20 (chunk 3/10) : 10000
+Total time elapsed: 122.36 s
+Calling variants ...
+Total processed positions in chr20 (chunk 2/10) : 10000
+Total time elapsed: 123.53 s
+
+real	2m6.049s
+user	16m32.611s
+sys	0m52.581s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr20: 35964
+[INFO] Full-alignment variants processed in chr20: 74344
+
+real	0m1.116s
+user	0m1.113s
+sys	0m0.115s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	4m21.554s
+user	27m58.893s
+sys	1m48.758s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr20: 57143, not found:460, not match:37, low_qual_count:0. Total normal:61825 Total tumor:57640, pro: 0.9914
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/vcf/chr20.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_chr20
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr20,25s)
+parsing total:  25s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 25s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_chr20.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_chr20.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr20
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 0s
+tag read start ...
+chr: chr20 ... 667s
+tag read 668s
+-------------------------------------------
+total process time:  668s
+total alignment:     784888
+total supplementary: 30142
+total secondary:     0
+total unmapped:      0
+total tag alignment: 403864
+total untagged:      381024
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr20 chunk 0/14: Total snv candidates found: 1070, total indel candidates found: 104
+[INFO] chr20 chunk 1/14: Total snv candidates found: 11957, total indel candidates found: 1867
+[INFO] chr20 chunk 7/14: Total snv candidates found: 534, total indel candidates found: 936
+[INFO] chr20 chunk 13/14: Total snv candidates found: 3413, total indel candidates found: 1701
+[faidx] Truncated sequence: chr20:63409487-66211299
+[INFO] chr20 chunk 5/14: Total snv candidates found: 287, total indel candidates found: 577
+[INFO] chr20 chunk 11/14: Total snv candidates found: 821, total indel candidates found: 885
+[INFO] chr20 chunk 8/14: Total snv candidates found: 1520, total indel candidates found: 926
+[INFO] chr20 chunk 2/14: Total snv candidates found: 2770, total indel candidates found: 1316
+[INFO] chr20 chunk 6/14: Total snv candidates found: 469, total indel candidates found: 780
+[INFO] chr20 chunk 3/14: Total snv candidates found: 391, total indel candidates found: 1105
+[INFO] chr20 chunk 4/14: Total snv candidates found: 464, total indel candidates found: 1081
+[INFO] chr20 chunk 12/14: Total snv candidates found: 666, total indel candidates found: 725
+[INFO] chr20 chunk 10/14: Total snv candidates found: 440, total indel candidates found: 728
+[INFO] chr20 chunk 9/14: Total snv candidates found: 430, total indel candidates found: 953
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/2-1_CPT.log
+
+[INFO] chr20 chunk 1-1/0 Tensors generated: 998
+[INFO] chr20 chunk 2-2/1 Tensors generated: 1950
+[INFO] chr20 chunk 1-1/5 Tensors generated: 287
+[INFO] chr20 chunk 1-1/3 Tensors generated: 391
+[INFO] chr20 chunk 1-1/10 Tensors generated: 440
+[INFO] chr20 chunk 1-1/9 Tensors generated: 430
+[INFO] chr20 chunk 1-1/6 Tensors generated: 469
+[INFO] chr20 chunk 1-1/4 Tensors generated: 464
+[INFO] chr20 chunk 1-1/12 Tensors generated: 665
+[INFO] chr20 chunk 1-1/7 Tensors generated: 533
+[INFO] chr20 chunk 1-1/11 Tensors generated: 821
+[INFO] chr20 chunk 1-1/8 Tensors generated: 1520
+[INFO] chr20 chunk 1-1/13 Tensors generated: 3368
+[INFO] chr20 chunk 1-1/2 Tensors generated: 2767
+[INFO] chr20 chunk 1-2/1 Tensors generated: 9999
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/2-2_PREDICT.log
+
+[INFO] chr20 total processed positions: 391, time elapsed: 0.8s
+[INFO] chr20 total processed positions: 287, time elapsed: 0.9s
+[INFO] chr20 total processed positions: 430, time elapsed: 1.2s
+[INFO] chr20 total processed positions: 440, time elapsed: 1.0s
+[INFO] chr20 total processed positions: 469, time elapsed: 1.2s
+[INFO] chr20 total processed positions: 533, time elapsed: 1.3s
+[INFO] chr20 total processed positions: 665, time elapsed: 1.3s
+[INFO] chr20 total processed positions: 464, time elapsed: 1.3s
+[INFO] chr20 total processed positions: 821, time elapsed: 1.5s
+[INFO] chr20 total processed positions: 998, time elapsed: 1.9s
+[INFO] chr20 total processed positions: 1520, time elapsed: 3.1s
+[INFO] chr20 total processed positions: 1950, time elapsed: 3.5s
+[INFO] chr20 total processed positions: 2767, time elapsed: 5.1s
+[INFO] chr20 total processed positions: 3368, time elapsed: 6.0s
+[INFO] chr20 total processed positions: 9999, time elapsed: 16.2s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/3-1_CPT.log
+
+[INFO] chr20 chunk 1-1/0 Tensors generated: 908
+[INFO] chr20 chunk 1-1/5 Tensors generated: 287
+[INFO] chr20 chunk 1-1/3 Tensors generated: 391
+[INFO] chr20 chunk 1-1/6 Tensors generated: 469
+[INFO] chr20 chunk 1-1/9 Tensors generated: 430
+[INFO] chr20 chunk 1-1/4 Tensors generated: 464
+[INFO] chr20 chunk 1-1/10 Tensors generated: 440
+[INFO] chr20 chunk 1-1/7 Tensors generated: 533
+[INFO] chr20 chunk 2-2/1 Tensors generated: 1895
+[INFO] chr20 chunk 1-1/12 Tensors generated: 665
+[INFO] chr20 chunk 1-1/11 Tensors generated: 821
+[INFO] chr20 chunk 1-1/8 Tensors generated: 1520
+[INFO] chr20 chunk 1-1/2 Tensors generated: 2761
+[INFO] chr20 chunk 1-1/13 Tensors generated: 3359
+[INFO] chr20 chunk 1-2/1 Tensors generated: 9830
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/3-2_PREDICT.log
+
+[INFO] chr20 total processed positions: 287, time elapsed: 51.0s
+[INFO] chr20 total processed positions: 391, time elapsed: 70.0s
+[INFO] chr20 total processed positions: 440, time elapsed: 78.2s
+[INFO] chr20 total processed positions: 430, time elapsed: 81.4s
+[INFO] chr20 total processed positions: 464, time elapsed: 82.3s
+[INFO] chr20 total processed positions: 469, time elapsed: 82.9s
+[INFO] chr20 total processed positions: 533, time elapsed: 99.1s
+[INFO] chr20 total processed positions: 665, time elapsed: 117.3s
+[INFO] chr20 total processed positions: 821, time elapsed: 145.1s
+[INFO] chr20 total processed positions: 908, time elapsed: 161.0s
+slurmstepd: error: *** JOB 2556290 ON n13 CANCELLED AT 2025-12-08T16:49:54 ***
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556290
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n13
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:21:40
+Job ended at:   2025-12-08 16:49:54
+Job Wall-clock time: 00:28:14
+CPU Utilized: 02:54:10
+CPU Efficiency: 15.42% of 18:49:20 core-walltime
+Memory Utilized: 21.68 GB
+Memory Efficiency: 54.19% of 40.00 GB

slurm-2556291.out

@@ -0,0 +1,644 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24 --region chr21:1-45090682 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr21
+[INFO] Number of chunks for each contig: 10
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr21:1-45090682
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output --ctg_name=chr21 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr21
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr21 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr21
+[INFO] Chunk number for each contig: 10
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr21 (chunk 1/10) : 21247
+Total time elapsed: 40.19 s
+Calling variants ...
+Total processed positions in chr21 (chunk 2/10) : 55447
+Total time elapsed: 86.41 s
+Calling variants ...
+Total processed positions in chr21 (chunk 5/10) : 65383
+Total time elapsed: 99.76 s
+Calling variants ...
+Total processed positions in chr21 (chunk 6/10) : 71156
+Total time elapsed: 100.33 s
+Calling variants ...
+Total processed positions in chr21 (chunk 4/10) : 73057
+Total time elapsed: 104.96 s
+Calling variants ...
+Total processed positions in chr21 (chunk 3/10) : 71284
+Total time elapsed: 107.34 s
+Calling variants ...
+Total processed positions in chr21 (chunk 7/10) : 75897
+Total time elapsed: 113.52 s
+Calling variants ...
+Total processed positions in chr21 (chunk 9/10) : 81308
+Total time elapsed: 118.65 s
+Calling variants ...
+Total processed positions in chr21 (chunk 8/10) : 78139
+Total time elapsed: 121.89 s
+Calling variants ...
+Total processed positions in chr21 (chunk 10/10) : 86992
+Total time elapsed: 128.36 s
+
+real	2m15.199s
+user	16m24.968s
+sys	1m1.295s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
+[INFO] Total heterozygous SNP positions selected: chr21: 38730
+
+real	0m1.926s
+user	0m1.806s
+sys	0m0.107s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr21.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr21
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr21,5s)
+parsing total:  5s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 5s
+
+real	0m5.642s
+user	0m11.272s
+sys	0m0.759s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 13.0
+[INFO] Low quality reference calls to be processed in chr21: 57899
+[INFO] Low quality variants to be processed in chr21: 69711
+
+real	0m1.996s
+user	0m1.789s
+sys	0m0.182s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr21 (chunk 13/13) : 7610
+Total time elapsed: 72.41 s
+Calling variants ...
+Total processed positions in chr21 (chunk 9/13) : 10000
+Total time elapsed: 75.76 s
+Calling variants ...
+Total processed positions in chr21 (chunk 3/13) : 10000
+Total time elapsed: 76.04 s
+Calling variants ...
+Total processed positions in chr21 (chunk 2/13) : 10000
+Total time elapsed: 76.76 s
+Calling variants ...
+Total processed positions in chr21 (chunk 11/13) : 10000
+Total time elapsed: 77.08 s
+Calling variants ...
+Total processed positions in chr21 (chunk 8/13) : 10000
+Total time elapsed: 78.05 s
+Calling variants ...
+Total processed positions in chr21 (chunk 10/13) : 10000
+Total time elapsed: 78.25 s
+Calling variants ...
+Total processed positions in chr21 (chunk 5/13) : 10000
+Total time elapsed: 80.58 s
+Calling variants ...
+Total processed positions in chr21 (chunk 1/13) : 10000
+Total time elapsed: 82.69 s
+Calling variants ...
+Total processed positions in chr21 (chunk 7/13) : 10000
+Total time elapsed: 84.85 s
+Calling variants ...
+Total processed positions in chr21 (chunk 4/13) : 10000
+Total time elapsed: 84.74 s
+Calling variants ...
+Total processed positions in chr21 (chunk 12/13) : 10000
+Total time elapsed: 86.04 s
+Calling variants ...
+Total processed positions in chr21 (chunk 6/13) : 10000
+Total time elapsed: 86.95 s
+
+real	1m30.619s
+user	16m49.687s
+sys	1m7.751s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr21: 29908
+[INFO] Full-alignment variants processed in chr21: 74068
+
+real	0m2.641s
+user	0m2.759s
+sys	0m0.179s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	4m8.696s
+user	33m41.706s
+sys	2m11.367s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output --ctg_name=chr21 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr21
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr21 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr21
+[INFO] Chunk number for each contig: 10
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr21 (chunk 5/10) : 11068
+Total time elapsed: 44.07 s
+Calling variants ...
+Total processed positions in chr21 (chunk 7/10) : 9368
+Total time elapsed: 44.86 s
+Calling variants ...
+Total processed positions in chr21 (chunk 4/10) : 10732
+Total time elapsed: 45.33 s
+Calling variants ...
+Total processed positions in chr21 (chunk 6/10) : 10461
+Total time elapsed: 45.62 s
+Calling variants ...
+Total processed positions in chr21 (chunk 9/10) : 11777
+Total time elapsed: 48.59 s
+Calling variants ...
+Total processed positions in chr21 (chunk 8/10) : 11175
+Total time elapsed: 50.18 s
+Calling variants ...
+Total processed positions in chr21 (chunk 10/10) : 15430
+Total time elapsed: 53.54 s
+Calling variants ...
+Total processed positions in chr21 (chunk 1/10) : 36882
+Total time elapsed: 81.42 s
+Calling variants ...
+Total processed positions in chr21 (chunk 3/10) : 32029
+Total time elapsed: 89.59 s
+Calling variants ...
+Total processed positions in chr21 (chunk 2/10) : 75635
+Total time elapsed: 132.33 s
+
+real	2m15.749s
+user	8m50.712s
+sys	0m36.304s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 17
+[INFO] Total heterozygous SNP positions selected: chr21: 39429
+
+real	0m1.077s
+user	0m0.967s
+sys	0m0.103s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr21.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr21
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr21,18s)
+parsing total:  18s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 19s
+
+real	0m18.951s
+user	0m46.210s
+sys	0m3.036s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 9.0
+[INFO] Low quality reference calls to be processed in chr21: 11425
+[INFO] Low quality variants to be processed in chr21: 77112
+
+real	0m1.032s
+user	0m0.893s
+sys	0m0.124s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr21 (chunk 1/9) : 10000
+Total time elapsed: 85.71 s
+Calling variants ...
+Total processed positions in chr21 (chunk 3/9) : 10000
+Total time elapsed: 89.12 s
+Calling variants ...
+Total processed positions in chr21 (chunk 4/9) : 10000
+Total time elapsed: 98.05 s
+Calling variants ...
+Total processed positions in chr21 (chunk 2/9) : 10000
+Total time elapsed: 101.27 s
+Calling variants ...
+Total processed positions in chr21 (chunk 6/9) : 10000
+Total time elapsed: 103.79 s
+Calling variants ...
+Total processed positions in chr21 (chunk 7/9) : 10000
+Total time elapsed: 105.16 s
+Calling variants ...
+Total processed positions in chr21 (chunk 9/9) : 8537
+Total time elapsed: 105.70 s
+Calling variants ...
+Total processed positions in chr21 (chunk 5/9) : 10000
+Total time elapsed: 110.43 s
+Calling variants ...
+Total processed positions in chr21 (chunk 8/9) : 10000
+Total time elapsed: 110.81 s
+
+real	1m54.184s
+user	14m27.321s
+sys	0m46.063s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr21: 33077
+[INFO] Full-alignment variants processed in chr21: 73272
+
+real	0m1.619s
+user	0m1.597s
+sys	0m0.153s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	4m38.770s
+user	24m12.848s
+sys	1m26.479s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr21: 54974, not found:1251, not match:50, low_qual_count:0. Total normal:57735 Total tumor:56275, pro: 0.9769
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf/chr21.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_chr21
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr21,34s)
+parsing total:  34s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 35s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_chr21.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_chr21.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr21
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 1s
+tag read start ...
+chr: chr21 ... 615s
+tag read 616s
+-------------------------------------------
+total process time:  617s
+total alignment:     890148
+total supplementary: 22088
+total secondary:     0
+total unmapped:      0
+total tag alignment: 306829
+total untagged:      583319
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr21 chunk 0/10: Total snv candidates found: 5072, total indel candidates found: 757
+[INFO] chr21 chunk 1/10: Total snv candidates found: 20319, total indel candidates found: 4282
+[INFO] chr21 chunk 2/10: Total snv candidates found: 6136, total indel candidates found: 1125
+[INFO] chr21 chunk 8/10: Total snv candidates found: 912, total indel candidates found: 1199
+[INFO] chr21 chunk 9/10: Total snv candidates found: 3112, total indel candidates found: 2027
+[faidx] Truncated sequence: chr21:40580649-45091721
+[INFO] chr21 chunk 6/10: Total snv candidates found: 736, total indel candidates found: 1237
+[INFO] chr21 chunk 7/10: Total snv candidates found: 1248, total indel candidates found: 1555
+[INFO] chr21 chunk 3/10: Total snv candidates found: 616, total indel candidates found: 964
+[INFO] chr21 chunk 4/10: Total snv candidates found: 805, total indel candidates found: 947
+[INFO] chr21 chunk 5/10: Total snv candidates found: 741, total indel candidates found: 1069
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/2-1_CPT.log
+
+[INFO] chr21 chunk 3-3/1 Tensors generated: 318
+[INFO] chr21 chunk 1-1/3 Tensors generated: 616
+[INFO] chr21 chunk 1-1/5 Tensors generated: 741
+[INFO] chr21 chunk 1-1/4 Tensors generated: 805
+[INFO] chr21 chunk 1-1/6 Tensors generated: 729
+[INFO] chr21 chunk 1-1/8 Tensors generated: 912
+[INFO] chr21 chunk 1-1/0 Tensors generated: 5057
+[INFO] chr21 chunk 1-1/7 Tensors generated: 1248
+[INFO] chr21 chunk 2-3/1 Tensors generated: 9316
+[INFO] chr21 chunk 1-1/9 Tensors generated: 3109
+[faidx] Truncated sequence: chr21:40603737-45091575
+[INFO] chr21 chunk 1-3/1 Tensors generated: 9761
+[INFO] chr21 chunk 1-1/2 Tensors generated: 6135
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/2-2_PREDICT.log
+
+[INFO] chr21 total processed positions: 318, time elapsed: 1.2s
+[INFO] chr21 total processed positions: 616, time elapsed: 1.7s
+[INFO] chr21 total processed positions: 729, time elapsed: 2.0s
+[INFO] chr21 total processed positions: 741, time elapsed: 2.0s
+[INFO] chr21 total processed positions: 805, time elapsed: 2.2s
+[INFO] chr21 total processed positions: 912, time elapsed: 2.4s
+[INFO] chr21 total processed positions: 1248, time elapsed: 3.0s
+[INFO] chr21 total processed positions: 3109, time elapsed: 6.7s
+[INFO] chr21 total processed positions: 5057, time elapsed: 10.3s
+[INFO] chr21 total processed positions: 6135, time elapsed: 12.9s
+[INFO] chr21 total processed positions: 9316, time elapsed: 18.5s
+[INFO] chr21 total processed positions: 9761, time elapsed: 20.0s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/3-1_CPT.log
+
+[INFO] chr21 chunk 3-3/1 Tensors generated: 316
+[INFO] chr21 chunk 1-1/3 Tensors generated: 616
+[INFO] chr21 chunk 1-1/6 Tensors generated: 729
+[INFO] chr21 chunk 1-1/5 Tensors generated: 741
+[INFO] chr21 chunk 1-1/4 Tensors generated: 805
+[INFO] chr21 chunk 1-1/8 Tensors generated: 912
+[INFO] chr21 chunk 1-1/7 Tensors generated: 1248
+[INFO] chr21 chunk 1-1/0 Tensors generated: 4472
+[INFO] chr21 chunk 2-3/1 Tensors generated: 8494
+[INFO] chr21 chunk 1-1/9 Tensors generated: 3109
+[faidx] Truncated sequence: chr21:40603737-45091575
+[INFO] chr21 chunk 1-1/2 Tensors generated: 6067
+[INFO] chr21 chunk 1-3/1 Tensors generated: 9502
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/3-2_PREDICT.log
+
+[INFO] chr21 total processed positions: 316, time elapsed: 37.3s
+[INFO] chr21 total processed positions: 616, time elapsed: 71.5s
+slurmstepd: error: *** JOB 2556291 ON n01 CANCELLED AT 2025-12-08T16:49:54 ***
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556291
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n01
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:24:11
+Job ended at:   2025-12-08 16:49:54
+Job Wall-clock time: 00:25:43
+CPU Utilized: 02:07:35
+CPU Efficiency: 12.40% of 17:08:40 core-walltime
+Memory Utilized: 16.69 GB
+Memory Efficiency: 41.71% of 40.00 GB

slurm-2556292.out

@@ -0,0 +1,322 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27 --region chr3:20251704-176116306 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr3
+[INFO] Number of chunks for each contig: 41
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr3:20251704-176116306
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output --ctg_name=chr3 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr3
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr3 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr3
+[INFO] Chunk number for each contig: 41
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr3 (chunk 20/41) : 46480
+Total time elapsed: 170.63 s
+Calling variants ...
+Total processed positions in chr3 (chunk 19/41) : 56068
+Total time elapsed: 196.00 s
+Calling variants ...
+Total processed positions in chr3 (chunk 17/41) : 69035
+Total time elapsed: 236.76 s
+Calling variants ...
+Total processed positions in chr3 (chunk 21/41) : 70599
+Total time elapsed: 237.59 s
+Calling variants ...
+Total processed positions in chr3 (chunk 5/41) : 74479
+Total time elapsed: 243.32 s
+Calling variants ...
+Total processed positions in chr3 (chunk 14/41) : 74855
+Total time elapsed: 246.58 s
+Calling variants ...
+Total processed positions in chr3 (chunk 1/41) : 79390
+Total time elapsed: 247.69 s
+Calling variants ...
+Total processed positions in chr3 (chunk 6/41) : 75949
+Total time elapsed: 249.08 s
+Calling variants ...
+Total processed positions in chr3 (chunk 18/41) : 74745
+Total time elapsed: 250.59 s
+Calling variants ...
+Total processed positions in chr3 (chunk 22/41) : 78103
+Total time elapsed: 253.62 s
+Calling variants ...
+Total processed positions in chr3 (chunk 9/41) : 81163
+Total time elapsed: 260.02 s
+Calling variants ...
+Total processed positions in chr3 (chunk 16/41) : 76388
+Total time elapsed: 261.10 s
+Calling variants ...
+Total processed positions in chr3 (chunk 23/41) : 79301
+Total time elapsed: 262.87 s
+Calling variants ...
+Total processed positions in chr3 (chunk 25/41) : 78250
+Total time elapsed: 263.37 s
+Calling variants ...
+Total processed positions in chr3 (chunk 24/41) : 81383
+Total time elapsed: 265.82 s
+Calling variants ...
+Total processed positions in chr3 (chunk 7/41) : 82908
+Total time elapsed: 266.83 s
+Calling variants ...
+Total processed positions in chr3 (chunk 4/41) : 79370
+Total time elapsed: 267.67 s
+Calling variants ...
+Total processed positions in chr3 (chunk 12/41) : 80581
+Total time elapsed: 271.61 s
+Calling variants ...
+Total processed positions in chr3 (chunk 26/41) : 79342
+Total time elapsed: 243.81 s
+Calling variants ...
+Total processed positions in chr3 (chunk 8/41) : 83199
+Total time elapsed: 276.33 s
+Calling variants ...
+Total processed positions in chr3 (chunk 28/41) : 77518
+Total time elapsed: 245.70 s
+Calling variants ...
+Total processed positions in chr3 (chunk 29/41) : 75850
+Total time elapsed: 248.04 s
+Calling variants ...
+Total processed positions in chr3 (chunk 13/41) : 80100
+Total time elapsed: 248.50 s
+Calling variants ...
+Total processed positions in chr3 (chunk 30/41) : 77260
+Total time elapsed: 248.39 s
+Calling variants ...
+Total processed positions in chr3 (chunk 10/41) : 79740
+Total time elapsed: 251.52 s
+Calling variants ...
+Total processed positions in chr3 (chunk 11/41) : 82947
+Total time elapsed: 260.02 s
+Calling variants ...
+Total processed positions in chr3 (chunk 27/41) : 86290
+Total time elapsed: 291.60 s
+Calling variants ...
+Total processed positions in chr3 (chunk 2/41) : 83369
+Total time elapsed: 261.26 s
+Calling variants ...
+Total processed positions in chr3 (chunk 15/41) : 82728
+Total time elapsed: 261.34 s
+Calling variants ...
+Total processed positions in chr3 (chunk 3/41) : 87168
+Total time elapsed: 263.77 s
+Calling variants ...
+Total processed positions in chr3 (chunk 31/41) : 77286
+Total time elapsed: 189.04 s
+Calling variants ...
+Total processed positions in chr3 (chunk 32/41) : 83710
+Total time elapsed: 200.27 s
+Calling variants ...
+Total processed positions in chr3 (chunk 33/41) : 75437
+Total time elapsed: 161.14 s
+Calling variants ...
+Total processed positions in chr3 (chunk 34/41) : 75899
+Total time elapsed: 168.99 s
+Calling variants ...
+Total processed positions in chr3 (chunk 36/41) : 77630
+Total time elapsed: 165.08 s
+Calling variants ...
+Total processed positions in chr3 (chunk 38/41) : 75120
+Total time elapsed: 163.08 s
+Calling variants ...
+Total processed positions in chr3 (chunk 35/41) : 74299
+Total time elapsed: 169.32 s
+Calling variants ...
+Total processed positions in chr3 (chunk 37/41) : 75513
+Total time elapsed: 166.41 s
+Calling variants ...
+Total processed positions in chr3 (chunk 39/41) : 82603
+Total time elapsed: 175.52 s
+Calling variants ...
+Total processed positions in chr3 (chunk 40/41) : 83507
+Total time elapsed: 175.41 s
+Calling variants ...
+Total processed positions in chr3 (chunk 41/41) : 89682
+Total time elapsed: 174.30 s
+
+real	7m29.196s
+user	153m14.000s
+sys	7m27.400s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16
+[INFO] Total heterozygous SNP positions selected: chr3: 123767
+
+real	0m5.433s
+user	0m4.980s
+sys	0m0.357s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr3.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr3
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr3,15s)
+parsing total:  15s
+merge results ... 0s
+writeResult SNP ... 2s
+
+total process: 19s
+
+real	0m19.284s
+user	1m2.234s
+sys	0m3.715s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 20.0
+[INFO] Set reference calls quality cutoff 14.0
+[INFO] Low quality reference calls to be processed in chr3: 283652
+[INFO] Low quality variants to be processed in chr3: 238359
+
+real	0m6.292s
+user	0m5.718s
+sys	0m0.454s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+slurmstepd: error: *** JOB 2556292 ON n11 CANCELLED AT 2025-12-08T16:49:54 ***
+slurmstepd: error: Detected 10 oom_kill events in StepId=2556292.batch. Some of the step tasks have been OOM Killed.
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556292
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n11
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:41:15
+Job ended at:   2025-12-08 16:49:54
+Job Wall-clock time: 00:08:39
+CPU Utilized: 02:45:28
+CPU Efficiency: 47.82% of 05:46:00 core-walltime
+Memory Utilized: 32.81 GB
+Memory Efficiency: 82.02% of 40.00 GB

slurm-2556293.out

@@ -0,0 +1,449 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15 --region chr17:1-28642702 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr17
+[INFO] Number of chunks for each contig: 17
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr17:1-28642702
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output --ctg_name=chr17 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr17
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr17 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr17
+[INFO] Chunk number for each contig: 17
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr17 (chunk 6/17) : 38596
+Total time elapsed: 95.29 s
+Calling variants ...
+Total processed positions in chr17 (chunk 5/17) : 61627
+Total time elapsed: 143.16 s
+Calling variants ...
+Total processed positions in chr17 (chunk 13/17) : 78825
+Total time elapsed: 173.07 s
+Calling variants ...
+Total processed positions in chr17 (chunk 3/17) : 85876
+Total time elapsed: 181.43 s
+Calling variants ...
+Total processed positions in chr17 (chunk 4/17) : 84539
+Total time elapsed: 181.84 s
+Calling variants ...
+Total processed positions in chr17 (chunk 14/17) : 81181
+Total time elapsed: 181.83 s
+Calling variants ...
+Total processed positions in chr17 (chunk 15/17) : 81543
+Total time elapsed: 182.32 s
+Calling variants ...
+Total processed positions in chr17 (chunk 10/17) : 83514
+Total time elapsed: 183.69 s
+Calling variants ...
+Total processed positions in chr17 (chunk 12/17) : 83512
+Total time elapsed: 187.00 s
+Calling variants ...
+Total processed positions in chr17 (chunk 8/17) : 83634
+Total time elapsed: 188.40 s
+Calling variants ...
+Total processed positions in chr17 (chunk 11/17) : 83228
+Total time elapsed: 188.88 s
+Calling variants ...
+Total processed positions in chr17 (chunk 16/17) : 93033
+Total time elapsed: 191.89 s
+Calling variants ...
+Total processed positions in chr17 (chunk 7/17) : 82191
+Total time elapsed: 194.59 s
+Calling variants ...
+Total processed positions in chr17 (chunk 9/17) : 92357
+Total time elapsed: 198.54 s
+Calling variants ...
+Total processed positions in chr17 (chunk 1/17) : 90481
+Total time elapsed: 201.20 s
+Calling variants ...
+Total processed positions in chr17 (chunk 2/17) : 89155
+Total time elapsed: 202.31 s
+Calling variants ...
+Total processed positions in chr17 (chunk 17/17) : 98267
+Total time elapsed: 214.09 s
+
+real	3m44.304s
+user	50m1.430s
+sys	2m26.943s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15
+[INFO] Total heterozygous SNP positions selected: chr17: 53664
+
+real	0m2.855s
+user	0m2.653s
+sys	0m0.172s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr17.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr17
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr17,6s)
+parsing total:  6s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 8s
+
+real	0m8.006s
+user	0m26.299s
+sys	0m1.603s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 13.0
+[INFO] Low quality reference calls to be processed in chr17: 123647
+[INFO] Low quality variants to be processed in chr17: 107365
+
+real	0m3.208s
+user	0m2.830s
+sys	0m0.319s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr17 (chunk 24/24) : 1012
+Total time elapsed: 15.71 s
+Calling variants ...
+Total processed positions in chr17 (chunk 16/24) : 10000
+Total time elapsed: 119.10 s
+Calling variants ...
+Total processed positions in chr17 (chunk 14/24) : 10000
+Total time elapsed: 121.61 s
+Calling variants ...
+Total processed positions in chr17 (chunk 19/24) : 10000
+Total time elapsed: 121.63 s
+Calling variants ...
+Total processed positions in chr17 (chunk 18/24) : 10000
+Total time elapsed: 121.65 s
+Calling variants ...
+Total processed positions in chr17 (chunk 6/24) : 10000
+Total time elapsed: 122.69 s
+Calling variants ...
+Total processed positions in chr17 (chunk 22/24) : 10000
+Total time elapsed: 123.51 s
+Calling variants ...
+Total processed positions in chr17 (chunk 21/24) : 10000
+Total time elapsed: 124.82 s
+Calling variants ...
+Total processed positions in chr17 (chunk 9/24) : 10000
+Total time elapsed: 125.01 s
+Calling variants ...
+Total processed positions in chr17 (chunk 4/24) : 10000
+Total time elapsed: 125.55 s
+Calling variants ...
+Total processed positions in chr17 (chunk 3/24) : 10000
+Total time elapsed: 126.30 s
+Calling variants ...
+Total processed positions in chr17 (chunk 12/24) : 10000
+Total time elapsed: 127.36 s
+Calling variants ...
+Total processed positions in chr17 (chunk 5/24) : 10000
+Total time elapsed: 127.54 s
+Calling variants ...
+Total processed positions in chr17 (chunk 10/24) : 10000
+Total time elapsed: 127.68 s
+Calling variants ...
+Total processed positions in chr17 (chunk 15/24) : 10000
+Total time elapsed: 128.53 s
+Calling variants ...
+Total processed positions in chr17 (chunk 20/24) : 10000
+Total time elapsed: 128.48 s
+Calling variants ...
+Total processed positions in chr17 (chunk 13/24) : 10000
+Total time elapsed: 130.01 s
+Calling variants ...
+Total processed positions in chr17 (chunk 11/24) : 10000
+Total time elapsed: 130.35 s
+Calling variants ...
+Total processed positions in chr17 (chunk 17/24) : 10000
+Total time elapsed: 129.08 s
+Calling variants ...
+Total processed positions in chr17 (chunk 2/24) : 10000
+Total time elapsed: 130.48 s
+Calling variants ...
+Total processed positions in chr17 (chunk 23/24) : 10000
+Total time elapsed: 131.76 s
+Calling variants ...
+Total processed positions in chr17 (chunk 7/24) : 10000
+Total time elapsed: 132.22 s
+Calling variants ...
+Total processed positions in chr17 (chunk 1/24) : 10000
+Total time elapsed: 133.61 s
+Calling variants ...
+Total processed positions in chr17 (chunk 8/24) : 10000
+Total time elapsed: 135.06 s
+
+real	2m19.593s
+user	47m42.523s
+sys	2m20.775s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr17: 46074
+[INFO] Full-alignment variants processed in chr17: 113883
+
+real	0m3.762s
+user	0m4.756s
+sys	0m0.345s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	6m41.397s
+user	98m39.308s
+sys	4m52.491s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output --ctg_name=chr17 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr17
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr17 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr17
+[INFO] Chunk number for each contig: 17
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr17 (chunk 15/17) : 11069
+Total time elapsed: 73.46 s
+Calling variants ...
+Total processed positions in chr17 (chunk 11/17) : 10550
+Total time elapsed: 73.77 s
+Calling variants ...
+Total processed positions in chr17 (chunk 12/17) : 10782
+Total time elapsed: 74.56 s
+Calling variants ...
+Total processed positions in chr17 (chunk 10/17) : 11845
+Total time elapsed: 75.71 s
+Calling variants ...
+Total processed positions in chr17 (chunk 14/17) : 11398
+Total time elapsed: 75.65 s
+Calling variants ...
+Total processed positions in chr17 (chunk 7/17) : 12155
+Total time elapsed: 78.00 s
+Calling variants ...
+Total processed positions in chr17 (chunk 3/17) : 12437
+Total time elapsed: 78.22 s
+Calling variants ...
+Total processed positions in chr17 (chunk 2/17) : 13822
+Total time elapsed: 78.40 s
+Calling variants ...
+Total processed positions in chr17 (chunk 6/17) : 13099
+Total time elapsed: 78.92 s
+Calling variants ...
+Total processed positions in chr17 (chunk 8/17) : 13984
+Total time elapsed: 79.86 s
+Calling variants ...
+Total processed positions in chr17 (chunk 16/17) : 15105
+Total time elapsed: 81.61 s
+Calling variants ...
+Total processed positions in chr17 (chunk 4/17) : 13833
+Total time elapsed: 82.04 s
+Calling variants ...
+Total processed positions in chr17 (chunk 17/17) : 16957
+Total time elapsed: 82.85 s
+Calling variants ...
+Total processed positions in chr17 (chunk 1/17) : 18647
+Total time elapsed: 90.68 s
+Calling variants ...
+Total processed positions in chr17 (chunk 5/17) : 23171
+Total time elapsed: 93.07 s
+slurmstepd: error: *** JOB 2556293 ON n12 CANCELLED AT 2025-12-08T16:49:54 ***
+slurmstepd: error: Detected 2 oom_kill events in StepId=2556293.batch. Some of the step tasks have been OOM Killed.
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556293
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n12
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:41:15
+Job ended at:   2025-12-08 16:49:54
+Job Wall-clock time: 00:08:39
+CPU Utilized: 02:04:09
+CPU Efficiency: 35.88% of 05:46:00 core-walltime
+Memory Utilized: 34.06 GB
+Memory Efficiency: 85.15% of 40.00 GB

slurm-2556294.out

@@ -0,0 +1,298 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35 --region chr7:1-50721758 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr7
+[INFO] Number of chunks for each contig: 33
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr7:1-50721758
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output --ctg_name=chr7 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr7
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr7 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr7
+[INFO] Chunk number for each contig: 33
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr7 (chunk 13/33) : 22241
+Total time elapsed: 76.23 s
+Calling variants ...
+Total processed positions in chr7 (chunk 18/33) : 70139
+Total time elapsed: 180.60 s
+Calling variants ...
+Total processed positions in chr7 (chunk 25/33) : 69867
+Total time elapsed: 192.97 s
+Calling variants ...
+Total processed positions in chr7 (chunk 23/33) : 74428
+Total time elapsed: 194.37 s
+Calling variants ...
+Total processed positions in chr7 (chunk 22/33) : 73065
+Total time elapsed: 196.55 s
+Calling variants ...
+Total processed positions in chr7 (chunk 24/33) : 73684
+Total time elapsed: 196.68 s
+Calling variants ...
+Total processed positions in chr7 (chunk 9/33) : 75541
+Total time elapsed: 199.46 s
+Calling variants ...
+Total processed positions in chr7 (chunk 12/33) : 74720
+Total time elapsed: 200.92 s
+Calling variants ...
+Total processed positions in chr7 (chunk 11/33) : 76047
+Total time elapsed: 201.97 s
+Calling variants ...
+Total processed positions in chr7 (chunk 7/33) : 80296
+Total time elapsed: 202.79 s
+Calling variants ...
+Total processed positions in chr7 (chunk 17/33) : 80009
+Total time elapsed: 203.21 s
+Calling variants ...
+Total processed positions in chr7 (chunk 3/33) : 76077
+Total time elapsed: 204.37 s
+Calling variants ...
+Total processed positions in chr7 (chunk 20/33) : 75524
+Total time elapsed: 204.22 s
+Calling variants ...
+Total processed positions in chr7 (chunk 15/33) : 82326
+Total time elapsed: 207.43 s
+Calling variants ...
+Total processed positions in chr7 (chunk 27/33) : 77596
+Total time elapsed: 208.35 s
+Calling variants ...
+Total processed positions in chr7 (chunk 21/33) : 78446
+Total time elapsed: 208.68 s
+Calling variants ...
+Total processed positions in chr7 (chunk 29/33) : 82170
+Total time elapsed: 208.62 s
+Calling variants ...
+Total processed positions in chr7 (chunk 14/33) : 69296
+Total time elapsed: 184.90 s
+Calling variants ...
+Total processed positions in chr7 (chunk 4/33) : 75243
+Total time elapsed: 189.34 s
+Calling variants ...
+Total processed positions in chr7 (chunk 19/33) : 72947
+Total time elapsed: 189.56 s
+Calling variants ...
+Total processed positions in chr7 (chunk 16/33) : 74245
+Total time elapsed: 190.73 s
+Calling variants ...
+Total processed positions in chr7 (chunk 5/33) : 83328
+Total time elapsed: 214.77 s
+Calling variants ...
+Total processed positions in chr7 (chunk 28/33) : 82266
+Total time elapsed: 216.35 s
+Calling variants ...
+Total processed positions in chr7 (chunk 6/33) : 80708
+Total time elapsed: 217.18 s
+Calling variants ...
+Total processed positions in chr7 (chunk 8/33) : 73966
+Total time elapsed: 194.26 s
+Calling variants ...
+Total processed positions in chr7 (chunk 26/33) : 77513
+Total time elapsed: 195.12 s
+Calling variants ...
+Total processed positions in chr7 (chunk 30/33) : 79092
+Total time elapsed: 197.61 s
+Calling variants ...
+Total processed positions in chr7 (chunk 10/33) : 83424
+Total time elapsed: 199.29 s
+Calling variants ...
+Total processed positions in chr7 (chunk 2/33) : 84481
+Total time elapsed: 201.74 s
+Calling variants ...
+Total processed positions in chr7 (chunk 1/33) : 95891
+Total time elapsed: 218.87 s
+Calling variants ...
+Total processed positions in chr7 (chunk 31/33) : 80772
+Total time elapsed: 172.06 s
+Calling variants ...
+Total processed positions in chr7 (chunk 32/33) : 87130
+Total time elapsed: 127.73 s
+Calling variants ...
+Total processed positions in chr7 (chunk 33/33) : 91433
+Total time elapsed: 128.40 s
+
+real	5m32.252s
+user	102m25.761s
+sys	4m21.024s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16
+[INFO] Total heterozygous SNP positions selected: chr7: 91608
+
+real	0m3.670s
+user	0m3.361s
+sys	0m0.201s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr7.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part35/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr7
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr7,10s)
+parsing total:  10s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 13s
+
+real	0m12.535s
+user	0m24.203s
+sys	0m1.755s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 20.0
+[INFO] Set reference calls quality cutoff 14.0
+[INFO] Low quality reference calls to be processed in chr7: 224670
+[INFO] Low quality variants to be processed in chr7: 197578
+
+real	0m4.202s
+user	0m3.753s
+sys	0m0.344s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+slurmstepd: error: *** JOB 2556294 ON n17 CANCELLED AT 2025-12-08T16:49:54 ***
+slurmstepd: error: Detected 10 oom_kill events in StepId=2556294.batch. Some of the step tasks have been OOM Killed.
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556294
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n17
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:42:45
+Job ended at:   2025-12-08 16:49:54
+Job Wall-clock time: 00:07:09
+CPU Utilized: 02:14:38
+CPU Efficiency: 47.07% of 04:46:00 core-walltime
+Memory Utilized: 26.77 GB
+Memory Efficiency: 66.93% of 40.00 GB

slurm-2556295.out

@@ -0,0 +1,228 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30 --region chr4:130874962-193574945 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr4
+[INFO] Number of chunks for each contig: 39
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr4:130874962-193574945
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output --ctg_name=chr4 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr4
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr4 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part30/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr4
+[INFO] Chunk number for each contig: 39
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr4 (chunk 11/39) : 24000
+Total time elapsed: 87.69 s
+Calling variants ...
+Total processed positions in chr4 (chunk 27/39) : 76194
+Total time elapsed: 197.90 s
+Calling variants ...
+Total processed positions in chr4 (chunk 7/39) : 72299
+Total time elapsed: 198.05 s
+Calling variants ...
+Total processed positions in chr4 (chunk 5/39) : 75668
+Total time elapsed: 197.94 s
+Calling variants ...
+Total processed positions in chr4 (chunk 18/39) : 78644
+Total time elapsed: 203.64 s
+Calling variants ...
+Total processed positions in chr4 (chunk 20/39) : 76838
+Total time elapsed: 205.57 s
+Calling variants ...
+Total processed positions in chr4 (chunk 17/39) : 73881
+Total time elapsed: 205.83 s
+Calling variants ...
+Total processed positions in chr4 (chunk 13/39) : 73534
+Total time elapsed: 206.94 s
+Calling variants ...
+Total processed positions in chr4 (chunk 19/39) : 76183
+Total time elapsed: 207.48 s
+Calling variants ...
+Total processed positions in chr4 (chunk 15/39) : 77480
+Total time elapsed: 208.43 s
+Calling variants ...
+Total processed positions in chr4 (chunk 12/39) : 77912
+Total time elapsed: 209.44 s
+Calling variants ...
+Total processed positions in chr4 (chunk 4/39) : 79537
+Total time elapsed: 209.59 s
+Calling variants ...
+Total processed positions in chr4 (chunk 30/39) : 77091
+Total time elapsed: 210.15 s
+Calling variants ...
+Total processed positions in chr4 (chunk 16/39) : 68268
+Total time elapsed: 182.26 s
+Calling variants ...
+Total processed positions in chr4 (chunk 25/39) : 75406
+Total time elapsed: 184.73 s
+Calling variants ...
+Total processed positions in chr4 (chunk 21/39) : 80640
+Total time elapsed: 214.29 s
+Calling variants ...
+Total processed positions in chr4 (chunk 10/39) : 81660
+Total time elapsed: 215.47 s
+Calling variants ...
+Total processed positions in chr4 (chunk 28/39) : 75230
+Total time elapsed: 216.37 s
+Calling variants ...
+Total processed positions in chr4 (chunk 24/39) : 70453
+Total time elapsed: 189.00 s
+Calling variants ...
+Total processed positions in chr4 (chunk 23/39) : 71595
+Total time elapsed: 192.95 s
+Calling variants ...
+Total processed positions in chr4 (chunk 9/39) : 75607
+Total time elapsed: 195.72 s
+Calling variants ...
+Total processed positions in chr4 (chunk 14/39) : 77473
+Total time elapsed: 225.40 s
+Calling variants ...
+Total processed positions in chr4 (chunk 6/39) : 79146
+Total time elapsed: 198.39 s
+Calling variants ...
+Total processed positions in chr4 (chunk 26/39) : 81483
+Total time elapsed: 201.34 s
+Calling variants ...
+Total processed positions in chr4 (chunk 8/39) : 82598
+Total time elapsed: 201.97 s
+Calling variants ...
+Total processed positions in chr4 (chunk 22/39) : 72618
+Total time elapsed: 202.32 s
+Calling variants ...
+Total processed positions in chr4 (chunk 2/39) : 92265
+Total time elapsed: 234.06 s
+Calling variants ...
+Total processed positions in chr4 (chunk 29/39) : 84342
+Total time elapsed: 236.48 s
+Calling variants ...
+Total processed positions in chr4 (chunk 3/39) : 86674
+Total time elapsed: 214.14 s
+Calling variants ...
+Total processed positions in chr4 (chunk 1/39) : 94679
+Total time elapsed: 245.62 s
+slurmstepd: error: *** JOB 2556295 ON n18 CANCELLED AT 2025-12-08T16:49:54 ***
+slurmstepd: error: Detected 10 oom_kill events in StepId=2556295.batch. Some of the step tasks have been OOM Killed.
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556295
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n18
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:45:15
+Job ended at:   2025-12-08 16:49:54
+Job Wall-clock time: 00:04:39
+CPU Utilized: 01:54:27
+CPU Efficiency: 61.53% of 03:06:00 core-walltime
+Memory Utilized: 38.72 GB
+Memory Efficiency: 96.81% of 40.00 GB

slurm-2536607.out → slurm-2556296.out

@@ -1,35 +1,36 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4': destination is already in the mount point list
 
-[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26 --region chr3:1-20251703 --sample_name DUMCO_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4 --region chr10:63341881-134758134 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
 
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/logs
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/split_beds
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/candidates
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/pileup_tensor_can
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/fa_tensor_can
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/vcf_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/tmp_vcf_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/logs/clair3_log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/phased_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/vcf
 [INFO] --include_all_ctgs enabled
-[INFO] Call variants in contigs: chr3
-[INFO] Number of chunks for each contig: 41
+[INFO] Call variants in contigs: chr10
+[INFO] Number of chunks for each contig: 27
 
 [INFO] CALLER VERSION: 0.4.4
-[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
-[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
 [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
 [INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
 [INFO] THREADS: 40
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26
-[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/output.vcf.gz
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/output.vcf.gz
 [INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
 [INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
-[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/region.bed
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/region.bed
 [INFO] GENOTYPING MODE VCF FILE PATH: None
 [INFO] HYBRID MODE VCF FILE PATH: None
-[INFO] REGION FOR CALLING: chr3:1-20251703
+[INFO] REGION FOR CALLING: chr10:63341881-134758134
 [INFO] CONTIGS FOR CALLING: None
 [INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
 [INFO] SAMTOOLS BINARY PATH: samtools
@@ -55,19 +56,18 @@
 
 [INFO] Call Germline Variants in Normal BAM using Clair3
 [INFO] RUN THE FOLLOWING COMMAND:
-( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output --ctg_name=chr3 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/logs/clair3_log/1_CLAIR3_NORMAL.log
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output --ctg_name=chr10 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/logs/clair3_log/1_CLAIR3_NORMAL.log
 
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
 [INFO] CLAIR3 VERSION: v1.0.8
-[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
 [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
 [INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
-[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output
 [INFO] PLATFORM: ont
 [INFO] THREADS: 40
 [INFO] BED FILE PATH: EMPTY
 [INFO] VCF FILE PATH: EMPTY
-[INFO] CONTIGS: chr3
+[INFO] CONTIGS: chr10
 [INFO] CONDA PREFIX: 
 [INFO] SAMTOOLS PATH: samtools
 [INFO] PYTHON PATH: python3
@@ -102,19 +102,37 @@
 [INFO] ENABLE LONG INDEL CALLING: False
 [INFO] ENABLE C_IMPLEMENT: True
 
-+ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr3 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
-/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr10 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
 
 [INFO] Check environment variables
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/log
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/tmp/merge_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/tmp/phase_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
-[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part26/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
-[INFO] Call variant in contigs: chr3
-[INFO] Chunk number for each contig: 41
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr10
+[INFO] Chunk number for each contig: 27
 [INFO] 1/7 Call variants using pileup model
+slurmstepd: error: *** JOB 2556296 ON n05 CANCELLED AT 2025-12-08T16:49:54 ***
+slurmstepd: error: Detected 8 oom_kill events in StepId=2556296.batch. Some of the step tasks have been OOM Killed.
+
+----------------------------------------------
+|                SLURM EPILOG                |
+----------------------------------------------
+Job ID: 2556296
+Cluster: flamingo
+User/Group: t_steimle/gs_hpc_biopath
+Nodelist: n05
+Nodes: 1
+Cores per node: 40
+Job started at: 2025-12-08 16:47:24
+Job ended at:   2025-12-08 16:49:54
+Job Wall-clock time: 00:02:30
+CPU Utilized: 00:59:54
+CPU Efficiency: 59.90% of 01:40:00 core-walltime
+Memory Utilized: 39.58 GB
+Memory Efficiency: 98.96% of 40.00 GB

slurm-2557974.out

@@ -0,0 +1,1106 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29 --region chr4:1-130874961 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr4
+[INFO] Number of chunks for each contig: 39
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr4:1-130874961
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output --ctg_name=chr4 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr4
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr4 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr4
+[INFO] Chunk number for each contig: 39
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr4 (chunk 11/39) : 24000
+Total time elapsed: 70.18 s
+Calling variants ...
+Total processed positions in chr4 (chunk 24/39) : 70453
+Total time elapsed: 143.41 s
+Calling variants ...
+Total processed positions in chr4 (chunk 16/39) : 68268
+Total time elapsed: 145.92 s
+Calling variants ...
+Total processed positions in chr4 (chunk 13/39) : 73534
+Total time elapsed: 148.75 s
+Calling variants ...
+Total processed positions in chr4 (chunk 25/39) : 75406
+Total time elapsed: 149.04 s
+Calling variants ...
+Total processed positions in chr4 (chunk 5/39) : 75668
+Total time elapsed: 149.73 s
+Calling variants ...
+Total processed positions in chr4 (chunk 28/39) : 75230
+Total time elapsed: 149.87 s
+Calling variants ...
+Total processed positions in chr4 (chunk 14/39) : 77473
+Total time elapsed: 151.72 s
+Calling variants ...
+Total processed positions in chr4 (chunk 30/39) : 77091
+Total time elapsed: 153.13 s
+Calling variants ...
+Total processed positions in chr4 (chunk 22/39) : 72618
+Total time elapsed: 153.66 s
+Calling variants ...
+Total processed positions in chr4 (chunk 27/39) : 76194
+Total time elapsed: 155.23 s
+Calling variants ...
+Total processed positions in chr4 (chunk 6/39) : 79146
+Total time elapsed: 156.66 s
+Calling variants ...
+Total processed positions in chr4 (chunk 7/39) : 72299
+Total time elapsed: 158.26 s
+Calling variants ...
+Total processed positions in chr4 (chunk 19/39) : 76183
+Total time elapsed: 158.36 s
+Calling variants ...
+Total processed positions in chr4 (chunk 26/39) : 81483
+Total time elapsed: 158.68 s
+Calling variants ...
+Total processed positions in chr4 (chunk 9/39) : 75607
+Total time elapsed: 159.75 s
+Calling variants ...
+Total processed positions in chr4 (chunk 20/39) : 76838
+Total time elapsed: 162.96 s
+Calling variants ...
+Total processed positions in chr4 (chunk 8/39) : 82598
+Total time elapsed: 163.69 s
+Calling variants ...
+Total processed positions in chr4 (chunk 23/39) : 71595
+Total time elapsed: 141.04 s
+Calling variants ...
+Total processed positions in chr4 (chunk 4/39) : 79537
+Total time elapsed: 168.09 s
+Calling variants ...
+Total processed positions in chr4 (chunk 10/39) : 81660
+Total time elapsed: 168.78 s
+Calling variants ...
+Total processed positions in chr4 (chunk 12/39) : 77912
+Total time elapsed: 169.22 s
+Calling variants ...
+Total processed positions in chr4 (chunk 17/39) : 73881
+Total time elapsed: 145.86 s
+Calling variants ...
+Total processed positions in chr4 (chunk 21/39) : 80640
+Total time elapsed: 171.20 s
+Calling variants ...
+Total processed positions in chr4 (chunk 18/39) : 78644
+Total time elapsed: 149.29 s
+Calling variants ...
+Total processed positions in chr4 (chunk 29/39) : 84342
+Total time elapsed: 174.90 s
+Calling variants ...
+Total processed positions in chr4 (chunk 2/39) : 92265
+Total time elapsed: 177.16 s
+Calling variants ...
+Total processed positions in chr4 (chunk 1/39) : 94679
+Total time elapsed: 180.70 s
+Calling variants ...
+Total processed positions in chr4 (chunk 15/39) : 77480
+Total time elapsed: 156.85 s
+Calling variants ...
+Total processed positions in chr4 (chunk 3/39) : 86674
+Total time elapsed: 161.63 s
+Calling variants ...
+Total processed positions in chr4 (chunk 31/39) : 78672
+Total time elapsed: 127.41 s
+Calling variants ...
+Total processed positions in chr4 (chunk 33/39) : 78533
+Total time elapsed: 106.12 s
+Calling variants ...
+Total processed positions in chr4 (chunk 35/39) : 75009
+Total time elapsed: 107.49 s
+Calling variants ...
+Total processed positions in chr4 (chunk 36/39) : 80260
+Total time elapsed: 107.59 s
+Calling variants ...
+Total processed positions in chr4 (chunk 32/39) : 81846
+Total time elapsed: 114.83 s
+Calling variants ...
+Total processed positions in chr4 (chunk 34/39) : 74811
+Total time elapsed: 113.50 s
+Calling variants ...
+Total processed positions in chr4 (chunk 37/39) : 82261
+Total time elapsed: 114.01 s
+Calling variants ...
+Total processed positions in chr4 (chunk 38/39) : 85427
+Total time elapsed: 121.06 s
+Calling variants ...
+Total processed positions in chr4 (chunk 39/39) : 83447
+Total time elapsed: 119.38 s
+
+real	4m44.258s
+user	90m33.855s
+sys	5m26.005s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16
+[INFO] Total heterozygous SNP positions selected: chr4: 120251
+
+real	0m7.056s
+user	0m6.717s
+sys	0m0.247s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr4.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr4
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr4,15s)
+parsing total:  15s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 18s
+
+real	0m18.515s
+user	0m34.635s
+sys	0m2.785s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 20.0
+[INFO] Set reference calls quality cutoff 14.0
+[INFO] Low quality reference calls to be processed in chr4: 266081
+[INFO] Low quality variants to be processed in chr4: 239599
+
+real	0m7.775s
+user	0m7.257s
+sys	0m0.410s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr4 (chunk 27/51) : 10000
+Total time elapsed: 90.58 s
+Calling variants ...
+Total processed positions in chr4 (chunk 2/51) : 10000
+Total time elapsed: 90.98 s
+Calling variants ...
+Total processed positions in chr4 (chunk 11/51) : 10000
+Total time elapsed: 94.20 s
+Calling variants ...
+Total processed positions in chr4 (chunk 24/51) : 10000
+Total time elapsed: 95.38 s
+Calling variants ...
+Total processed positions in chr4 (chunk 9/51) : 10000
+Total time elapsed: 95.94 s
+Calling variants ...
+Total processed positions in chr4 (chunk 18/51) : 10000
+Total time elapsed: 96.07 s
+Calling variants ...
+Total processed positions in chr4 (chunk 6/51) : 10000
+Total time elapsed: 97.74 s
+Calling variants ...
+Total processed positions in chr4 (chunk 28/51) : 10000
+Total time elapsed: 98.19 s
+Calling variants ...
+Total processed positions in chr4 (chunk 14/51) : 10000
+Total time elapsed: 101.22 s
+Calling variants ...
+Total processed positions in chr4 (chunk 12/51) : 10000
+Total time elapsed: 102.23 s
+Calling variants ...
+Total processed positions in chr4 (chunk 21/51) : 10000
+Total time elapsed: 102.73 s
+Calling variants ...
+Total processed positions in chr4 (chunk 30/51) : 10000
+Total time elapsed: 103.47 s
+Calling variants ...
+Total processed positions in chr4 (chunk 23/51) : 10000
+Total time elapsed: 103.43 s
+Calling variants ...
+Total processed positions in chr4 (chunk 5/51) : 10000
+Total time elapsed: 104.26 s
+Calling variants ...
+Total processed positions in chr4 (chunk 29/51) : 10000
+Total time elapsed: 104.25 s
+Calling variants ...
+Total processed positions in chr4 (chunk 15/51) : 10000
+Total time elapsed: 104.98 s
+Calling variants ...
+Total processed positions in chr4 (chunk 19/51) : 10000
+Total time elapsed: 105.38 s
+Calling variants ...
+Total processed positions in chr4 (chunk 4/51) : 10000
+Total time elapsed: 105.77 s
+Calling variants ...
+Total processed positions in chr4 (chunk 10/51) : 10000
+Total time elapsed: 106.84 s
+Calling variants ...
+Total processed positions in chr4 (chunk 17/51) : 10000
+Total time elapsed: 107.02 s
+Calling variants ...
+Total processed positions in chr4 (chunk 26/51) : 10000
+Total time elapsed: 107.53 s
+Calling variants ...
+Total processed positions in chr4 (chunk 3/51) : 10000
+Total time elapsed: 107.84 s
+Calling variants ...
+Total processed positions in chr4 (chunk 16/51) : 10000
+Total time elapsed: 108.47 s
+Calling variants ...
+Total processed positions in chr4 (chunk 8/51) : 10000
+Total time elapsed: 108.63 s
+Calling variants ...
+Total processed positions in chr4 (chunk 22/51) : 10000
+Total time elapsed: 108.81 s
+Calling variants ...
+Total processed positions in chr4 (chunk 13/51) : 10000
+Total time elapsed: 110.05 s
+Calling variants ...
+Total processed positions in chr4 (chunk 1/51) : 10000
+Total time elapsed: 110.09 s
+Calling variants ...
+Total processed positions in chr4 (chunk 20/51) : 10000
+Total time elapsed: 110.35 s
+Calling variants ...
+Total processed positions in chr4 (chunk 25/51) : 10000
+Total time elapsed: 110.58 s
+Calling variants ...
+Total processed positions in chr4 (chunk 7/51) : 10000
+Total time elapsed: 110.83 s
+Calling variants ...
+Total processed positions in chr4 (chunk 51/51) : 5680
+Total time elapsed: 58.98 s
+Calling variants ...
+Total processed positions in chr4 (chunk 38/51) : 10000
+Total time elapsed: 78.77 s
+Calling variants ...
+Total processed positions in chr4 (chunk 32/51) : 10000
+Total time elapsed: 86.12 s
+Calling variants ...
+Total processed positions in chr4 (chunk 39/51) : 10000
+Total time elapsed: 77.54 s
+Calling variants ...
+Total processed positions in chr4 (chunk 34/51) : 10000
+Total time elapsed: 83.29 s
+Calling variants ...
+Total processed positions in chr4 (chunk 37/51) : 10000
+Total time elapsed: 83.31 s
+Calling variants ...
+Total processed positions in chr4 (chunk 33/51) : 10000
+Total time elapsed: 86.47 s
+Calling variants ...
+Total processed positions in chr4 (chunk 31/51) : 10000
+Total time elapsed: 90.67 s
+Calling variants ...
+Total processed positions in chr4 (chunk 35/51) : 10000
+Total time elapsed: 85.48 s
+Calling variants ...
+Total processed positions in chr4 (chunk 47/51) : 10000
+Total time elapsed: 79.94 s
+Calling variants ...
+Total processed positions in chr4 (chunk 36/51) : 10000
+Total time elapsed: 89.40 s
+Calling variants ...
+Total processed positions in chr4 (chunk 46/51) : 10000
+Total time elapsed: 81.23 s
+Calling variants ...
+Total processed positions in chr4 (chunk 44/51) : 10000
+Total time elapsed: 82.69 s
+Calling variants ...
+Total processed positions in chr4 (chunk 42/51) : 10000
+Total time elapsed: 83.85 s
+Calling variants ...
+Total processed positions in chr4 (chunk 41/51) : 10000
+Total time elapsed: 84.51 s
+Calling variants ...
+Total processed positions in chr4 (chunk 40/51) : 10000
+Total time elapsed: 85.44 s
+Calling variants ...
+Total processed positions in chr4 (chunk 45/51) : 10000
+Total time elapsed: 86.60 s
+Calling variants ...
+Total processed positions in chr4 (chunk 48/51) : 10000
+Total time elapsed: 84.92 s
+Calling variants ...
+Total processed positions in chr4 (chunk 49/51) : 10000
+Total time elapsed: 85.67 s
+Calling variants ...
+Total processed positions in chr4 (chunk 50/51) : 10000
+Total time elapsed: 86.42 s
+Calling variants ...
+Total processed positions in chr4 (chunk 43/51) : 10000
+Total time elapsed: 88.89 s
+
+real	3m21.051s
+user	78m38.604s
+sys	4m48.871s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr4: 103037
+[INFO] Full-alignment variants processed in chr4: 249575
+
+real	0m10.582s
+user	0m11.421s
+sys	0m0.423s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	9m26.550s
+user	170m47.807s
+sys	10m21.421s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output --ctg_name=chr4 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr4
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr4 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr4
+[INFO] Chunk number for each contig: 39
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr4 (chunk 17/39) : 6938
+Total time elapsed: 97.96 s
+Calling variants ...
+Total processed positions in chr4 (chunk 30/39) : 6275
+Total time elapsed: 97.48 s
+Calling variants ...
+Total processed positions in chr4 (chunk 22/39) : 7168
+Total time elapsed: 98.65 s
+Calling variants ...
+Total processed positions in chr4 (chunk 24/39) : 8033
+Total time elapsed: 101.32 s
+Calling variants ...
+Total processed positions in chr4 (chunk 4/39) : 8859
+Total time elapsed: 101.78 s
+Calling variants ...
+Total processed positions in chr4 (chunk 27/39) : 10107
+Total time elapsed: 104.20 s
+Calling variants ...
+Total processed positions in chr4 (chunk 19/39) : 10456
+Total time elapsed: 105.48 s
+Calling variants ...
+Total processed positions in chr4 (chunk 28/39) : 11973
+Total time elapsed: 106.60 s
+Calling variants ...
+Total processed positions in chr4 (chunk 7/39) : 11742
+Total time elapsed: 107.70 s
+Calling variants ...
+Total processed positions in chr4 (chunk 14/39) : 11319
+Total time elapsed: 107.88 s
+Calling variants ...
+Total processed positions in chr4 (chunk 3/39) : 12191
+Total time elapsed: 108.00 s
+Calling variants ...
+Total processed positions in chr4 (chunk 13/39) : 12378
+Total time elapsed: 108.85 s
+Calling variants ...
+Total processed positions in chr4 (chunk 8/39) : 14322
+Total time elapsed: 109.55 s
+Calling variants ...
+Total processed positions in chr4 (chunk 25/39) : 12826
+Total time elapsed: 109.58 s
+Calling variants ...
+Total processed positions in chr4 (chunk 1/39) : 16761
+Total time elapsed: 115.41 s
+Calling variants ...
+Total processed positions in chr4 (chunk 2/39) : 19043
+Total time elapsed: 116.88 s
+Calling variants ...
+Total processed positions in chr4 (chunk 12/39) : 25433
+Total time elapsed: 124.54 s
+Calling variants ...
+Total processed positions in chr4 (chunk 23/39) : 6875
+Total time elapsed: 51.25 s
+Calling variants ...
+Total processed positions in chr4 (chunk 5/39) : 7383
+Total time elapsed: 52.95 s
+Calling variants ...
+Total processed positions in chr4 (chunk 26/39) : 9155
+Total time elapsed: 53.62 s
+Calling variants ...
+Total processed positions in chr4 (chunk 21/39) : 9342
+Total time elapsed: 54.15 s
+Calling variants ...
+Total processed positions in chr4 (chunk 16/39) : 9070
+Total time elapsed: 54.90 s
+Calling variants ...
+Total processed positions in chr4 (chunk 29/39) : 9144
+Total time elapsed: 55.66 s
+Calling variants ...
+Total processed positions in chr4 (chunk 9/39) : 9194
+Total time elapsed: 56.32 s
+Calling variants ...
+Total processed positions in chr4 (chunk 20/39) : 9952
+Total time elapsed: 59.17 s
+Calling variants ...
+Total processed positions in chr4 (chunk 18/39) : 10631
+Total time elapsed: 59.37 s
+Calling variants ...
+Total processed positions in chr4 (chunk 6/39) : 10917
+Total time elapsed: 60.33 s
+Calling variants ...
+Total processed positions in chr4 (chunk 10/39) : 13221
+Total time elapsed: 62.54 s
+Calling variants ...
+Total processed positions in chr4 (chunk 31/39) : 9517
+Total time elapsed: 50.48 s
+Calling variants ...
+Total processed positions in chr4 (chunk 32/39) : 10951
+Total time elapsed: 51.58 s
+Calling variants ...
+Total processed positions in chr4 (chunk 33/39) : 11317
+Total time elapsed: 50.80 s
+Calling variants ...
+Total processed positions in chr4 (chunk 15/39) : 18241
+Total time elapsed: 68.67 s
+Calling variants ...
+Total processed positions in chr4 (chunk 35/39) : 10750
+Total time elapsed: 50.93 s
+Calling variants ...
+Total processed positions in chr4 (chunk 34/39) : 12049
+Total time elapsed: 52.42 s
+Calling variants ...
+Total processed positions in chr4 (chunk 36/39) : 10096
+Total time elapsed: 49.80 s
+Calling variants ...
+Total processed positions in chr4 (chunk 37/39) : 11340
+Total time elapsed: 49.39 s
+Calling variants ...
+Total processed positions in chr4 (chunk 38/39) : 12999
+Total time elapsed: 51.90 s
+Calling variants ...
+Total processed positions in chr4 (chunk 39/39) : 21385
+Total time elapsed: 61.33 s
+Calling variants ...
+Total processed positions in chr4 (chunk 11/39) : 59320
+Total time elapsed: 182.79 s
+
+real	3m6.972s
+user	35m10.970s
+sys	16m37.256s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 20
+[INFO] Total heterozygous SNP positions selected: chr4: 125541
+
+real	0m2.138s
+user	0m1.875s
+sys	0m0.182s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr4.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr4
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr4,77s)
+parsing total:  77s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 80s
+
+real	1m20.651s
+user	2m23.459s
+sys	0m9.362s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 22.0
+[INFO] Set reference calls quality cutoff 7.0
+[INFO] Low quality reference calls to be processed in chr4: 15242
+[INFO] Low quality variants to be processed in chr4: 242179
+
+real	0m2.055s
+user	0m1.823s
+sys	0m0.180s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr4 (chunk 26/26) : 7421
+Total time elapsed: 98.11 s
+Calling variants ...
+Total processed positions in chr4 (chunk 8/26) : 10000
+Total time elapsed: 99.93 s
+Calling variants ...
+Total processed positions in chr4 (chunk 2/26) : 10000
+Total time elapsed: 106.12 s
+Calling variants ...
+Total processed positions in chr4 (chunk 1/26) : 10000
+Total time elapsed: 112.32 s
+Calling variants ...
+Total processed positions in chr4 (chunk 24/26) : 10000
+Total time elapsed: 116.91 s
+Calling variants ...
+Total processed positions in chr4 (chunk 9/26) : 10000
+Total time elapsed: 123.12 s
+Calling variants ...
+Total processed positions in chr4 (chunk 11/26) : 10000
+Total time elapsed: 125.15 s
+Calling variants ...
+Total processed positions in chr4 (chunk 10/26) : 10000
+Total time elapsed: 129.96 s
+Calling variants ...
+Total processed positions in chr4 (chunk 22/26) : 10000
+Total time elapsed: 129.91 s
+Calling variants ...
+Total processed positions in chr4 (chunk 7/26) : 10000
+Total time elapsed: 130.76 s
+Calling variants ...
+Total processed positions in chr4 (chunk 17/26) : 10000
+Total time elapsed: 131.61 s
+Calling variants ...
+Total processed positions in chr4 (chunk 25/26) : 10000
+Total time elapsed: 132.40 s
+Calling variants ...
+Total processed positions in chr4 (chunk 12/26) : 10000
+Total time elapsed: 133.40 s
+Calling variants ...
+Total processed positions in chr4 (chunk 3/26) : 10000
+Total time elapsed: 133.90 s
+Calling variants ...
+Total processed positions in chr4 (chunk 21/26) : 10000
+Total time elapsed: 134.24 s
+Calling variants ...
+Total processed positions in chr4 (chunk 23/26) : 10000
+Total time elapsed: 134.58 s
+Calling variants ...
+Total processed positions in chr4 (chunk 6/26) : 10000
+Total time elapsed: 134.47 s
+Calling variants ...
+Total processed positions in chr4 (chunk 5/26) : 10000
+Total time elapsed: 135.31 s
+Calling variants ...
+Total processed positions in chr4 (chunk 15/26) : 10000
+Total time elapsed: 136.86 s
+Calling variants ...
+Total processed positions in chr4 (chunk 14/26) : 10000
+Total time elapsed: 137.60 s
+Calling variants ...
+Total processed positions in chr4 (chunk 19/26) : 10000
+Total time elapsed: 140.33 s
+Calling variants ...
+Total processed positions in chr4 (chunk 20/26) : 10000
+Total time elapsed: 141.75 s
+Calling variants ...
+Total processed positions in chr4 (chunk 13/26) : 10000
+Total time elapsed: 141.61 s
+Calling variants ...
+Total processed positions in chr4 (chunk 18/26) : 10000
+Total time elapsed: 148.75 s
+Calling variants ...
+Total processed positions in chr4 (chunk 4/26) : 10000
+Total time elapsed: 161.91 s
+Calling variants ...
+Total processed positions in chr4 (chunk 16/26) : 10000
+Total time elapsed: 174.46 s
+
+real	2m58.186s
+user	53m55.414s
+sys	2m45.006s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr4: 104058
+[INFO] Full-alignment variants processed in chr4: 223475
+
+real	0m3.608s
+user	0m3.707s
+sys	0m0.216s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	7m46.215s
+user	91m47.732s
+sys	19m33.629s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr4: 162879, not found:920, not match:65, low_qual_count:0. Total normal:165926 Total tumor:163864, pro: 0.994
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/vcf/chr4.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_phased_chr4
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr4,81s)
+parsing total:  81s
+merge results ... 0s
+writeResult SNP ... 2s
+
+total process: 86s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_phased_chr4.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_chr4.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr4
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 1s
+tag read start ...
+chr: chr4 ... 1638s
+tag read 1641s
+-------------------------------------------
+total process time:  1642s
+total alignment:     2126232
+total supplementary: 91198
+total secondary:     0
+total unmapped:      0
+total tag alignment: 1100175
+total untagged:      1026057
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr4 chunk 15/39: Total snv candidates found: 5441, total indel candidates found: 298
+[INFO] chr4 chunk 16/39: Total snv candidates found: 4972, total indel candidates found: 649
+[INFO] chr4 chunk 14/39: Total snv candidates found: 4283, total indel candidates found: 912
+[INFO] chr4 chunk 2/39: Total snv candidates found: 1796, total indel candidates found: 885
+[INFO] chr4 chunk 0/39: Total snv candidates found: 1735, total indel candidates found: 1346
+[INFO] chr4 chunk 7/39: Total snv candidates found: 406, total indel candidates found: 909
+[INFO] chr4 chunk 11/39: Total snv candidates found: 929, total indel candidates found: 1229
+[INFO] chr4 chunk 1/39: Total snv candidates found: 1671, total indel candidates found: 996
+[INFO] chr4 chunk 5/39: Total snv candidates found: 487, total indel candidates found: 731
+[INFO] chr4 chunk 17/39: Total snv candidates found: 558, total indel candidates found: 942
+[INFO] chr4 chunk 9/39: Total snv candidates found: 465, total indel candidates found: 653
+[INFO] chr4 chunk 4/39: Total snv candidates found: 539, total indel candidates found: 726
+[INFO] chr4 chunk 12/39: Total snv candidates found: 346, total indel candidates found: 805
+[INFO] chr4 chunk 8/39: Total snv candidates found: 456, total indel candidates found: 662
+[INFO] chr4 chunk 6/39: Total snv candidates found: 226, total indel candidates found: 558
+[INFO] chr4 chunk 3/39: Total snv candidates found: 571, total indel candidates found: 719
+[INFO] chr4 chunk 10/39: Total snv candidates found: 656, total indel candidates found: 662
+[INFO] chr4 chunk 18/39: Total snv candidates found: 583, total indel candidates found: 644
+[INFO] chr4 chunk 20/39: Total snv candidates found: 529, total indel candidates found: 620
+[INFO] chr4 chunk 21/39: Total snv candidates found: 1317, total indel candidates found: 687
+[INFO] chr4 chunk 13/39: Total snv candidates found: 294, total indel candidates found: 580
+[INFO] chr4 chunk 34/39: Total snv candidates found: 257, total indel candidates found: 663
+[INFO] chr4 chunk 31/39: Total snv candidates found: 276, total indel candidates found: 622
+[INFO] chr4 chunk 22/39: Total snv candidates found: 287, total indel candidates found: 729
+[INFO] chr4 chunk 38/39: Total snv candidates found: 366, total indel candidates found: 558
+[INFO] chr4 chunk 25/39: Total snv candidates found: 527, total indel candidates found: 916
+[INFO] chr4 chunk 33/39: Total snv candidates found: 379, total indel candidates found: 786
+[INFO] chr4 chunk 26/39: Total snv candidates found: 875, total indel candidates found: 831
+[INFO] chr4 chunk 37/39: Total snv candidates found: 391, total indel candidates found: 753
+[INFO] chr4 chunk 27/39: Total snv candidates found: 538, total indel candidates found: 762
+[INFO] chr4 chunk 19/39: Total snv candidates found: 351, total indel candidates found: 614
+[INFO] chr4 chunk 23/39: Total snv candidates found: 458, total indel candidates found: 779
+[INFO] chr4 chunk 32/39: Total snv candidates found: 210, total indel candidates found: 664
+[INFO] chr4 chunk 35/39: Total snv candidates found: 344, total indel candidates found: 588
+[INFO] chr4 chunk 24/39: Total snv candidates found: 277, total indel candidates found: 706
+[INFO] chr4 chunk 28/39: Total snv candidates found: 439, total indel candidates found: 670
+[INFO] chr4 chunk 29/39: Total snv candidates found: 588, total indel candidates found: 687
+[INFO] chr4 chunk 30/39: Total snv candidates found: 416, total indel candidates found: 641
+[INFO] chr4 chunk 36/39: Total snv candidates found: 736, total indel candidates found: 736
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/2-1_CPT.log
+
+[INFO] chr4 chunk 1-1/34 Tensors generated: 257
+[INFO] chr4 chunk 1-1/32 Tensors generated: 210
+[INFO] chr4 chunk 1-1/24 Tensors generated: 276
+[INFO] chr4 chunk 1-1/6 Tensors generated: 226
+[INFO] chr4 chunk 1-1/31 Tensors generated: 275
+[INFO] chr4 chunk 1-1/13 Tensors generated: 294
+[INFO] chr4 chunk 1-1/22 Tensors generated: 287
+[INFO] chr4 chunk 1-1/35 Tensors generated: 344
+[INFO] chr4 chunk 1-1/12 Tensors generated: 340
+[INFO] chr4 chunk 1-1/19 Tensors generated: 351
+[INFO] chr4 chunk 1-1/38 Tensors generated: 366
+[INFO] chr4 chunk 1-1/33 Tensors generated: 378
+[INFO] chr4 chunk 1-1/7 Tensors generated: 406
+[INFO] chr4 chunk 1-1/37 Tensors generated: 391
+[INFO] chr4 chunk 1-1/23 Tensors generated: 458
+[INFO] chr4 chunk 1-1/30 Tensors generated: 415
+[INFO] chr4 chunk 1-1/9 Tensors generated: 465
+[INFO] chr4 chunk 1-1/25 Tensors generated: 525
+[INFO] chr4 chunk 1-1/28 Tensors generated: 439
+[INFO] chr4 chunk 1-1/5 Tensors generated: 485
+[INFO] chr4 chunk 1-1/8 Tensors generated: 456
+[INFO] chr4 chunk 1-1/1 Tensors generated: 1671
+[INFO] chr4 chunk 1-1/4 Tensors generated: 539
+[INFO] chr4 chunk 1-1/29 Tensors generated: 588
+[INFO] chr4 chunk 1-1/20 Tensors generated: 529
+[INFO] chr4 chunk 1-1/27 Tensors generated: 538
+[INFO] chr4 chunk 1-1/17 Tensors generated: 554
+[INFO] chr4 chunk 1-1/18 Tensors generated: 583
+[INFO] chr4 chunk 1-1/26 Tensors generated: 875
+[INFO] chr4 chunk 1-1/3 Tensors generated: 569
+[INFO] chr4 chunk 1-1/2 Tensors generated: 1780
+[INFO] chr4 chunk 1-1/0 Tensors generated: 1732
+[INFO] chr4 chunk 1-1/10 Tensors generated: 652
+[INFO] chr4 chunk 1-1/36 Tensors generated: 736
+[INFO] chr4 chunk 1-1/11 Tensors generated: 926
+[INFO] chr4 chunk 1-1/21 Tensors generated: 1317
+[INFO] chr4 chunk 1-1/15 Tensors generated: 5298
+[INFO] chr4 chunk 1-1/14 Tensors generated: 4283
+[INFO] chr4 chunk 1-1/16 Tensors generated: 4972
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/2-2_PREDICT.log
+
+[INFO] chr4 total processed positions: 226, time elapsed: 1.4s
+[INFO] chr4 total processed positions: 210, time elapsed: 1.4s
+[INFO] chr4 total processed positions: 294, time elapsed: 1.5s
+[INFO] chr4 total processed positions: 257, time elapsed: 1.5s
+[INFO] chr4 total processed positions: 275, time elapsed: 0.9s
+[INFO] chr4 total processed positions: 287, time elapsed: 1.6s
+[INFO] chr4 total processed positions: 340, time elapsed: 1.7s
+[INFO] chr4 total processed positions: 276, time elapsed: 1.6s
+[INFO] chr4 total processed positions: 366, time elapsed: 1.5s
+[INFO] chr4 total processed positions: 344, time elapsed: 1.3s
+[INFO] chr4 total processed positions: 378, time elapsed: 1.6s
+[INFO] chr4 total processed positions: 351, time elapsed: 1.5s
+[INFO] chr4 total processed positions: 439, time elapsed: 1.8s
+[INFO] chr4 total processed positions: 406, time elapsed: 1.5s
+[INFO] chr4 total processed positions: 458, time elapsed: 1.9s
+[INFO] chr4 total processed positions: 415, time elapsed: 1.7s
+[INFO] chr4 total processed positions: 456, time elapsed: 1.9s
+[INFO] chr4 total processed positions: 391, time elapsed: 1.3s
+[INFO] chr4 total processed positions: 529, time elapsed: 2.0s
+[INFO] chr4 total processed positions: 554, time elapsed: 1.8s
+[INFO] chr4 total processed positions: 465, time elapsed: 1.9s
+[INFO] chr4 total processed positions: 539, time elapsed: 1.8s
+[INFO] chr4 total processed positions: 485, time elapsed: 2.1s
+[INFO] chr4 total processed positions: 525, time elapsed: 2.1s
+[INFO] chr4 total processed positions: 538, time elapsed: 2.1s
+[INFO] chr4 total processed positions: 569, time elapsed: 2.2s
+[INFO] chr4 total processed positions: 583, time elapsed: 2.3s
+[INFO] chr4 total processed positions: 736, time elapsed: 2.2s
+[INFO] chr4 total processed positions: 588, time elapsed: 2.2s
+[INFO] chr4 total processed positions: 652, time elapsed: 2.0s
+[INFO] chr4 total processed positions: 875, time elapsed: 2.5s
+[INFO] chr4 total processed positions: 926, time elapsed: 2.7s
+[INFO] chr4 total processed positions: 1317, time elapsed: 3.4s
+[INFO] chr4 total processed positions: 1671, time elapsed: 4.2s
+[INFO] chr4 total processed positions: 1732, time elapsed: 4.0s
+[INFO] chr4 total processed positions: 1780, time elapsed: 4.6s
+[INFO] chr4 total processed positions: 4283, time elapsed: 9.3s
+[INFO] chr4 total processed positions: 4972, time elapsed: 10.5s
+[INFO] chr4 total processed positions: 5298, time elapsed: 11.5s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/3-1_CPT.log
+
+[INFO] chr4 chunk 1-1/32 Tensors generated: 210
+[INFO] chr4 chunk 1-1/34 Tensors generated: 257
+[INFO] chr4 chunk 1-1/6 Tensors generated: 226
+[INFO] chr4 chunk 1-1/24 Tensors generated: 276
+[INFO] chr4 chunk 1-1/22 Tensors generated: 287
+[INFO] chr4 chunk 1-1/31 Tensors generated: 275
+[INFO] chr4 chunk 1-1/13 Tensors generated: 294
+[INFO] chr4 chunk 1-1/12 Tensors generated: 340
+[INFO] chr4 chunk 1-1/35 Tensors generated: 344
+[INFO] chr4 chunk 1-1/33 Tensors generated: 378
+[INFO] chr4 chunk 1-1/7 Tensors generated: 406
+[INFO] chr4 chunk 1-1/19 Tensors generated: 351
+[INFO] chr4 chunk 1-1/38 Tensors generated: 366
+[INFO] chr4 chunk 1-1/37 Tensors generated: 391
+[INFO] chr4 chunk 1-1/23 Tensors generated: 458
+[INFO] chr4 chunk 1-1/30 Tensors generated: 415
+[INFO] chr4 chunk 1-1/9 Tensors generated: 465
+[INFO] chr4 chunk 1-1/28 Tensors generated: 439
+[INFO] chr4 chunk 1-1/5 Tensors generated: 485
+[INFO] chr4 chunk 1-1/8 Tensors generated: 456
+[INFO] chr4 chunk 1-1/4 Tensors generated: 539
+[INFO] chr4 chunk 1-1/25 Tensors generated: 525
+[INFO] chr4 chunk 1-1/27 Tensors generated: 538
+[INFO] chr4 chunk 1-1/20 Tensors generated: 529
+[INFO] chr4 chunk 1-1/17 Tensors generated: 554
+[INFO] chr4 chunk 1-1/29 Tensors generated: 588
+[INFO] chr4 chunk 1-1/18 Tensors generated: 583
+[INFO] chr4 chunk 1-1/3 Tensors generated: 569
+[INFO] chr4 chunk 1-1/10 Tensors generated: 652
+[INFO] chr4 chunk 1-1/36 Tensors generated: 736
+[INFO] chr4 chunk 1-1/26 Tensors generated: 875
+[INFO] chr4 chunk 1-1/11 Tensors generated: 926
+[INFO] chr4 chunk 1-1/1 Tensors generated: 1671
+[INFO] chr4 chunk 1-1/21 Tensors generated: 1317
+[INFO] chr4 chunk 1-1/2 Tensors generated: 1747
+[INFO] chr4 chunk 1-1/0 Tensors generated: 1672
+[INFO] chr4 chunk 1-1/15 Tensors generated: 4912
+[INFO] chr4 chunk 1-1/16 Tensors generated: 4699
+[INFO] chr4 chunk 1-1/14 Tensors generated: 4228
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part29/logs/3-2_PREDICT.log
+
+[INFO] chr4 total processed positions: 210, time elapsed: 27.7s
+[INFO] chr4 total processed positions: 226, time elapsed: 29.5s
+[INFO] chr4 total processed positions: 257, time elapsed: 33.4s
+[INFO] chr4 total processed positions: 276, time elapsed: 36.2s
+[INFO] chr4 total processed positions: 275, time elapsed: 35.9s
+[INFO] chr4 total processed positions: 287, time elapsed: 37.5s
+[INFO] chr4 total processed positions: 294, time elapsed: 38.1s
+[INFO] chr4 total processed positions: 340, time elapsed: 44.0s
+[INFO] chr4 total processed positions: 344, time elapsed: 44.8s
+[INFO] chr4 total processed positions: 351, time elapsed: 44.5s
+[INFO] chr4 total processed positions: 366, time elapsed: 47.8s
+[INFO] chr4 total processed positions: 378, time elapsed: 49.1s
+[INFO] chr4 total processed positions: 415, time elapsed: 50.2s
+[INFO] chr4 total processed positions: 391, time elapsed: 50.6s
+[INFO] chr4 total processed positions: 406, time elapsed: 52.5s
+[INFO] chr4 total processed positions: 439, time elapsed: 54.2s
+[INFO] chr4 total processed positions: 458, time elapsed: 56.5s
+[INFO] chr4 total processed positions: 465, time elapsed: 57.0s
+[INFO] chr4 total processed positions: 456, time elapsed: 57.2s
+[INFO] chr4 total processed positions: 485, time elapsed: 59.2s
+[INFO] chr4 total processed positions: 525, time elapsed: 63.9s
+[INFO] chr4 total processed positions: 529, time elapsed: 65.8s
+[INFO] chr4 total processed positions: 539, time elapsed: 66.4s
+[INFO] chr4 total processed positions: 538, time elapsed: 67.0s
+[INFO] chr4 total processed positions: 554, time elapsed: 69.8s
+[INFO] chr4 total processed positions: 569, time elapsed: 71.7s
+[INFO] chr4 total processed positions: 588, time elapsed: 73.2s
+[INFO] chr4 total processed positions: 583, time elapsed: 73.6s
+[INFO] chr4 total processed positions: 652, time elapsed: 81.3s
+[INFO] chr4 total processed positions: 736, time elapsed: 90.3s
+[INFO] chr4 total processed positions: 875, time elapsed: 109.0s
+[INFO] chr4 total processed positions: 926, time elapsed: 110.2s
+[INFO] chr4 total processed positions: 1317, time elapsed: 158.1s
+[INFO] chr4 total processed positions: 1671, time elapsed: 197.4s
+[INFO] chr4 total processed positions: 1672, time elapsed: 201.5s
+[INFO] chr4 total processed positions: 1747, time elapsed: 208.0s

slurm-2557976.out

@@ -0,0 +1,774 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19 --region chr19:19687872-61707364 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr19
+[INFO] Number of chunks for each contig: 13
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr19:19687872-61707364
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output --ctg_name=chr19 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr19
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr19 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr19
+[INFO] Chunk number for each contig: 13
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr19 (chunk 6/13) : 37439
+Total time elapsed: 68.25 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/13) : 71150
+Total time elapsed: 114.34 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/13) : 77159
+Total time elapsed: 127.54 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/13) : 77903
+Total time elapsed: 127.58 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/13) : 76878
+Total time elapsed: 129.30 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/13) : 86660
+Total time elapsed: 131.77 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/13) : 80468
+Total time elapsed: 131.99 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/13) : 80011
+Total time elapsed: 132.32 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/13) : 81026
+Total time elapsed: 135.00 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/13) : 83832
+Total time elapsed: 135.85 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/13) : 82264
+Total time elapsed: 137.91 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/13) : 82363
+Total time elapsed: 139.38 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/13) : 90012
+Total time elapsed: 146.27 s
+
+real	2m32.510s
+user	27m1.488s
+sys	0m52.206s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
+[INFO] Total heterozygous SNP positions selected: chr19: 52254
+
+real	0m1.699s
+user	0m1.552s
+sys	0m0.112s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr19,5s)
+parsing total:  5s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 6s
+
+real	0m5.817s
+user	0m11.244s
+sys	0m0.823s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 12.0
+[INFO] Low quality reference calls to be processed in chr19: 86848
+[INFO] Low quality variants to be processed in chr19: 96058
+
+real	0m1.918s
+user	0m1.644s
+sys	0m0.213s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr19 (chunk 19/19) : 2906
+Total time elapsed: 29.75 s
+Calling variants ...
+Total processed positions in chr19 (chunk 14/19) : 10000
+Total time elapsed: 97.02 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/19) : 10000
+Total time elapsed: 97.47 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/19) : 10000
+Total time elapsed: 97.72 s
+Calling variants ...
+Total processed positions in chr19 (chunk 16/19) : 10000
+Total time elapsed: 98.40 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/19) : 10000
+Total time elapsed: 100.37 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/19) : 10000
+Total time elapsed: 100.80 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/19) : 10000
+Total time elapsed: 100.91 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/19) : 10000
+Total time elapsed: 100.93 s
+Calling variants ...
+Total processed positions in chr19 (chunk 17/19) : 10000
+Total time elapsed: 101.42 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/19) : 10000
+Total time elapsed: 102.17 s
+Calling variants ...
+Total processed positions in chr19 (chunk 15/19) : 10000
+Total time elapsed: 102.37 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/19) : 10000
+Total time elapsed: 102.38 s
+Calling variants ...
+Total processed positions in chr19 (chunk 18/19) : 10000
+Total time elapsed: 103.28 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/19) : 10000
+Total time elapsed: 103.68 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/19) : 10000
+Total time elapsed: 103.95 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/19) : 10000
+Total time elapsed: 104.63 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/19) : 10000
+Total time elapsed: 104.89 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/19) : 10000
+Total time elapsed: 106.36 s
+
+real	1m49.108s
+user	29m56.686s
+sys	1m40.205s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr19: 41215
+[INFO] Full-alignment variants processed in chr19: 104681
+
+real	0m2.415s
+user	0m2.656s
+sys	0m0.189s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	4m44.025s
+user	57m24.571s
+sys	2m34.919s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output --ctg_name=chr19 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr19
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr19 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr19
+[INFO] Chunk number for each contig: 13
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr19 (chunk 10/13) : 10530
+Total time elapsed: 52.11 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/13) : 10757
+Total time elapsed: 53.05 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/13) : 11930
+Total time elapsed: 55.44 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/13) : 13827
+Total time elapsed: 56.45 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/13) : 13999
+Total time elapsed: 56.63 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/13) : 15113
+Total time elapsed: 56.87 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/13) : 15863
+Total time elapsed: 59.92 s
+Calling variants ...
+Total processed positions in chr19 (chunk 12/13) : 15431
+Total time elapsed: 61.25 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/13) : 18455
+Total time elapsed: 64.38 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/13) : 18004
+Total time elapsed: 64.17 s
+Calling variants ...
+Total processed positions in chr19 (chunk 13/13) : 19185
+Total time elapsed: 66.04 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/13) : 43919
+Total time elapsed: 97.09 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/13) : 53083
+Total time elapsed: 108.19 s
+
+real	1m50.923s
+user	11m5.290s
+sys	0m48.883s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 18
+[INFO] Total heterozygous SNP positions selected: chr19: 62515
+
+real	0m0.849s
+user	0m0.724s
+sys	0m0.094s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr19,30s)
+parsing total:  30s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 31s
+
+real	0m31.156s
+user	0m57.488s
+sys	0m3.131s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 7.0
+[INFO] Low quality reference calls to be processed in chr19: 10511
+[INFO] Low quality variants to be processed in chr19: 108203
+
+real	0m0.840s
+user	0m0.651s
+sys	0m0.139s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr19 (chunk 12/12) : 8714
+Total time elapsed: 94.43 s
+Calling variants ...
+Total processed positions in chr19 (chunk 6/12) : 10000
+Total time elapsed: 96.30 s
+Calling variants ...
+Total processed positions in chr19 (chunk 7/12) : 10000
+Total time elapsed: 98.32 s
+Calling variants ...
+Total processed positions in chr19 (chunk 8/12) : 10000
+Total time elapsed: 100.36 s
+Calling variants ...
+Total processed positions in chr19 (chunk 5/12) : 10000
+Total time elapsed: 102.17 s
+Calling variants ...
+Total processed positions in chr19 (chunk 4/12) : 10000
+Total time elapsed: 105.54 s
+Calling variants ...
+Total processed positions in chr19 (chunk 2/12) : 10000
+Total time elapsed: 111.36 s
+Calling variants ...
+Total processed positions in chr19 (chunk 11/12) : 10000
+Total time elapsed: 113.73 s
+Calling variants ...
+Total processed positions in chr19 (chunk 3/12) : 10000
+Total time elapsed: 116.21 s
+Calling variants ...
+Total processed positions in chr19 (chunk 1/12) : 10000
+Total time elapsed: 116.21 s
+Calling variants ...
+Total processed positions in chr19 (chunk 10/12) : 10000
+Total time elapsed: 118.94 s
+Calling variants ...
+Total processed positions in chr19 (chunk 9/12) : 10000
+Total time elapsed: 122.41 s
+
+real	2m4.968s
+user	20m27.392s
+sys	1m5.045s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr19: 46569
+[INFO] Full-alignment variants processed in chr19: 101152
+
+real	0m1.515s
+user	0m1.439s
+sys	0m0.132s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	4m35.468s
+user	32m37.343s
+sys	1m58.100s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr19: 84452, not found:765, not match:81, low_qual_count:0. Total normal:76459 Total tumor:85298, pro: 0.9901
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/vcf/chr19.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_chr19
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr19,39s)
+parsing total:  39s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 39s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_phased_chr19.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_chr19.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr19
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 0s
+tag read start ...
+chr: chr19 ... 625s
+tag read 626s
+-------------------------------------------
+total process time:  626s
+total alignment:     734582
+total supplementary: 28447
+total secondary:     0
+total unmapped:      0
+total tag alignment: 390188
+total untagged:      344394
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr19 chunk 2/13: Total snv candidates found: 8283, total indel candidates found: 192
+[INFO] chr19 chunk 1/13: Total snv candidates found: 8305, total indel candidates found: 982
+[INFO] chr19 chunk 7/13: Total snv candidates found: 774, total indel candidates found: 1459
+[INFO] chr19 chunk 5/13: Total snv candidates found: 930, total indel candidates found: 1172
+[INFO] chr19 chunk 9/13: Total snv candidates found: 1134, total indel candidates found: 1711
+[INFO] chr19 chunk 10/13: Total snv candidates found: 1091, total indel candidates found: 1615
+[INFO] chr19 chunk 12/13: Total snv candidates found: 1165, total indel candidates found: 1426
+[faidx] Truncated sequence: chr19:58474127-61708401
+[INFO] chr19 chunk 4/13: Total snv candidates found: 622, total indel candidates found: 1052
+[INFO] chr19 chunk 8/13: Total snv candidates found: 724, total indel candidates found: 1286
+[INFO] chr19 chunk 3/13: Total snv candidates found: 8985, total indel candidates found: 1029
+[INFO] chr19 chunk 6/13: Total snv candidates found: 1237, total indel candidates found: 1303
+[INFO] chr19 chunk 0/13: Total snv candidates found: 1028, total indel candidates found: 1065
+[INFO] chr19 chunk 11/13: Total snv candidates found: 1775, total indel candidates found: 1483
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/2-1_CPT.log
+
+[INFO] chr19 chunk 1-1/4 Tensors generated: 612
+[INFO] chr19 chunk 1-1/8 Tensors generated: 721
+[INFO] chr19 chunk 1-1/7 Tensors generated: 772
+[INFO] chr19 chunk 1-1/0 Tensors generated: 1025
+[INFO] chr19 chunk 1-1/5 Tensors generated: 908
+[INFO] chr19 chunk 1-1/9 Tensors generated: 1129
+[INFO] chr19 chunk 1-1/12 Tensors generated: 1143
+[INFO] chr19 chunk 1-1/10 Tensors generated: 1090
+[INFO] chr19 chunk 1-1/6 Tensors generated: 1221
+[INFO] chr19 chunk 1-1/11 Tensors generated: 1774
+[INFO] chr19 chunk 1-1/3 Tensors generated: 8980
+[INFO] chr19 chunk 1-1/1 Tensors generated: 8202
+[INFO] chr19 chunk 1-1/2 Tensors generated: 8263
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/2-2_PREDICT.log
+
+[INFO] chr19 total processed positions: 612, time elapsed: 1.4s
+[INFO] chr19 total processed positions: 721, time elapsed: 1.3s
+[INFO] chr19 total processed positions: 772, time elapsed: 1.4s
+[INFO] chr19 total processed positions: 908, time elapsed: 1.9s
+[INFO] chr19 total processed positions: 1025, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 1090, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 1129, time elapsed: 2.2s
+[INFO] chr19 total processed positions: 1143, time elapsed: 2.2s
+[INFO] chr19 total processed positions: 1221, time elapsed: 2.4s
+[INFO] chr19 total processed positions: 1774, time elapsed: 3.3s
+[INFO] chr19 total processed positions: 8202, time elapsed: 13.3s
+[INFO] chr19 total processed positions: 8263, time elapsed: 13.4s
+[INFO] chr19 total processed positions: 8980, time elapsed: 14.1s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/3-1_CPT.log
+
+[INFO] chr19 chunk 1-1/4 Tensors generated: 612
+[INFO] chr19 chunk 1-1/8 Tensors generated: 721
+[INFO] chr19 chunk 1-1/7 Tensors generated: 772
+[INFO] chr19 chunk 1-1/5 Tensors generated: 908
+[INFO] chr19 chunk 1-1/6 Tensors generated: 1091
+[INFO] chr19 chunk 1-1/0 Tensors generated: 1025
+[INFO] chr19 chunk 1-1/9 Tensors generated: 1121
+[INFO] chr19 chunk 1-1/10 Tensors generated: 1089
+[INFO] chr19 chunk 1-1/12 Tensors generated: 1139
+[INFO] chr19 chunk 1-1/11 Tensors generated: 1774
+[INFO] chr19 chunk 1-1/2 Tensors generated: 6524
+[INFO] chr19 chunk 1-1/1 Tensors generated: 7891
+[INFO] chr19 chunk 1-1/3 Tensors generated: 8612
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/3-2_PREDICT.log
+
+[INFO] chr19 total processed positions: 612, time elapsed: 108.1s
+[INFO] chr19 total processed positions: 721, time elapsed: 127.2s
+[INFO] chr19 total processed positions: 772, time elapsed: 136.3s
+[INFO] chr19 total processed positions: 908, time elapsed: 160.1s
+[INFO] chr19 total processed positions: 1025, time elapsed: 180.2s
+[INFO] chr19 total processed positions: 1089, time elapsed: 192.3s
+[INFO] chr19 total processed positions: 1091, time elapsed: 192.7s
+[INFO] chr19 total processed positions: 1121, time elapsed: 198.0s
+[INFO] chr19 total processed positions: 1139, time elapsed: 202.2s
+[INFO] chr19 total processed positions: 1774, time elapsed: 312.6s
+[INFO] chr19 total processed positions: 6524, time elapsed: 1146.3s
+[INFO] chr19 total processed positions: 7891, time elapsed: 1391.8s
+[INFO] chr19 total processed positions: 8612, time elapsed: 1519.5s
+
+[INFO] Merge Full-alignment VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --vcf_fn_prefix fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/full_alignment.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 4: Haplotype filtering
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/4_HAP_FILTER.log
+
+[INFO] Processing in chr19, total processed positions: 1000
+Total input calls: 4369, filtered by haplotype match 24
+
+[INFO] STEP 5: Merge and sort VCF
+[INFO] RUN THE FOLLOWING COMMAND:
+( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/output.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/5_MV.log
+
+[INFO] Full-alignment variants filtered by pileup:  400
+
+[INFO] STEP 6: Indel Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates --input_prefix INDEL_CANDIDATES_FILE_ --output_fn INDEL_CANDIDATES_FILES  && ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_6-1_create_pair_tensor_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/6-1_CPTI.log
+
+[INFO] chr19  Tensors generated: 192
+[INFO] chr19  Tensors generated: 1047
+[INFO] chr19  Tensors generated: 1063
+[INFO] chr19  Tensors generated: 1158
+[INFO] chr19  Tensors generated: 976
+[INFO] chr19  Tensors generated: 1281
+[INFO] chr19  Tensors generated: 1029
+[INFO] chr19  Tensors generated: 1299
+[INFO] chr19  Tensors generated: 1483
+[INFO] chr19  Tensors generated: 1456
+[INFO] chr19  Tensors generated: 1417
+[INFO] chr19  Tensors generated: 1707
+[INFO] chr19  Tensors generated: 1615
+
+[INFO] Indel Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_6-2_predict_indel.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/pileup_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/6-2_PREDICT_INDEL.log
+
+[INFO] chr19 total processed positions: 192, time elapsed: 0.4s
+[INFO] chr19 total processed positions: 1029, time elapsed: 1.8s
+[INFO] chr19 total processed positions: 976, time elapsed: 1.9s
+[INFO] chr19 total processed positions: 1047, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 1063, time elapsed: 1.8s
+[INFO] chr19 total processed positions: 1158, time elapsed: 2.1s
+[INFO] chr19 total processed positions: 1299, time elapsed: 2.3s
+[INFO] chr19 total processed positions: 1281, time elapsed: 2.4s
+[INFO] chr19 total processed positions: 1456, time elapsed: 2.5s
+[INFO] chr19 total processed positions: 1417, time elapsed: 2.8s
+[INFO] chr19 total processed positions: 1615, time elapsed: 2.9s
+[INFO] chr19 total processed positions: 1483, time elapsed: 2.6s
+[INFO] chr19 total processed positions: 1707, time elapsed: 3.2s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output --vcf_fn_prefix indel_p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 7: Indel Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_7-1_create_pair_tensor_fa_indel.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/7-1_CPTI.log
+
+[INFO] chr19  Tensors generated: 158
+[INFO] chr19  Tensors generated: 1014
+[INFO] chr19  Tensors generated: 960
+[INFO] chr19  Tensors generated: 1063
+[INFO] chr19  Tensors generated: 1047
+[INFO] chr19  Tensors generated: 1158
+[INFO] chr19  Tensors generated: 1293
+[INFO] chr19  Tensors generated: 1281
+[INFO] chr19  Tensors generated: 1417
+[INFO] chr19  Tensors generated: 1483
+[INFO] chr19  Tensors generated: 1456
+[INFO] chr19  Tensors generated: 1702
+[INFO] chr19  Tensors generated: 1613
+
+[INFO] Indel Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/parallel_7-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/fa_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/vcf_output/indel_fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part19/logs/7-2_PREDICT_INDEL.log
+

slurm-2557977.out

@@ -0,0 +1,964 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21 --region chr2:113845112-242696752 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr2
+[INFO] Number of chunks for each contig: 49
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr2:113845112-242696752
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output --ctg_name=chr2 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr2
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr2 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr2
+[INFO] Chunk number for each contig: 49
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr2 (chunk 11/49) : 74661
+Total time elapsed: 146.96 s
+Calling variants ...
+Total processed positions in chr2 (chunk 28/49) : 75612
+Total time elapsed: 147.58 s
+Calling variants ...
+Total processed positions in chr2 (chunk 17/49) : 71352
+Total time elapsed: 152.76 s
+Calling variants ...
+Total processed positions in chr2 (chunk 29/49) : 76038
+Total time elapsed: 154.24 s
+Calling variants ...
+Total processed positions in chr2 (chunk 13/49) : 75269
+Total time elapsed: 157.54 s
+Calling variants ...
+Total processed positions in chr2 (chunk 23/49) : 82668
+Total time elapsed: 159.10 s
+Calling variants ...
+Total processed positions in chr2 (chunk 8/49) : 80441
+Total time elapsed: 159.55 s
+Calling variants ...
+Total processed positions in chr2 (chunk 12/49) : 82008
+Total time elapsed: 161.83 s
+Calling variants ...
+Total processed positions in chr2 (chunk 9/49) : 81596
+Total time elapsed: 165.37 s
+Calling variants ...
+Total processed positions in chr2 (chunk 1/49) : 80838
+Total time elapsed: 165.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 20/49) : 75043
+Total time elapsed: 166.74 s
+Calling variants ...
+Total processed positions in chr2 (chunk 16/49) : 81038
+Total time elapsed: 166.96 s
+Calling variants ...
+Total processed positions in chr2 (chunk 22/49) : 80277
+Total time elapsed: 167.29 s
+Calling variants ...
+Total processed positions in chr2 (chunk 3/49) : 86183
+Total time elapsed: 167.52 s
+Calling variants ...
+Total processed positions in chr2 (chunk 14/49) : 81970
+Total time elapsed: 168.25 s
+Calling variants ...
+Total processed positions in chr2 (chunk 18/49) : 80235
+Total time elapsed: 168.36 s
+Calling variants ...
+Total processed positions in chr2 (chunk 7/49) : 88857
+Total time elapsed: 169.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 26/49) : 84734
+Total time elapsed: 169.91 s
+Calling variants ...
+Total processed positions in chr2 (chunk 21/49) : 81835
+Total time elapsed: 172.35 s
+Calling variants ...
+Total processed positions in chr2 (chunk 10/49) : 82733
+Total time elapsed: 172.41 s
+Calling variants ...
+Total processed positions in chr2 (chunk 30/49) : 73373
+Total time elapsed: 148.13 s
+Calling variants ...
+Total processed positions in chr2 (chunk 19/49) : 75283
+Total time elapsed: 173.63 s
+Calling variants ...
+Total processed positions in chr2 (chunk 2/49) : 84106
+Total time elapsed: 174.45 s
+Calling variants ...
+Total processed positions in chr2 (chunk 27/49) : 83387
+Total time elapsed: 174.70 s
+Calling variants ...
+Total processed positions in chr2 (chunk 15/49) : 87963
+Total time elapsed: 177.17 s
+Calling variants ...
+Total processed positions in chr2 (chunk 6/49) : 79351
+Total time elapsed: 156.14 s
+Calling variants ...
+Total processed positions in chr2 (chunk 24/49) : 79088
+Total time elapsed: 156.95 s
+Calling variants ...
+Total processed positions in chr2 (chunk 4/49) : 83480
+Total time elapsed: 159.75 s
+Calling variants ...
+Total processed positions in chr2 (chunk 5/49) : 83721
+Total time elapsed: 161.86 s
+Calling variants ...
+Total processed positions in chr2 (chunk 25/49) : 84883
+Total time elapsed: 165.15 s
+Calling variants ...
+Total processed positions in chr2 (chunk 31/49) : 73402
+Total time elapsed: 119.56 s
+Calling variants ...
+Total processed positions in chr2 (chunk 32/49) : 71337
+Total time elapsed: 128.49 s
+Calling variants ...
+Total processed positions in chr2 (chunk 34/49) : 79400
+Total time elapsed: 128.35 s
+Calling variants ...
+Total processed positions in chr2 (chunk 38/49) : 73991
+Total time elapsed: 124.13 s
+Calling variants ...
+Total processed positions in chr2 (chunk 33/49) : 82305
+Total time elapsed: 132.36 s
+Calling variants ...
+Total processed positions in chr2 (chunk 37/49) : 75613
+Total time elapsed: 127.08 s
+Calling variants ...
+Total processed positions in chr2 (chunk 42/49) : 75734
+Total time elapsed: 121.55 s
+Calling variants ...
+Total processed positions in chr2 (chunk 40/49) : 70806
+Total time elapsed: 124.40 s
+Calling variants ...
+Total processed positions in chr2 (chunk 47/49) : 74017
+Total time elapsed: 125.68 s
+Calling variants ...
+Total processed positions in chr2 (chunk 44/49) : 75892
+Total time elapsed: 129.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 39/49) : 79011
+Total time elapsed: 132.08 s
+Calling variants ...
+Total processed positions in chr2 (chunk 46/49) : 81534
+Total time elapsed: 130.11 s
+Calling variants ...
+Total processed positions in chr2 (chunk 41/49) : 80990
+Total time elapsed: 133.01 s
+Calling variants ...
+Total processed positions in chr2 (chunk 43/49) : 78010
+Total time elapsed: 133.53 s
+Calling variants ...
+Total processed positions in chr2 (chunk 35/49) : 84506
+Total time elapsed: 143.31 s
+Calling variants ...
+Total processed positions in chr2 (chunk 36/49) : 84088
+Total time elapsed: 142.80 s
+Calling variants ...
+Total processed positions in chr2 (chunk 45/49) : 86558
+Total time elapsed: 140.02 s
+Calling variants ...
+Total processed positions in chr2 (chunk 48/49) : 83848
+Total time elapsed: 139.39 s
+Calling variants ...
+Total processed positions in chr2 (chunk 49/49) : 92842
+Total time elapsed: 143.71 s
+
+real	5m27.391s
+user	116m19.862s
+sys	8m3.215s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16
+[INFO] Total heterozygous SNP positions selected: chr2: 150142
+
+real	0m8.783s
+user	0m8.442s
+sys	0m0.241s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr2.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr2
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 3s
+(chr2,17s)
+parsing total:  17s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 21s
+
+real	0m21.566s
+user	0m40.677s
+sys	0m2.645s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 20.0
+[INFO] Set reference calls quality cutoff 14.0
+[INFO] Low quality reference calls to be processed in chr2: 351297
+[INFO] Low quality variants to be processed in chr2: 282859
+
+real	0m9.508s
+user	0m8.948s
+sys	0m0.404s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr2 (chunk 11/64) : 10000
+Total time elapsed: 89.29 s
+Calling variants ...
+Total processed positions in chr2 (chunk 25/64) : 10000
+Total time elapsed: 98.33 s
+Calling variants ...
+Total processed positions in chr2 (chunk 4/64) : 10000
+Total time elapsed: 98.40 s
+Calling variants ...
+Total processed positions in chr2 (chunk 29/64) : 10000
+Total time elapsed: 98.52 s
+Calling variants ...
+Total processed positions in chr2 (chunk 30/64) : 10000
+Total time elapsed: 99.14 s
+Calling variants ...
+Total processed positions in chr2 (chunk 20/64) : 10000
+Total time elapsed: 99.39 s
+Calling variants ...
+Total processed positions in chr2 (chunk 24/64) : 10000
+Total time elapsed: 99.60 s
+Calling variants ...
+Total processed positions in chr2 (chunk 9/64) : 10000
+Total time elapsed: 100.06 s
+Calling variants ...
+Total processed positions in chr2 (chunk 19/64) : 10000
+Total time elapsed: 99.91 s
+Calling variants ...
+Total processed positions in chr2 (chunk 21/64) : 10000
+Total time elapsed: 99.82 s
+Calling variants ...
+Total processed positions in chr2 (chunk 13/64) : 10000
+Total time elapsed: 101.13 s
+Calling variants ...
+Total processed positions in chr2 (chunk 28/64) : 10000
+Total time elapsed: 102.62 s
+Calling variants ...
+Total processed positions in chr2 (chunk 22/64) : 10000
+Total time elapsed: 102.59 s
+Calling variants ...
+Total processed positions in chr2 (chunk 26/64) : 10000
+Total time elapsed: 103.18 s
+Calling variants ...
+Total processed positions in chr2 (chunk 23/64) : 10000
+Total time elapsed: 103.44 s
+Calling variants ...
+Total processed positions in chr2 (chunk 3/64) : 10000
+Total time elapsed: 104.47 s
+Calling variants ...
+Total processed positions in chr2 (chunk 14/64) : 10000
+Total time elapsed: 104.76 s
+Calling variants ...
+Total processed positions in chr2 (chunk 17/64) : 10000
+Total time elapsed: 105.01 s
+Calling variants ...
+Total processed positions in chr2 (chunk 7/64) : 10000
+Total time elapsed: 106.31 s
+Calling variants ...
+Total processed positions in chr2 (chunk 12/64) : 10000
+Total time elapsed: 106.32 s
+Calling variants ...
+Total processed positions in chr2 (chunk 6/64) : 10000
+Total time elapsed: 106.79 s
+Calling variants ...
+Total processed positions in chr2 (chunk 8/64) : 10000
+Total time elapsed: 107.08 s
+Calling variants ...
+Total processed positions in chr2 (chunk 10/64) : 10000
+Total time elapsed: 107.08 s
+Calling variants ...
+Total processed positions in chr2 (chunk 18/64) : 10000
+Total time elapsed: 107.54 s
+Calling variants ...
+Total processed positions in chr2 (chunk 16/64) : 10000
+Total time elapsed: 108.15 s
+Calling variants ...
+Total processed positions in chr2 (chunk 27/64) : 10000
+Total time elapsed: 108.69 s
+Calling variants ...
+Total processed positions in chr2 (chunk 5/64) : 10000
+Total time elapsed: 109.37 s
+Calling variants ...
+Total processed positions in chr2 (chunk 15/64) : 10000
+Total time elapsed: 109.37 s
+Calling variants ...
+Total processed positions in chr2 (chunk 2/64) : 10000
+Total time elapsed: 111.80 s
+Calling variants ...
+Total processed positions in chr2 (chunk 1/64) : 10000
+Total time elapsed: 113.45 s
+Calling variants ...
+Total processed positions in chr2 (chunk 38/64) : 10000
+Total time elapsed: 97.28 s
+Calling variants ...
+Total processed positions in chr2 (chunk 31/64) : 10000
+Total time elapsed: 108.49 s
+Calling variants ...
+Total processed positions in chr2 (chunk 32/64) : 10000
+Total time elapsed: 100.43 s
+Calling variants ...
+Total processed positions in chr2 (chunk 53/64) : 10000
+Total time elapsed: 92.84 s
+Calling variants ...
+Total processed positions in chr2 (chunk 35/64) : 10000
+Total time elapsed: 101.58 s
+Calling variants ...
+Total processed positions in chr2 (chunk 41/64) : 10000
+Total time elapsed: 99.16 s
+Calling variants ...
+Total processed positions in chr2 (chunk 34/64) : 10000
+Total time elapsed: 101.67 s
+Calling variants ...
+Total processed positions in chr2 (chunk 33/64) : 10000
+Total time elapsed: 105.70 s
+Calling variants ...
+Total processed positions in chr2 (chunk 46/64) : 10000
+Total time elapsed: 101.46 s
+Calling variants ...
+Total processed positions in chr2 (chunk 45/64) : 10000
+Total time elapsed: 102.47 s
+Calling variants ...
+Total processed positions in chr2 (chunk 36/64) : 10000
+Total time elapsed: 106.03 s
+Calling variants ...
+Total processed positions in chr2 (chunk 39/64) : 10000
+Total time elapsed: 106.59 s
+Calling variants ...
+Total processed positions in chr2 (chunk 37/64) : 10000
+Total time elapsed: 107.47 s
+Calling variants ...
+Total processed positions in chr2 (chunk 48/64) : 10000
+Total time elapsed: 102.60 s
+Calling variants ...
+Total processed positions in chr2 (chunk 47/64) : 10000
+Total time elapsed: 102.92 s
+Calling variants ...
+Total processed positions in chr2 (chunk 40/64) : 10000
+Total time elapsed: 107.45 s
+Calling variants ...
+Total processed positions in chr2 (chunk 42/64) : 10000
+Total time elapsed: 105.14 s
+Calling variants ...
+Total processed positions in chr2 (chunk 54/64) : 10000
+Total time elapsed: 100.39 s
+Calling variants ...
+Total processed positions in chr2 (chunk 44/64) : 10000
+Total time elapsed: 105.13 s
+Calling variants ...
+Total processed positions in chr2 (chunk 43/64) : 10000
+Total time elapsed: 106.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 57/64) : 10000
+Total time elapsed: 99.89 s
+Calling variants ...
+Total processed positions in chr2 (chunk 52/64) : 10000
+Total time elapsed: 102.98 s
+Calling variants ...
+Total processed positions in chr2 (chunk 50/64) : 10000
+Total time elapsed: 103.62 s
+Calling variants ...
+Total processed positions in chr2 (chunk 55/64) : 10000
+Total time elapsed: 102.01 s
+Calling variants ...
+Total processed positions in chr2 (chunk 56/64) : 10000
+Total time elapsed: 105.40 s
+Calling variants ...
+Total processed positions in chr2 (chunk 59/64) : 10000
+Total time elapsed: 102.12 s
+Calling variants ...
+Total processed positions in chr2 (chunk 58/64) : 10000
+Total time elapsed: 105.47 s
+Calling variants ...
+Total processed positions in chr2 (chunk 51/64) : 10000
+Total time elapsed: 109.28 s
+Calling variants ...
+Total processed positions in chr2 (chunk 49/64) : 10000
+Total time elapsed: 110.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 60/64) : 10000
+Total time elapsed: 103.25 s
+Calling variants ...
+Total processed positions in chr2 (chunk 64/64) : 4156
+Total time elapsed: 35.72 s
+Calling variants ...
+Total processed positions in chr2 (chunk 61/64) : 10000
+Total time elapsed: 72.73 s
+Calling variants ...
+Total processed positions in chr2 (chunk 62/64) : 10000
+Total time elapsed: 75.62 s
+Calling variants ...
+Total processed positions in chr2 (chunk 63/64) : 10000
+Total time elapsed: 76.10 s
+
+real	4m46.439s
+user	104m13.888s
+sys	6m17.660s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr2: 121260
+[INFO] Full-alignment variants processed in chr2: 298027
+
+real	0m11.649s
+user	0m12.884s
+sys	0m0.395s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	11m51.527s
+user	222m28.836s
+sys	14m27.506s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output --ctg_name=chr2 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr2
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr2 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr2
+[INFO] Chunk number for each contig: 49
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr2 (chunk 30/49) : 6472
+Total time elapsed: 133.58 s
+Calling variants ...
+Total processed positions in chr2 (chunk 28/49) : 7473
+Total time elapsed: 134.50 s
+Calling variants ...
+Total processed positions in chr2 (chunk 5/49) : 8455
+Total time elapsed: 136.84 s
+Calling variants ...
+Total processed positions in chr2 (chunk 23/49) : 8909
+Total time elapsed: 137.22 s
+Calling variants ...
+Total processed positions in chr2 (chunk 24/49) : 9129
+Total time elapsed: 138.77 s
+Calling variants ...
+Total processed positions in chr2 (chunk 7/49) : 11591
+Total time elapsed: 140.48 s
+Calling variants ...
+Total processed positions in chr2 (chunk 25/49) : 10438
+Total time elapsed: 140.48 s
+Calling variants ...
+Total processed positions in chr2 (chunk 16/49) : 11769
+Total time elapsed: 142.03 s
+Calling variants ...
+Total processed positions in chr2 (chunk 11/49) : 11806
+Total time elapsed: 142.04 s
+Calling variants ...
+Total processed positions in chr2 (chunk 26/49) : 11900
+Total time elapsed: 142.40 s
+Calling variants ...
+Total processed positions in chr2 (chunk 15/49) : 11490
+Total time elapsed: 142.16 s
+Calling variants ...
+Total processed positions in chr2 (chunk 18/49) : 11980
+Total time elapsed: 142.61 s
+Calling variants ...
+Total processed positions in chr2 (chunk 8/49) : 13128
+Total time elapsed: 143.45 s
+Calling variants ...
+Total processed positions in chr2 (chunk 27/49) : 14692
+Total time elapsed: 144.85 s
+Calling variants ...
+Total processed positions in chr2 (chunk 1/49) : 15284
+Total time elapsed: 146.08 s
+Calling variants ...
+Total processed positions in chr2 (chunk 3/49) : 13938
+Total time elapsed: 146.00 s
+Calling variants ...
+Total processed positions in chr2 (chunk 20/49) : 24047
+Total time elapsed: 157.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 17/49) : 7627
+Total time elapsed: 59.33 s
+Calling variants ...
+Total processed positions in chr2 (chunk 21/49) : 9171
+Total time elapsed: 60.12 s
+Calling variants ...
+Total processed positions in chr2 (chunk 2/49) : 10653
+Total time elapsed: 62.70 s
+Calling variants ...
+Total processed positions in chr2 (chunk 4/49) : 10602
+Total time elapsed: 63.56 s
+Calling variants ...
+Total processed positions in chr2 (chunk 13/49) : 10312
+Total time elapsed: 63.57 s
+Calling variants ...
+Total processed positions in chr2 (chunk 29/49) : 10495
+Total time elapsed: 63.77 s
+Calling variants ...
+Total processed positions in chr2 (chunk 12/49) : 12287
+Total time elapsed: 65.11 s
+Calling variants ...
+Total processed positions in chr2 (chunk 10/49) : 12602
+Total time elapsed: 65.76 s
+Calling variants ...
+Total processed positions in chr2 (chunk 31/49) : 7977
+Total time elapsed: 54.46 s
+Calling variants ...
+Total processed positions in chr2 (chunk 32/49) : 8410
+Total time elapsed: 54.90 s
+Calling variants ...
+Total processed positions in chr2 (chunk 39/49) : 7943
+Total time elapsed: 57.35 s
+Calling variants ...
+Total processed positions in chr2 (chunk 35/49) : 11348
+Total time elapsed: 60.67 s
+Calling variants ...
+Total processed positions in chr2 (chunk 37/49) : 9564
+Total time elapsed: 59.96 s
+Calling variants ...
+Total processed positions in chr2 (chunk 40/49) : 8407
+Total time elapsed: 58.77 s
+Calling variants ...
+Total processed positions in chr2 (chunk 38/49) : 8387
+Total time elapsed: 58.73 s
+Calling variants ...
+Total processed positions in chr2 (chunk 36/49) : 9813
+Total time elapsed: 61.02 s
+Calling variants ...
+Total processed positions in chr2 (chunk 43/49) : 9185
+Total time elapsed: 58.58 s
+Calling variants ...
+Total processed positions in chr2 (chunk 42/49) : 9050
+Total time elapsed: 60.16 s
+Calling variants ...
+Total processed positions in chr2 (chunk 44/49) : 8253
+Total time elapsed: 58.38 s
+Calling variants ...
+Total processed positions in chr2 (chunk 41/49) : 9364
+Total time elapsed: 61.60 s
+Calling variants ...
+Total processed positions in chr2 (chunk 45/49) : 9880
+Total time elapsed: 59.25 s
+Calling variants ...
+Total processed positions in chr2 (chunk 46/49) : 10647
+Total time elapsed: 59.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 6/49) : 9236
+Total time elapsed: 49.48 s
+Calling variants ...
+Total processed positions in chr2 (chunk 22/49) : 9821
+Total time elapsed: 51.70 s
+Calling variants ...
+Total processed positions in chr2 (chunk 9/49) : 10082
+Total time elapsed: 51.89 s
+Calling variants ...
+Total processed positions in chr2 (chunk 14/49) : 12324
+Total time elapsed: 53.35 s
+Calling variants ...
+Total processed positions in chr2 (chunk 47/49) : 11754
+Total time elapsed: 54.64 s
+Calling variants ...
+Total processed positions in chr2 (chunk 19/49) : 64666
+Total time elapsed: 224.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 33/49) : 10165
+Total time elapsed: 45.64 s
+Calling variants ...
+Total processed positions in chr2 (chunk 34/49) : 10438
+Total time elapsed: 47.55 s
+Calling variants ...
+Total processed positions in chr2 (chunk 48/49) : 12378
+Total time elapsed: 48.60 s
+Calling variants ...
+Total processed positions in chr2 (chunk 49/49) : 16414
+Total time elapsed: 52.81 s
+
+real	4m2.239s
+user	42m58.746s
+sys	36m7.828s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 20
+[INFO] Total heterozygous SNP positions selected: chr2: 154655
+
+real	0m2.357s
+user	0m2.095s
+sys	0m0.189s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr2.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr2
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 3s
+(chr2,66s)
+parsing total:  66s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 70s
+
+real	1m11.184s
+user	2m59.151s
+sys	0m10.796s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 22.0
+[INFO] Set reference calls quality cutoff 7.0
+[INFO] Low quality reference calls to be processed in chr2: 18408
+[INFO] Low quality variants to be processed in chr2: 277651
+
+real	0m2.246s
+user	0m1.992s
+sys	0m0.198s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr2 (chunk 30/30) : 6059
+Total time elapsed: 83.49 s
+Calling variants ...
+Total processed positions in chr2 (chunk 13/30) : 10000
+Total time elapsed: 104.21 s
+Calling variants ...
+Total processed positions in chr2 (chunk 14/30) : 10000
+Total time elapsed: 127.96 s
+Calling variants ...
+Total processed positions in chr2 (chunk 12/30) : 10000
+Total time elapsed: 130.89 s
+Calling variants ...
+Total processed positions in chr2 (chunk 5/30) : 10000
+Total time elapsed: 134.21 s
+Calling variants ...
+Total processed positions in chr2 (chunk 10/30) : 10000
+Total time elapsed: 136.37 s
+Calling variants ...
+Total processed positions in chr2 (chunk 2/30) : 10000
+Total time elapsed: 136.44 s
+Calling variants ...
+Total processed positions in chr2 (chunk 7/30) : 10000
+Total time elapsed: 137.33 s
+Calling variants ...
+Total processed positions in chr2 (chunk 6/30) : 10000
+Total time elapsed: 137.52 s
+Calling variants ...
+Total processed positions in chr2 (chunk 22/30) : 10000
+Total time elapsed: 137.75 s
+Calling variants ...
+Total processed positions in chr2 (chunk 29/30) : 10000
+Total time elapsed: 139.04 s
+Calling variants ...
+Total processed positions in chr2 (chunk 25/30) : 10000
+Total time elapsed: 140.17 s
+Calling variants ...
+Total processed positions in chr2 (chunk 9/30) : 10000
+Total time elapsed: 140.75 s
+Calling variants ...
+Total processed positions in chr2 (chunk 28/30) : 10000
+Total time elapsed: 142.51 s
+Calling variants ...
+Total processed positions in chr2 (chunk 27/30) : 10000
+Total time elapsed: 143.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 18/30) : 10000
+Total time elapsed: 143.82 s
+Calling variants ...
+Total processed positions in chr2 (chunk 8/30) : 10000
+Total time elapsed: 144.15 s
+Calling variants ...
+Total processed positions in chr2 (chunk 3/30) : 10000
+Total time elapsed: 145.48 s
+Calling variants ...
+Total processed positions in chr2 (chunk 17/30) : 10000
+Total time elapsed: 148.69 s
+Calling variants ...
+Total processed positions in chr2 (chunk 23/30) : 10000
+Total time elapsed: 149.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 19/30) : 10000
+Total time elapsed: 149.90 s
+Calling variants ...
+Total processed positions in chr2 (chunk 21/30) : 10000
+Total time elapsed: 150.16 s
+Calling variants ...
+Total processed positions in chr2 (chunk 1/30) : 10000
+Total time elapsed: 150.67 s
+Calling variants ...
+Total processed positions in chr2 (chunk 24/30) : 10000
+Total time elapsed: 152.04 s
+Calling variants ...
+Total processed positions in chr2 (chunk 15/30) : 10000
+Total time elapsed: 151.80 s
+Calling variants ...
+Total processed positions in chr2 (chunk 4/30) : 10000
+Total time elapsed: 152.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 26/30) : 10000
+Total time elapsed: 153.33 s
+Calling variants ...
+Total processed positions in chr2 (chunk 11/30) : 10000
+Total time elapsed: 154.04 s
+Calling variants ...
+Total processed positions in chr2 (chunk 16/30) : 10000
+Total time elapsed: 154.28 s
+Calling variants ...
+Total processed positions in chr2 (chunk 20/30) : 10000
+Total time elapsed: 156.51 s
+
+real	2m40.250s
+user	63m44.864s
+sys	3m31.391s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr2: 119513
+[INFO] Full-alignment variants processed in chr2: 256477
+
+real	0m4.082s
+user	0m4.234s
+sys	0m0.219s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	8m16.175s
+user	110m2.943s
+sys	39m51.958s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr2: 199643, not found:792, not match:54, low_qual_count:0. Total normal:208641 Total tumor:200489, pro: 0.9958
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/vcf/chr2.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/phased_output/tumor_phased_chr2
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 3s
+(chr2,85s)
+parsing total:  85s
+merge results ... 0s
+writeResult SNP ... 2s
+
+total process: 90s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part21/tmp/CONTIGS
+

slurm-2557978.out

@@ -0,0 +1,774 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40 --region chr9:55624206-150617247 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr9
+[INFO] Number of chunks for each contig: 31
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr9:55624206-150617247
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output --ctg_name=chr9 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr9
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr9 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr9
+[INFO] Chunk number for each contig: 31
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr9 (chunk 12/31) : 1257
+Total time elapsed: 17.96 s
+Calling variants ...
+Total processed positions in chr9 (chunk 13/31) : 2641
+Total time elapsed: 20.38 s
+Calling variants ...
+Total processed positions in chr9 (chunk 15/31) : 17476
+Total time elapsed: 48.85 s
+Calling variants ...
+Total processed positions in chr9 (chunk 14/31) : 21538
+Total time elapsed: 53.60 s
+Calling variants ...
+Total processed positions in chr9 (chunk 10/31) : 33522
+Total time elapsed: 78.54 s
+Calling variants ...
+Total processed positions in chr9 (chunk 11/31) : 37053
+Total time elapsed: 86.05 s
+Calling variants ...
+Total processed positions in chr9 (chunk 16/31) : 56455
+Total time elapsed: 119.76 s
+Calling variants ...
+Total processed positions in chr9 (chunk 17/31) : 62283
+Total time elapsed: 127.62 s
+Calling variants ...
+Total processed positions in chr9 (chunk 9/31) : 63514
+Total time elapsed: 131.78 s
+Calling variants ...
+Total processed positions in chr9 (chunk 3/31) : 71362
+Total time elapsed: 135.99 s
+Calling variants ...
+Total processed positions in chr9 (chunk 5/31) : 74395
+Total time elapsed: 139.66 s
+Calling variants ...
+Total processed positions in chr9 (chunk 24/31) : 79394
+Total time elapsed: 141.54 s
+Calling variants ...
+Total processed positions in chr9 (chunk 29/31) : 78305
+Total time elapsed: 142.68 s
+Calling variants ...
+Total processed positions in chr9 (chunk 7/31) : 76859
+Total time elapsed: 143.38 s
+Calling variants ...
+Total processed positions in chr9 (chunk 8/31) : 79476
+Total time elapsed: 144.97 s
+Calling variants ...
+Total processed positions in chr9 (chunk 25/31) : 76301
+Total time elapsed: 145.07 s
+Calling variants ...
+Total processed positions in chr9 (chunk 6/31) : 72961
+Total time elapsed: 146.47 s
+Calling variants ...
+Total processed positions in chr9 (chunk 26/31) : 82443
+Total time elapsed: 148.27 s
+Calling variants ...
+Total processed positions in chr9 (chunk 20/31) : 75744
+Total time elapsed: 148.83 s
+Calling variants ...
+Total processed positions in chr9 (chunk 23/31) : 81576
+Total time elapsed: 150.46 s
+Calling variants ...
+Total processed positions in chr9 (chunk 2/31) : 77468
+Total time elapsed: 151.04 s
+Calling variants ...
+Total processed positions in chr9 (chunk 4/31) : 76648
+Total time elapsed: 151.73 s
+Calling variants ...
+Total processed positions in chr9 (chunk 22/31) : 81615
+Total time elapsed: 154.06 s
+Calling variants ...
+Total processed positions in chr9 (chunk 19/31) : 78752
+Total time elapsed: 154.05 s
+Calling variants ...
+Total processed positions in chr9 (chunk 28/31) : 79687
+Total time elapsed: 155.51 s
+Calling variants ...
+Total processed positions in chr9 (chunk 18/31) : 77860
+Total time elapsed: 155.64 s
+Calling variants ...
+Total processed positions in chr9 (chunk 27/31) : 81764
+Total time elapsed: 157.11 s
+Calling variants ...
+Total processed positions in chr9 (chunk 1/31) : 85324
+Total time elapsed: 159.15 s
+Calling variants ...
+Total processed positions in chr9 (chunk 30/31) : 88072
+Total time elapsed: 162.12 s
+Calling variants ...
+Total processed positions in chr9 (chunk 21/31) : 89341
+Total time elapsed: 152.60 s
+Calling variants ...
+Total processed positions in chr9 (chunk 31/31) : 95505
+Total time elapsed: 155.05 s
+
+real	3m4.784s
+user	62m4.077s
+sys	3m33.310s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
+[INFO] Total heterozygous SNP positions selected: chr9: 77784
+
+real	0m4.754s
+user	0m4.489s
+sys	0m0.192s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr9.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr9
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr9,10s)
+parsing total:  10s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 12s
+
+real	0m12.323s
+user	0m23.247s
+sys	0m1.686s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 13.0
+[INFO] Low quality reference calls to be processed in chr9: 181543
+[INFO] Low quality variants to be processed in chr9: 165238
+
+real	0m5.203s
+user	0m4.807s
+sys	0m0.313s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr9 (chunk 19/35) : 10000
+Total time elapsed: 92.62 s
+Calling variants ...
+Total processed positions in chr9 (chunk 17/35) : 10000
+Total time elapsed: 96.32 s
+Calling variants ...
+Total processed positions in chr9 (chunk 29/35) : 10000
+Total time elapsed: 96.61 s
+Calling variants ...
+Total processed positions in chr9 (chunk 2/35) : 10000
+Total time elapsed: 96.49 s
+Calling variants ...
+Total processed positions in chr9 (chunk 26/35) : 10000
+Total time elapsed: 98.14 s
+Calling variants ...
+Total processed positions in chr9 (chunk 10/35) : 10000
+Total time elapsed: 98.23 s
+Calling variants ...
+Total processed positions in chr9 (chunk 7/35) : 10000
+Total time elapsed: 98.31 s
+Calling variants ...
+Total processed positions in chr9 (chunk 1/35) : 10000
+Total time elapsed: 102.22 s
+Calling variants ...
+Total processed positions in chr9 (chunk 30/35) : 10000
+Total time elapsed: 102.47 s
+Calling variants ...
+Total processed positions in chr9 (chunk 25/35) : 10000
+Total time elapsed: 102.89 s
+Calling variants ...
+Total processed positions in chr9 (chunk 4/35) : 10000
+Total time elapsed: 103.42 s
+Calling variants ...
+Total processed positions in chr9 (chunk 23/35) : 10000
+Total time elapsed: 103.94 s
+Calling variants ...
+Total processed positions in chr9 (chunk 28/35) : 10000
+Total time elapsed: 104.38 s
+Calling variants ...
+Total processed positions in chr9 (chunk 6/35) : 10000
+Total time elapsed: 104.32 s
+Calling variants ...
+Total processed positions in chr9 (chunk 3/35) : 10000
+Total time elapsed: 104.69 s
+Calling variants ...
+Total processed positions in chr9 (chunk 20/35) : 10000
+Total time elapsed: 104.80 s
+Calling variants ...
+Total processed positions in chr9 (chunk 15/35) : 10000
+Total time elapsed: 105.81 s
+Calling variants ...
+Total processed positions in chr9 (chunk 24/35) : 10000
+Total time elapsed: 106.00 s
+Calling variants ...
+Total processed positions in chr9 (chunk 12/35) : 10000
+Total time elapsed: 106.02 s
+Calling variants ...
+Total processed positions in chr9 (chunk 18/35) : 10000
+Total time elapsed: 106.35 s
+Calling variants ...
+Total processed positions in chr9 (chunk 16/35) : 10000
+Total time elapsed: 106.68 s
+Calling variants ...
+Total processed positions in chr9 (chunk 8/35) : 10000
+Total time elapsed: 106.87 s
+Calling variants ...
+Total processed positions in chr9 (chunk 9/35) : 10000
+Total time elapsed: 106.89 s
+Calling variants ...
+Total processed positions in chr9 (chunk 27/35) : 10000
+Total time elapsed: 107.09 s
+Calling variants ...
+Total processed positions in chr9 (chunk 21/35) : 10000
+Total time elapsed: 107.27 s
+Calling variants ...
+Total processed positions in chr9 (chunk 14/35) : 10000
+Total time elapsed: 107.48 s
+Calling variants ...
+Total processed positions in chr9 (chunk 13/35) : 10000
+Total time elapsed: 107.50 s
+Calling variants ...
+Total processed positions in chr9 (chunk 11/35) : 10000
+Total time elapsed: 107.78 s
+Calling variants ...
+Total processed positions in chr9 (chunk 5/35) : 10000
+Total time elapsed: 107.99 s
+Calling variants ...
+Total processed positions in chr9 (chunk 22/35) : 10000
+Total time elapsed: 108.92 s
+Calling variants ...
+Total processed positions in chr9 (chunk 35/35) : 6781
+Total time elapsed: 55.49 s
+Calling variants ...
+Total processed positions in chr9 (chunk 32/35) : 10000
+Total time elapsed: 69.14 s
+Calling variants ...
+Total processed positions in chr9 (chunk 31/35) : 10000
+Total time elapsed: 74.70 s
+Calling variants ...
+Total processed positions in chr9 (chunk 34/35) : 10000
+Total time elapsed: 78.02 s
+Calling variants ...
+Total processed positions in chr9 (chunk 33/35) : 10000
+Total time elapsed: 81.45 s
+
+real	3m4.889s
+user	55m57.941s
+sys	3m16.335s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr9: 70909
+[INFO] Full-alignment variants processed in chr9: 180962
+
+real	0m6.255s
+user	0m6.847s
+sys	0m0.266s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	7m3.909s
+user	119m5.300s
+sys	6m54.136s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output --ctg_name=chr9 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr9
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr9 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr9
+[INFO] Chunk number for each contig: 31
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr9 (chunk 12/31) : 3313
+Total time elapsed: 63.75 s
+Calling variants ...
+Total processed positions in chr9 (chunk 13/31) : 9677
+Total time elapsed: 75.54 s
+Calling variants ...
+Total processed positions in chr9 (chunk 8/31) : 8048
+Total time elapsed: 76.99 s
+Calling variants ...
+Total processed positions in chr9 (chunk 5/31) : 8157
+Total time elapsed: 78.17 s
+Calling variants ...
+Total processed positions in chr9 (chunk 18/31) : 8449
+Total time elapsed: 78.96 s
+Calling variants ...
+Total processed positions in chr9 (chunk 23/31) : 9152
+Total time elapsed: 80.13 s
+Calling variants ...
+Total processed positions in chr9 (chunk 27/31) : 10222
+Total time elapsed: 80.37 s
+Calling variants ...
+Total processed positions in chr9 (chunk 9/31) : 7557
+Total time elapsed: 81.04 s
+Calling variants ...
+Total processed positions in chr9 (chunk 19/31) : 11050
+Total time elapsed: 81.73 s
+Calling variants ...
+Total processed positions in chr9 (chunk 4/31) : 11173
+Total time elapsed: 81.98 s
+Calling variants ...
+Total processed positions in chr9 (chunk 6/31) : 10501
+Total time elapsed: 82.23 s
+Calling variants ...
+Total processed positions in chr9 (chunk 20/31) : 11420
+Total time elapsed: 83.61 s
+Calling variants ...
+Total processed positions in chr9 (chunk 24/31) : 11713
+Total time elapsed: 84.00 s
+Calling variants ...
+Total processed positions in chr9 (chunk 26/31) : 12517
+Total time elapsed: 84.11 s
+Calling variants ...
+Total processed positions in chr9 (chunk 2/31) : 13146
+Total time elapsed: 86.25 s
+Calling variants ...
+Total processed positions in chr9 (chunk 17/31) : 11841
+Total time elapsed: 87.22 s
+Calling variants ...
+Total processed positions in chr9 (chunk 1/31) : 15967
+Total time elapsed: 89.50 s
+Calling variants ...
+Total processed positions in chr9 (chunk 15/31) : 22912
+Total time elapsed: 93.68 s
+Calling variants ...
+Total processed positions in chr9 (chunk 28/31) : 6980
+Total time elapsed: 47.43 s
+Calling variants ...
+Total processed positions in chr9 (chunk 7/31) : 10077
+Total time elapsed: 48.37 s
+Calling variants ...
+Total processed positions in chr9 (chunk 29/31) : 8642
+Total time elapsed: 49.57 s
+Calling variants ...
+Total processed positions in chr9 (chunk 3/31) : 9920
+Total time elapsed: 49.92 s
+Calling variants ...
+Total processed positions in chr9 (chunk 25/31) : 9578
+Total time elapsed: 50.63 s
+Calling variants ...
+Total processed positions in chr9 (chunk 22/31) : 12435
+Total time elapsed: 51.57 s
+Calling variants ...
+Total processed positions in chr9 (chunk 11/31) : 40307
+Total time elapsed: 115.89 s
+Calling variants ...
+Total processed positions in chr9 (chunk 30/31) : 12175
+Total time elapsed: 53.41 s
+Calling variants ...
+Total processed positions in chr9 (chunk 21/31) : 11701
+Total time elapsed: 54.40 s
+Calling variants ...
+Total processed positions in chr9 (chunk 10/31) : 17506
+Total time elapsed: 58.44 s
+Calling variants ...
+Total processed positions in chr9 (chunk 31/31) : 16000
+Total time elapsed: 55.65 s
+Calling variants ...
+Total processed positions in chr9 (chunk 14/31) : 27421
+Total time elapsed: 65.13 s
+Calling variants ...
+Total processed positions in chr9 (chunk 16/31) : 56368
+Total time elapsed: 141.70 s
+
+real	2m25.563s
+user	26m45.350s
+sys	3m12.482s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19
+[INFO] Total heterozygous SNP positions selected: chr9: 77791
+
+real	0m1.682s
+user	0m1.459s
+sys	0m0.151s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr9.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr9
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr9,45s)
+parsing total:  45s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 48s
+
+real	0m47.622s
+user	1m39.107s
+sys	0m6.712s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 22.0
+[INFO] Set reference calls quality cutoff 8.0
+[INFO] Low quality reference calls to be processed in chr9: 19049
+[INFO] Low quality variants to be processed in chr9: 171149
+
+real	0m1.655s
+user	0m1.429s
+sys	0m0.187s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr9 (chunk 20/20) : 198
+Total time elapsed: 5.14 s
+Calling variants ...
+Total processed positions in chr9 (chunk 9/20) : 10000
+Total time elapsed: 103.97 s
+Calling variants ...
+Total processed positions in chr9 (chunk 6/20) : 10000
+Total time elapsed: 106.05 s
+Calling variants ...
+Total processed positions in chr9 (chunk 1/20) : 10000
+Total time elapsed: 108.09 s
+Calling variants ...
+Total processed positions in chr9 (chunk 8/20) : 10000
+Total time elapsed: 109.62 s
+Calling variants ...
+Total processed positions in chr9 (chunk 2/20) : 10000
+Total time elapsed: 112.64 s
+Calling variants ...
+Total processed positions in chr9 (chunk 3/20) : 10000
+Total time elapsed: 115.34 s
+Calling variants ...
+Total processed positions in chr9 (chunk 19/20) : 10000
+Total time elapsed: 118.04 s
+Calling variants ...
+Total processed positions in chr9 (chunk 13/20) : 10000
+Total time elapsed: 118.74 s
+Calling variants ...
+Total processed positions in chr9 (chunk 17/20) : 10000
+Total time elapsed: 119.76 s
+Calling variants ...
+Total processed positions in chr9 (chunk 10/20) : 10000
+Total time elapsed: 119.63 s
+Calling variants ...
+Total processed positions in chr9 (chunk 14/20) : 10000
+Total time elapsed: 120.51 s
+Calling variants ...
+Total processed positions in chr9 (chunk 7/20) : 10000
+Total time elapsed: 121.34 s
+Calling variants ...
+Total processed positions in chr9 (chunk 15/20) : 10000
+Total time elapsed: 123.04 s
+Calling variants ...
+Total processed positions in chr9 (chunk 18/20) : 10000
+Total time elapsed: 123.50 s
+Calling variants ...
+Total processed positions in chr9 (chunk 4/20) : 10000
+Total time elapsed: 125.47 s
+Calling variants ...
+Total processed positions in chr9 (chunk 12/20) : 10000
+Total time elapsed: 131.99 s
+Calling variants ...
+Total processed positions in chr9 (chunk 16/20) : 10000
+Total time elapsed: 134.56 s
+Calling variants ...
+Total processed positions in chr9 (chunk 11/20) : 10000
+Total time elapsed: 139.32 s
+Calling variants ...
+Total processed positions in chr9 (chunk 5/20) : 10000
+Total time elapsed: 155.07 s
+
+real	2m38.507s
+user	35m49.457s
+sys	1m53.587s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr9: 73865
+[INFO] Full-alignment variants processed in chr9: 160201
+
+real	0m2.867s
+user	0m2.939s
+sys	0m0.181s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	6m8.256s
+user	64m28.253s
+sys	5m14.468s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr9: 107191, not found:2348, not match:108, low_qual_count:0. Total normal:119728 Total tumor:109647, pro: 0.9776
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf/chr9.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_chr9
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr9,49s)
+parsing total:  49s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 52s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_chr9.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_chr9.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr9
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 1s
+tag read start ...
+chr: chr9 ... 1322s
+tag read 1325s
+-------------------------------------------
+total process time:  1326s
+total alignment:     1870680
+total supplementary: 62722
+total secondary:     0
+total unmapped:      0
+total tag alignment: 709540
+total untagged:      1161140
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr9 chunk 0/31: Total snv candidates found: 74, total indel candidates found: 46
+[INFO] chr9 chunk 1/31: Total snv candidates found: 1194, total indel candidates found: 371
+[INFO] chr9 chunk 4/31: Total snv candidates found: 656, total indel candidates found: 215

slurm-2557979.out

@@ -0,0 +1,964 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20 --region chr2:1-113845111 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr2
+[INFO] Number of chunks for each contig: 49
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr2:1-113845111
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output --ctg_name=chr2 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr2
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr2 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr2
+[INFO] Chunk number for each contig: 49
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr2 (chunk 13/49) : 75269
+Total time elapsed: 199.75 s
+Calling variants ...
+Total processed positions in chr2 (chunk 17/49) : 71352
+Total time elapsed: 202.02 s
+Calling variants ...
+Total processed positions in chr2 (chunk 30/49) : 73373
+Total time elapsed: 202.96 s
+Calling variants ...
+Total processed positions in chr2 (chunk 20/49) : 75043
+Total time elapsed: 203.11 s
+Calling variants ...
+Total processed positions in chr2 (chunk 11/49) : 74661
+Total time elapsed: 209.92 s
+Calling variants ...
+Total processed positions in chr2 (chunk 8/49) : 80441
+Total time elapsed: 210.76 s
+Calling variants ...
+Total processed positions in chr2 (chunk 9/49) : 81596
+Total time elapsed: 211.37 s
+Calling variants ...
+Total processed positions in chr2 (chunk 6/49) : 79351
+Total time elapsed: 212.10 s
+Calling variants ...
+Total processed positions in chr2 (chunk 10/49) : 82733
+Total time elapsed: 212.80 s
+Calling variants ...
+Total processed positions in chr2 (chunk 1/49) : 80838
+Total time elapsed: 214.27 s
+Calling variants ...
+Total processed positions in chr2 (chunk 29/49) : 76038
+Total time elapsed: 214.57 s
+Calling variants ...
+Total processed positions in chr2 (chunk 24/49) : 79088
+Total time elapsed: 215.10 s
+Calling variants ...
+Total processed positions in chr2 (chunk 16/49) : 81038
+Total time elapsed: 215.99 s
+Calling variants ...
+Total processed positions in chr2 (chunk 23/49) : 82668
+Total time elapsed: 216.47 s
+Calling variants ...
+Total processed positions in chr2 (chunk 27/49) : 83387
+Total time elapsed: 216.81 s
+Calling variants ...
+Total processed positions in chr2 (chunk 18/49) : 80235
+Total time elapsed: 219.85 s
+Calling variants ...
+Total processed positions in chr2 (chunk 22/49) : 80277
+Total time elapsed: 224.08 s
+Calling variants ...
+Total processed positions in chr2 (chunk 4/49) : 83480
+Total time elapsed: 224.07 s
+Calling variants ...
+Total processed positions in chr2 (chunk 14/49) : 81970
+Total time elapsed: 224.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 19/49) : 75283
+Total time elapsed: 225.15 s
+Calling variants ...
+Total processed positions in chr2 (chunk 2/49) : 84106
+Total time elapsed: 227.83 s
+Calling variants ...
+Total processed positions in chr2 (chunk 21/49) : 81835
+Total time elapsed: 229.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 26/49) : 84734
+Total time elapsed: 231.67 s
+Calling variants ...
+Total processed positions in chr2 (chunk 28/49) : 75612
+Total time elapsed: 201.90 s
+Calling variants ...
+Total processed positions in chr2 (chunk 3/49) : 86183
+Total time elapsed: 233.85 s
+Calling variants ...
+Total processed positions in chr2 (chunk 12/49) : 82008
+Total time elapsed: 206.01 s
+Calling variants ...
+Total processed positions in chr2 (chunk 25/49) : 84883
+Total time elapsed: 209.79 s
+Calling variants ...
+Total processed positions in chr2 (chunk 5/49) : 83721
+Total time elapsed: 210.17 s
+Calling variants ...
+Total processed positions in chr2 (chunk 15/49) : 87963
+Total time elapsed: 213.68 s
+Calling variants ...
+Total processed positions in chr2 (chunk 7/49) : 88857
+Total time elapsed: 217.49 s
+Calling variants ...
+Total processed positions in chr2 (chunk 31/49) : 73402
+Total time elapsed: 151.18 s
+Calling variants ...
+Total processed positions in chr2 (chunk 40/49) : 70806
+Total time elapsed: 138.01 s
+Calling variants ...
+Total processed positions in chr2 (chunk 37/49) : 75613
+Total time elapsed: 142.20 s
+Calling variants ...
+Total processed positions in chr2 (chunk 32/49) : 71337
+Total time elapsed: 152.09 s
+Calling variants ...
+Total processed positions in chr2 (chunk 47/49) : 74017
+Total time elapsed: 134.36 s
+Calling variants ...
+Total processed positions in chr2 (chunk 42/49) : 75734
+Total time elapsed: 144.37 s
+Calling variants ...
+Total processed positions in chr2 (chunk 39/49) : 79011
+Total time elapsed: 149.41 s
+Calling variants ...
+Total processed positions in chr2 (chunk 36/49) : 84088
+Total time elapsed: 153.45 s
+Calling variants ...
+Total processed positions in chr2 (chunk 38/49) : 73991
+Total time elapsed: 154.35 s
+Calling variants ...
+Total processed positions in chr2 (chunk 33/49) : 82305
+Total time elapsed: 164.60 s
+Calling variants ...
+Total processed positions in chr2 (chunk 41/49) : 80990
+Total time elapsed: 153.46 s
+Calling variants ...
+Total processed positions in chr2 (chunk 34/49) : 79400
+Total time elapsed: 166.04 s
+Calling variants ...
+Total processed positions in chr2 (chunk 44/49) : 75892
+Total time elapsed: 155.48 s
+Calling variants ...
+Total processed positions in chr2 (chunk 48/49) : 83848
+Total time elapsed: 152.05 s
+Calling variants ...
+Total processed positions in chr2 (chunk 35/49) : 84506
+Total time elapsed: 167.45 s
+Calling variants ...
+Total processed positions in chr2 (chunk 43/49) : 78010
+Total time elapsed: 162.44 s
+Calling variants ...
+Total processed positions in chr2 (chunk 46/49) : 81534
+Total time elapsed: 162.72 s
+Calling variants ...
+Total processed positions in chr2 (chunk 45/49) : 86558
+Total time elapsed: 175.83 s
+Calling variants ...
+Total processed positions in chr2 (chunk 49/49) : 92842
+Total time elapsed: 181.53 s
+
+real	6m56.137s
+user	148m38.462s
+sys	7m29.296s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16
+[INFO] Total heterozygous SNP positions selected: chr2: 150142
+
+real	0m5.569s
+user	0m5.216s
+sys	0m0.241s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr2.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr2
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr2,16s)
+parsing total:  16s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 18s
+
+real	0m18.252s
+user	0m39.624s
+sys	0m2.736s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 20.0
+[INFO] Set reference calls quality cutoff 14.0
+[INFO] Low quality reference calls to be processed in chr2: 351297
+[INFO] Low quality variants to be processed in chr2: 282859
+
+real	0m6.395s
+user	0m5.824s
+sys	0m0.430s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr2 (chunk 19/64) : 10000
+Total time elapsed: 136.19 s
+Calling variants ...
+Total processed positions in chr2 (chunk 9/64) : 10000
+Total time elapsed: 136.95 s
+Calling variants ...
+Total processed positions in chr2 (chunk 30/64) : 10000
+Total time elapsed: 141.06 s
+Calling variants ...
+Total processed positions in chr2 (chunk 17/64) : 10000
+Total time elapsed: 142.38 s
+Calling variants ...
+Total processed positions in chr2 (chunk 6/64) : 10000
+Total time elapsed: 142.84 s
+Calling variants ...
+Total processed positions in chr2 (chunk 16/64) : 10000
+Total time elapsed: 145.46 s
+Calling variants ...
+Total processed positions in chr2 (chunk 10/64) : 10000
+Total time elapsed: 145.78 s
+Calling variants ...
+Total processed positions in chr2 (chunk 21/64) : 10000
+Total time elapsed: 145.87 s
+Calling variants ...
+Total processed positions in chr2 (chunk 2/64) : 10000
+Total time elapsed: 146.26 s
+Calling variants ...
+Total processed positions in chr2 (chunk 11/64) : 10000
+Total time elapsed: 146.61 s
+Calling variants ...
+Total processed positions in chr2 (chunk 28/64) : 10000
+Total time elapsed: 147.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 3/64) : 10000
+Total time elapsed: 148.00 s
+Calling variants ...
+Total processed positions in chr2 (chunk 5/64) : 10000
+Total time elapsed: 148.47 s
+Calling variants ...
+Total processed positions in chr2 (chunk 27/64) : 10000
+Total time elapsed: 149.41 s
+Calling variants ...
+Total processed positions in chr2 (chunk 7/64) : 10000
+Total time elapsed: 149.28 s
+Calling variants ...
+Total processed positions in chr2 (chunk 29/64) : 10000
+Total time elapsed: 149.50 s
+Calling variants ...
+Total processed positions in chr2 (chunk 26/64) : 10000
+Total time elapsed: 149.59 s
+Calling variants ...
+Total processed positions in chr2 (chunk 18/64) : 10000
+Total time elapsed: 150.10 s
+Calling variants ...
+Total processed positions in chr2 (chunk 8/64) : 10000
+Total time elapsed: 151.30 s
+Calling variants ...
+Total processed positions in chr2 (chunk 23/64) : 10000
+Total time elapsed: 152.13 s
+Calling variants ...
+Total processed positions in chr2 (chunk 4/64) : 10000
+Total time elapsed: 153.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 25/64) : 10000
+Total time elapsed: 154.11 s
+Calling variants ...
+Total processed positions in chr2 (chunk 15/64) : 10000
+Total time elapsed: 153.49 s
+Calling variants ...
+Total processed positions in chr2 (chunk 12/64) : 10000
+Total time elapsed: 154.56 s
+Calling variants ...
+Total processed positions in chr2 (chunk 20/64) : 10000
+Total time elapsed: 154.74 s
+Calling variants ...
+Total processed positions in chr2 (chunk 22/64) : 10000
+Total time elapsed: 156.87 s
+Calling variants ...
+Total processed positions in chr2 (chunk 14/64) : 10000
+Total time elapsed: 157.18 s
+Calling variants ...
+Total processed positions in chr2 (chunk 13/64) : 10000
+Total time elapsed: 158.06 s
+Calling variants ...
+Total processed positions in chr2 (chunk 24/64) : 10000
+Total time elapsed: 159.71 s
+Calling variants ...
+Total processed positions in chr2 (chunk 1/64) : 10000
+Total time elapsed: 162.45 s
+Calling variants ...
+Total processed positions in chr2 (chunk 31/64) : 10000
+Total time elapsed: 139.95 s
+Calling variants ...
+Total processed positions in chr2 (chunk 32/64) : 10000
+Total time elapsed: 149.41 s
+Calling variants ...
+Total processed positions in chr2 (chunk 44/64) : 10000
+Total time elapsed: 140.36 s
+Calling variants ...
+Total processed positions in chr2 (chunk 41/64) : 10000
+Total time elapsed: 142.69 s
+Calling variants ...
+Total processed positions in chr2 (chunk 49/64) : 10000
+Total time elapsed: 140.69 s
+Calling variants ...
+Total processed positions in chr2 (chunk 56/64) : 10000
+Total time elapsed: 134.70 s
+Calling variants ...
+Total processed positions in chr2 (chunk 45/64) : 10000
+Total time elapsed: 141.91 s
+Calling variants ...
+Total processed positions in chr2 (chunk 38/64) : 10000
+Total time elapsed: 147.31 s
+Calling variants ...
+Total processed positions in chr2 (chunk 37/64) : 10000
+Total time elapsed: 148.15 s
+Calling variants ...
+Total processed positions in chr2 (chunk 42/64) : 10000
+Total time elapsed: 144.90 s
+Calling variants ...
+Total processed positions in chr2 (chunk 50/64) : 10000
+Total time elapsed: 143.17 s
+Calling variants ...
+Total processed positions in chr2 (chunk 35/64) : 10000
+Total time elapsed: 153.02 s
+Calling variants ...
+Total processed positions in chr2 (chunk 51/64) : 10000
+Total time elapsed: 142.60 s
+Calling variants ...
+Total processed positions in chr2 (chunk 46/64) : 10000
+Total time elapsed: 147.12 s
+Calling variants ...
+Total processed positions in chr2 (chunk 52/64) : 10000
+Total time elapsed: 145.77 s
+Calling variants ...
+Total processed positions in chr2 (chunk 57/64) : 10000
+Total time elapsed: 142.08 s
+Calling variants ...
+Total processed positions in chr2 (chunk 33/64) : 10000
+Total time elapsed: 158.96 s
+Calling variants ...
+Total processed positions in chr2 (chunk 59/64) : 10000
+Total time elapsed: 140.68 s
+Calling variants ...
+Total processed positions in chr2 (chunk 53/64) : 10000
+Total time elapsed: 146.33 s
+Calling variants ...
+Total processed positions in chr2 (chunk 39/64) : 10000
+Total time elapsed: 154.28 s
+Calling variants ...
+Total processed positions in chr2 (chunk 36/64) : 10000
+Total time elapsed: 154.64 s
+Calling variants ...
+Total processed positions in chr2 (chunk 40/64) : 10000
+Total time elapsed: 153.95 s
+Calling variants ...
+Total processed positions in chr2 (chunk 34/64) : 10000
+Total time elapsed: 158.39 s
+Calling variants ...
+Total processed positions in chr2 (chunk 55/64) : 10000
+Total time elapsed: 146.24 s
+Calling variants ...
+Total processed positions in chr2 (chunk 58/64) : 10000
+Total time elapsed: 143.60 s
+Calling variants ...
+Total processed positions in chr2 (chunk 48/64) : 10000
+Total time elapsed: 151.82 s
+Calling variants ...
+Total processed positions in chr2 (chunk 43/64) : 10000
+Total time elapsed: 154.28 s
+Calling variants ...
+Total processed positions in chr2 (chunk 47/64) : 10000
+Total time elapsed: 155.12 s
+Calling variants ...
+Total processed positions in chr2 (chunk 54/64) : 10000
+Total time elapsed: 152.51 s
+Calling variants ...
+Total processed positions in chr2 (chunk 60/64) : 10000
+Total time elapsed: 147.03 s
+Calling variants ...
+Total processed positions in chr2 (chunk 64/64) : 4156
+Total time elapsed: 40.98 s
+Calling variants ...
+Total processed positions in chr2 (chunk 61/64) : 10000
+Total time elapsed: 96.41 s
+Calling variants ...
+Total processed positions in chr2 (chunk 62/64) : 10000
+Total time elapsed: 90.96 s
+Calling variants ...
+Total processed positions in chr2 (chunk 63/64) : 10000
+Total time elapsed: 91.35 s
+
+real	6m32.438s
+user	149m33.204s
+sys	6m35.289s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr2: 121260
+[INFO] Full-alignment variants processed in chr2: 298027
+
+real	0m7.682s
+user	0m8.986s
+sys	0m0.390s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	14m39.872s
+user	299m42.740s
+sys	14m11.207s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output --ctg_name=chr2 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr2
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr2 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr2
+[INFO] Chunk number for each contig: 49
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr2 (chunk 17/49) : 7627
+Total time elapsed: 101.22 s
+Calling variants ...
+Total processed positions in chr2 (chunk 5/49) : 8455
+Total time elapsed: 103.54 s
+Calling variants ...
+Total processed positions in chr2 (chunk 21/49) : 9171
+Total time elapsed: 104.85 s
+Calling variants ...
+Total processed positions in chr2 (chunk 6/49) : 9236
+Total time elapsed: 104.97 s
+Calling variants ...
+Total processed positions in chr2 (chunk 23/49) : 8909
+Total time elapsed: 105.24 s
+Calling variants ...
+Total processed positions in chr2 (chunk 22/49) : 9821
+Total time elapsed: 106.19 s
+Calling variants ...
+Total processed positions in chr2 (chunk 24/49) : 9129
+Total time elapsed: 106.40 s
+Calling variants ...
+Total processed positions in chr2 (chunk 29/49) : 10495
+Total time elapsed: 108.59 s
+Calling variants ...
+Total processed positions in chr2 (chunk 18/49) : 11980
+Total time elapsed: 108.93 s
+Calling variants ...
+Total processed positions in chr2 (chunk 7/49) : 11591
+Total time elapsed: 109.33 s
+Calling variants ...
+Total processed positions in chr2 (chunk 11/49) : 11806
+Total time elapsed: 109.32 s
+Calling variants ...
+Total processed positions in chr2 (chunk 4/49) : 10602
+Total time elapsed: 109.98 s
+Calling variants ...
+Total processed positions in chr2 (chunk 26/49) : 11900
+Total time elapsed: 112.11 s
+Calling variants ...
+Total processed positions in chr2 (chunk 12/49) : 12287
+Total time elapsed: 112.73 s
+Calling variants ...
+Total processed positions in chr2 (chunk 3/49) : 13938
+Total time elapsed: 114.59 s
+Calling variants ...
+Total processed positions in chr2 (chunk 27/49) : 14692
+Total time elapsed: 115.74 s
+Calling variants ...
+Total processed positions in chr2 (chunk 20/49) : 24047
+Total time elapsed: 131.50 s
+Calling variants ...
+Total processed positions in chr2 (chunk 28/49) : 7473
+Total time elapsed: 66.78 s
+Calling variants ...
+Total processed positions in chr2 (chunk 9/49) : 10082
+Total time elapsed: 69.67 s
+Calling variants ...
+Total processed positions in chr2 (chunk 2/49) : 10653
+Total time elapsed: 71.83 s
+Calling variants ...
+Total processed positions in chr2 (chunk 13/49) : 10312
+Total time elapsed: 73.61 s
+Calling variants ...
+Total processed positions in chr2 (chunk 16/49) : 11769
+Total time elapsed: 76.02 s
+Calling variants ...
+Total processed positions in chr2 (chunk 15/49) : 11490
+Total time elapsed: 77.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 14/49) : 12324
+Total time elapsed: 76.89 s
+Calling variants ...
+Total processed positions in chr2 (chunk 8/49) : 13128
+Total time elapsed: 77.71 s
+Calling variants ...
+Total processed positions in chr2 (chunk 31/49) : 7977
+Total time elapsed: 61.62 s
+Calling variants ...
+Total processed positions in chr2 (chunk 1/49) : 15284
+Total time elapsed: 81.62 s
+Calling variants ...
+Total processed positions in chr2 (chunk 36/49) : 9813
+Total time elapsed: 64.59 s
+Calling variants ...
+Total processed positions in chr2 (chunk 34/49) : 10438
+Total time elapsed: 66.29 s
+Calling variants ...
+Total processed positions in chr2 (chunk 37/49) : 9564
+Total time elapsed: 64.73 s
+Calling variants ...
+Total processed positions in chr2 (chunk 39/49) : 7943
+Total time elapsed: 62.60 s
+Calling variants ...
+Total processed positions in chr2 (chunk 44/49) : 8253
+Total time elapsed: 58.74 s
+Calling variants ...
+Total processed positions in chr2 (chunk 35/49) : 11348
+Total time elapsed: 67.32 s
+Calling variants ...
+Total processed positions in chr2 (chunk 38/49) : 8387
+Total time elapsed: 63.79 s
+Calling variants ...
+Total processed positions in chr2 (chunk 42/49) : 9050
+Total time elapsed: 63.53 s
+Calling variants ...
+Total processed positions in chr2 (chunk 41/49) : 9364
+Total time elapsed: 64.39 s
+Calling variants ...
+Total processed positions in chr2 (chunk 43/49) : 9185
+Total time elapsed: 62.50 s
+Calling variants ...
+Total processed positions in chr2 (chunk 46/49) : 10647
+Total time elapsed: 61.22 s
+Calling variants ...
+Total processed positions in chr2 (chunk 45/49) : 9880
+Total time elapsed: 62.34 s
+Calling variants ...
+Total processed positions in chr2 (chunk 30/49) : 6472
+Total time elapsed: 50.40 s
+Calling variants ...
+Total processed positions in chr2 (chunk 25/49) : 10438
+Total time elapsed: 54.55 s
+Calling variants ...
+Total processed positions in chr2 (chunk 47/49) : 11754
+Total time elapsed: 56.15 s
+Calling variants ...
+Total processed positions in chr2 (chunk 10/49) : 12602
+Total time elapsed: 57.65 s
+Calling variants ...
+Total processed positions in chr2 (chunk 32/49) : 8410
+Total time elapsed: 45.98 s
+Calling variants ...
+Total processed positions in chr2 (chunk 33/49) : 10165
+Total time elapsed: 49.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 40/49) : 8407
+Total time elapsed: 44.81 s
+Calling variants ...
+Total processed positions in chr2 (chunk 48/49) : 12378
+Total time elapsed: 48.29 s
+Calling variants ...
+Total processed positions in chr2 (chunk 19/49) : 64666
+Total time elapsed: 214.06 s
+Calling variants ...
+Total processed positions in chr2 (chunk 49/49) : 16414
+Total time elapsed: 54.77 s
+
+real	3m38.990s
+user	49m2.698s
+sys	12m29.771s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 20
+[INFO] Total heterozygous SNP positions selected: chr2: 154655
+
+real	0m1.575s
+user	0m1.297s
+sys	0m0.177s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr2.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr2
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr2,60s)
+parsing total:  60s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 63s
+
+real	1m3.199s
+user	3m4.039s
+sys	0m11.635s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 22.0
+[INFO] Set reference calls quality cutoff 7.0
+[INFO] Low quality reference calls to be processed in chr2: 18408
+[INFO] Low quality variants to be processed in chr2: 277651
+
+real	0m1.581s
+user	0m1.339s
+sys	0m0.173s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr2 (chunk 30/30) : 6059
+Total time elapsed: 102.23 s
+Calling variants ...
+Total processed positions in chr2 (chunk 13/30) : 10000
+Total time elapsed: 154.87 s
+Calling variants ...
+Total processed positions in chr2 (chunk 2/30) : 10000
+Total time elapsed: 176.62 s
+Calling variants ...
+Total processed positions in chr2 (chunk 29/30) : 10000
+Total time elapsed: 177.89 s
+Calling variants ...
+Total processed positions in chr2 (chunk 14/30) : 10000
+Total time elapsed: 180.12 s
+Calling variants ...
+Total processed positions in chr2 (chunk 25/30) : 10000
+Total time elapsed: 181.74 s
+Calling variants ...
+Total processed positions in chr2 (chunk 3/30) : 10000
+Total time elapsed: 182.47 s
+Calling variants ...
+Total processed positions in chr2 (chunk 11/30) : 10000
+Total time elapsed: 185.54 s
+Calling variants ...
+Total processed positions in chr2 (chunk 9/30) : 10000
+Total time elapsed: 186.85 s
+Calling variants ...
+Total processed positions in chr2 (chunk 6/30) : 10000
+Total time elapsed: 186.98 s
+Calling variants ...
+Total processed positions in chr2 (chunk 18/30) : 10000
+Total time elapsed: 186.71 s
+Calling variants ...
+Total processed positions in chr2 (chunk 5/30) : 10000
+Total time elapsed: 187.14 s
+Calling variants ...
+Total processed positions in chr2 (chunk 23/30) : 10000
+Total time elapsed: 189.44 s
+Calling variants ...
+Total processed positions in chr2 (chunk 22/30) : 10000
+Total time elapsed: 189.09 s
+Calling variants ...
+Total processed positions in chr2 (chunk 15/30) : 10000
+Total time elapsed: 189.34 s
+Calling variants ...
+Total processed positions in chr2 (chunk 16/30) : 10000
+Total time elapsed: 189.71 s
+Calling variants ...
+Total processed positions in chr2 (chunk 28/30) : 10000
+Total time elapsed: 190.87 s
+Calling variants ...
+Total processed positions in chr2 (chunk 7/30) : 10000
+Total time elapsed: 191.68 s
+Calling variants ...
+Total processed positions in chr2 (chunk 12/30) : 10000
+Total time elapsed: 190.92 s
+Calling variants ...
+Total processed positions in chr2 (chunk 19/30) : 10000
+Total time elapsed: 192.52 s
+Calling variants ...
+Total processed positions in chr2 (chunk 8/30) : 10000
+Total time elapsed: 193.53 s
+Calling variants ...
+Total processed positions in chr2 (chunk 10/30) : 10000
+Total time elapsed: 194.41 s
+Calling variants ...
+Total processed positions in chr2 (chunk 17/30) : 10000
+Total time elapsed: 196.52 s
+Calling variants ...
+Total processed positions in chr2 (chunk 1/30) : 10000
+Total time elapsed: 198.59 s
+Calling variants ...
+Total processed positions in chr2 (chunk 24/30) : 10000
+Total time elapsed: 198.82 s
+Calling variants ...
+Total processed positions in chr2 (chunk 4/30) : 10000
+Total time elapsed: 200.41 s
+Calling variants ...
+Total processed positions in chr2 (chunk 27/30) : 10000
+Total time elapsed: 203.01 s
+Calling variants ...
+Total processed positions in chr2 (chunk 20/30) : 10000
+Total time elapsed: 202.15 s
+Calling variants ...
+Total processed positions in chr2 (chunk 26/30) : 10000
+Total time elapsed: 204.48 s
+Calling variants ...
+Total processed positions in chr2 (chunk 21/30) : 10000
+Total time elapsed: 206.71 s
+
+real	3m31.628s
+user	86m24.557s
+sys	3m59.700s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr2: 119513
+[INFO] Full-alignment variants processed in chr2: 256477
+
+real	0m2.788s
+user	0m2.943s
+sys	0m0.205s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	8m30.472s
+user	138m45.707s
+sys	16m43.041s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr2: 199643, not found:792, not match:54, low_qual_count:0. Total normal:208641 Total tumor:200489, pro: 0.9958
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/vcf/chr2.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_phased_chr2
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr2,93s)
+parsing total:  93s
+merge results ... 1s
+writeResult SNP ... 1s
+
+total process: 97s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS
+

slurm-2557980.out

@@ -0,0 +1,632 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44 --region chrY:1-62460029 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chrY
+[INFO] Number of chunks for each contig: 13
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chrY:1-62460029
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output --ctg_name=chrY --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chrY
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chrY --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chrY
+[INFO] Chunk number for each contig: 13
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chrY (chunk 10/13) : 2510
+Total time elapsed: 14.69 s
+Calling variants ...
+Total processed positions in chrY (chunk 8/13) : 3198
+Total time elapsed: 15.01 s
+Calling variants ...
+Total processed positions in chrY (chunk 9/13) : 5363
+Total time elapsed: 19.82 s
+Calling variants ...
+Total processed positions in chrY (chunk 7/13) : 13555
+Total time elapsed: 31.66 s
+Calling variants ...
+Total processed positions in chrY (chunk 13/13) : 20440
+Total time elapsed: 40.73 s
+Calling variants ...
+Total processed positions in chrY (chunk 12/13) : 19252
+Total time elapsed: 41.61 s
+Calling variants ...
+Total processed positions in chrY (chunk 6/13) : 20091
+Total time elapsed: 46.89 s
+Calling variants ...
+Total processed positions in chrY (chunk 11/13) : 23275
+Total time elapsed: 48.80 s
+Calling variants ...
+Total processed positions in chrY (chunk 4/13) : 37911
+Total time elapsed: 64.24 s
+Calling variants ...
+Total processed positions in chrY (chunk 5/13) : 36533
+Total time elapsed: 65.91 s
+Calling variants ...
+Total processed positions in chrY (chunk 3/13) : 38723
+Total time elapsed: 66.37 s
+Calling variants ...
+Total processed positions in chrY (chunk 2/13) : 43770
+Total time elapsed: 72.50 s
+Calling variants ...
+Total processed positions in chrY (chunk 1/13) : 47658
+Total time elapsed: 80.74 s
+
+real	1m26.989s
+user	9m48.882s
+sys	0m30.243s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 11
+[INFO] Total heterozygous SNP positions selected: chrY: 21687
+
+real	0m0.762s
+user	0m0.656s
+sys	0m0.088s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chrY.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chrY
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chrY,3s)
+parsing total:  3s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 3s
+
+real	0m3.472s
+user	0m8.235s
+sys	0m0.764s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 17.0
+[INFO] Set reference calls quality cutoff 11.0
+[INFO] Low quality reference calls to be processed in chrY: 26213
+[INFO] Low quality variants to be processed in chrY: 34866
+
+real	0m0.792s
+user	0m0.667s
+sys	0m0.106s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chrY (chunk 7/7) : 1079
+Total time elapsed: 11.23 s
+Calling variants ...
+Total processed positions in chrY (chunk 2/7) : 10000
+Total time elapsed: 91.05 s
+Calling variants ...
+Total processed positions in chrY (chunk 1/7) : 10000
+Total time elapsed: 91.43 s
+Calling variants ...
+Total processed positions in chrY (chunk 3/7) : 10000
+Total time elapsed: 92.16 s
+Calling variants ...
+Total processed positions in chrY (chunk 5/7) : 10000
+Total time elapsed: 92.18 s
+Calling variants ...
+Total processed positions in chrY (chunk 4/7) : 10000
+Total time elapsed: 93.21 s
+Calling variants ...
+Total processed positions in chrY (chunk 6/7) : 10000
+Total time elapsed: 93.30 s
+
+real	1m35.777s
+user	9m8.817s
+sys	0m28.111s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chrY: 14986
+[INFO] Full-alignment variants processed in chrY: 38380
+
+real	0m1.052s
+user	0m1.067s
+sys	0m0.117s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	3m13.768s
+user	19m12.062s
+sys	1m0.250s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output --ctg_name=chrY --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chrY
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chrY --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chrY
+[INFO] Chunk number for each contig: 13
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chrY (chunk 8/13) : 7329
+Total time elapsed: 39.08 s
+Calling variants ...
+Total processed positions in chrY (chunk 4/13) : 9532
+Total time elapsed: 43.30 s
+Calling variants ...
+Total processed positions in chrY (chunk 2/13) : 7989
+Total time elapsed: 44.10 s
+Calling variants ...
+Total processed positions in chrY (chunk 10/13) : 9348
+Total time elapsed: 46.20 s
+Calling variants ...
+Total processed positions in chrY (chunk 9/13) : 13536
+Total time elapsed: 51.94 s
+Calling variants ...
+Total processed positions in chrY (chunk 5/13) : 15812
+Total time elapsed: 52.23 s
+Calling variants ...
+Total processed positions in chrY (chunk 3/13) : 16514
+Total time elapsed: 54.48 s
+Calling variants ...
+Total processed positions in chrY (chunk 7/13) : 20564
+Total time elapsed: 59.94 s
+Calling variants ...
+Total processed positions in chrY (chunk 13/13) : 23851
+Total time elapsed: 66.40 s
+Calling variants ...
+Total processed positions in chrY (chunk 1/13) : 25344
+Total time elapsed: 67.41 s
+Calling variants ...
+Total processed positions in chrY (chunk 6/13) : 27005
+Total time elapsed: 70.73 s
+Calling variants ...
+Total processed positions in chrY (chunk 12/13) : 27326
+Total time elapsed: 75.58 s
+Calling variants ...
+Total processed positions in chrY (chunk 11/13) : 32618
+Total time elapsed: 80.59 s
+
+real	1m23.256s
+user	9m43.700s
+sys	0m39.007s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 12
+[INFO] Total heterozygous SNP positions selected: chrY: 31855
+
+real	0m0.720s
+user	0m0.592s
+sys	0m0.097s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chrY.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chrY
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chrY,13s)
+parsing total:  13s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 14s
+
+real	0m13.758s
+user	0m41.538s
+sys	0m2.887s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 20.0
+[INFO] Set reference calls quality cutoff 10.0
+[INFO] Low quality reference calls to be processed in chrY: 15293
+[INFO] Low quality variants to be processed in chrY: 58497
+
+real	0m0.761s
+user	0m0.602s
+sys	0m0.098s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chrY (chunk 8/8) : 3790
+Total time elapsed: 41.07 s
+Calling variants ...
+Total processed positions in chrY (chunk 3/8) : 10000
+Total time elapsed: 100.57 s
+Calling variants ...
+Total processed positions in chrY (chunk 5/8) : 10000
+Total time elapsed: 102.89 s
+Calling variants ...
+Total processed positions in chrY (chunk 6/8) : 10000
+Total time elapsed: 103.29 s
+Calling variants ...
+Total processed positions in chrY (chunk 7/8) : 10000
+Total time elapsed: 103.39 s
+Calling variants ...
+Total processed positions in chrY (chunk 1/8) : 10000
+Total time elapsed: 110.52 s
+Calling variants ...
+Total processed positions in chrY (chunk 4/8) : 10000
+Total time elapsed: 111.71 s
+Calling variants ...
+Total processed positions in chrY (chunk 2/8) : 10000
+Total time elapsed: 113.96 s
+
+real	1m56.455s
+user	12m24.097s
+sys	0m37.720s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chrY: 25148
+[INFO] Full-alignment variants processed in chrY: 60787
+
+real	0m1.113s
+user	0m1.054s
+sys	0m0.123s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	3m40.589s
+user	22m55.153s
+sys	1m20.559s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chrY: 51398, not found:568, not match:45, low_qual_count:0. Total normal:36068 Total tumor:52011, pro: 0.9882
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/vcf/chrY.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_chrY
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chrY,23s)
+parsing total:  23s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 23s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_chrY.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_chrY.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chrY
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 0s
+tag read start ...
+chr: chrY ... 723s
+tag read 724s
+-------------------------------------------
+total process time:  724s
+total alignment:     1029125
+total supplementary: 12705
+total secondary:     0
+total unmapped:      0
+total tag alignment: 118794
+total untagged:      910331
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chrY chunk 7/13: Total snv candidates found: 761, total indel candidates found: 37
+[INFO] chrY chunk 9/13: Total snv candidates found: 309, total indel candidates found: 16
+[INFO] chrY chunk 8/13: Total snv candidates found: 821, total indel candidates found: 52
+[INFO] chrY chunk 6/13: Total snv candidates found: 3048, total indel candidates found: 258
+[INFO] chrY chunk 5/13: Total snv candidates found: 2009, total indel candidates found: 445
+[INFO] chrY chunk 11/13: Total snv candidates found: 4319, total indel candidates found: 270
+[INFO] chrY chunk 12/13: Total snv candidates found: 5416, total indel candidates found: 610
+[faidx] Truncated sequence: chrY:57654453-62461074
+[INFO] chrY chunk 10/13: Total snv candidates found: 5980, total indel candidates found: 374
+[INFO] chrY chunk 4/13: Total snv candidates found: 2127, total indel candidates found: 1355
+[INFO] chrY chunk 0/13: Total snv candidates found: 4192, total indel candidates found: 3001
+[INFO] chrY chunk 2/13: Total snv candidates found: 2871, total indel candidates found: 1731
+[INFO] chrY chunk 3/13: Total snv candidates found: 357, total indel candidates found: 1566
+[INFO] chrY chunk 1/13: Total snv candidates found: 421, total indel candidates found: 1763
+
+[INFO] STEP 2: Pileup Model Calling
+[INFO] Create Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/2-1_CPT.log
+
+[INFO] chrY chunk 1-1/3 Tensors generated: 352
+[INFO] chrY chunk 1-1/1 Tensors generated: 405
+[INFO] chrY chunk 1-1/7 Tensors generated: 758
+[INFO] chrY chunk 1-1/9 Tensors generated: 309
+[INFO] chrY chunk 1-1/8 Tensors generated: 812
+[INFO] chrY chunk 1-1/2 Tensors generated: 2762
+[INFO] chrY chunk 1-1/5 Tensors generated: 1950
+[INFO] chrY chunk 1-1/0 Tensors generated: 4115
+[INFO] chrY chunk 1-1/4 Tensors generated: 2055
+[INFO] chrY chunk 1-1/6 Tensors generated: 3015
+[INFO] chrY chunk 1-1/11 Tensors generated: 4309
+[INFO] chrY chunk 1-1/10 Tensors generated: 5972
+[INFO] chrY chunk 1-1/12 Tensors generated: 5342
+
+[INFO] Pileup Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/2-2_PREDICT.log
+
+[INFO] chrY total processed positions: 309, time elapsed: 0.7s
+[INFO] No variant output for p_chrY.9_0_1.vcf, remove empty VCF
+[INFO] chrY total processed positions: 352, time elapsed: 1.0s
+[INFO] chrY total processed positions: 405, time elapsed: 1.0s
+[INFO] chrY total processed positions: 758, time elapsed: 1.4s
+[INFO] No variant output for p_chrY.7_0_1.vcf, remove empty VCF
+[INFO] chrY total processed positions: 812, time elapsed: 1.5s
+[INFO] chrY total processed positions: 1950, time elapsed: 3.2s
+[INFO] chrY total processed positions: 2055, time elapsed: 3.6s
+[INFO] chrY total processed positions: 2762, time elapsed: 4.7s
+[INFO] chrY total processed positions: 3015, time elapsed: 5.0s
+[INFO] chrY total processed positions: 4115, time elapsed: 6.7s
+[INFO] chrY total processed positions: 4309, time elapsed: 7.2s
+[INFO] chrY total processed positions: 5342, time elapsed: 8.5s
+[INFO] chrY total processed positions: 5972, time elapsed: 9.5s
+
+[INFO] Merge Pileup VCFs
+[INFO] RUN THE FOLLOWING COMMAND:
+pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output/pileup.vcf
+
+[INFO] Sorting VCFs...
+[INFO] Finished VCF sorting!
+
+[INFO] STEP 3: Full-alignment Model Calling
+[INFO] Create Full-alignment Paired Tensors
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/3-1_CPT.log
+
+[INFO] chrY chunk 1-1/3 Tensors generated: 347
+[INFO] chrY chunk 1-1/9 Tensors generated: 173
+[INFO] chrY chunk 1-1/1 Tensors generated: 399
+[INFO] chrY chunk 1-1/8 Tensors generated: 396
+[INFO] chrY chunk 1-1/7 Tensors generated: 588
+[INFO] chrY chunk 1-1/5 Tensors generated: 1815
+[INFO] chrY chunk 1-1/6 Tensors generated: 2359
+[INFO] chrY chunk 1-1/2 Tensors generated: 2616
+[INFO] chrY chunk 1-1/0 Tensors generated: 3907
+[INFO] chrY chunk 1-1/4 Tensors generated: 2046
+[INFO] chrY chunk 1-1/11 Tensors generated: 3394
+[INFO] chrY chunk 1-1/12 Tensors generated: 4768
+[INFO] chrY chunk 1-1/10 Tensors generated: 5087
+
+[INFO] Full-alignment Model Prediction
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/3-2_PREDICT.log
+
+[INFO] chrY total processed positions: 173, time elapsed: 30.6s
+[INFO] chrY total processed positions: 347, time elapsed: 61.0s
+[INFO] chrY total processed positions: 396, time elapsed: 69.7s
+[INFO] chrY total processed positions: 399, time elapsed: 70.2s
+[INFO] chrY total processed positions: 588, time elapsed: 104.2s

slurm-2557981.out

@@ -0,0 +1,562 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25 --region chr22:1-51324926 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr22
+[INFO] Number of chunks for each contig: 11
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr22:1-51324926
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output --ctg_name=chr22 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr22
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr22 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr22
+[INFO] Chunk number for each contig: 11
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr22 (chunk 2/11) : 47403
+Total time elapsed: 76.59 s
+Calling variants ...
+Total processed positions in chr22 (chunk 3/11) : 53800
+Total time elapsed: 78.51 s
+Calling variants ...
+Total processed positions in chr22 (chunk 4/11) : 55146
+Total time elapsed: 84.17 s
+Calling variants ...
+Total processed positions in chr22 (chunk 1/11) : 54744
+Total time elapsed: 91.37 s
+Calling variants ...
+Total processed positions in chr22 (chunk 7/11) : 77013
+Total time elapsed: 103.88 s
+Calling variants ...
+Total processed positions in chr22 (chunk 9/11) : 78760
+Total time elapsed: 108.34 s
+Calling variants ...
+Total processed positions in chr22 (chunk 10/11) : 84773
+Total time elapsed: 110.66 s
+Calling variants ...
+Total processed positions in chr22 (chunk 11/11) : 85609
+Total time elapsed: 111.64 s
+Calling variants ...
+Total processed positions in chr22 (chunk 6/11) : 87769
+Total time elapsed: 114.11 s
+Calling variants ...
+Total processed positions in chr22 (chunk 5/11) : 86212
+Total time elapsed: 115.06 s
+Calling variants ...
+Total processed positions in chr22 (chunk 8/11) : 84558
+Total time elapsed: 117.46 s
+
+real	2m3.931s
+user	18m5.961s
+sys	0m48.172s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 13
+[INFO] Total heterozygous SNP positions selected: chr22: 46311
+
+real	0m2.154s
+user	0m2.043s
+sys	0m0.098s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr22.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr22
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr22,5s)
+parsing total:  5s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 6s
+
+real	0m6.434s
+user	0m13.166s
+sys	0m0.864s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 12.0
+[INFO] Low quality reference calls to be processed in chr22: 67750
+[INFO] Low quality variants to be processed in chr22: 82189
+
+real	0m2.278s
+user	0m2.071s
+sys	0m0.173s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr22 (chunk 12/15) : 10000
+Total time elapsed: 72.79 s
+Calling variants ...
+Total processed positions in chr22 (chunk 4/15) : 10000
+Total time elapsed: 73.40 s
+Calling variants ...
+Total processed positions in chr22 (chunk 13/15) : 10000
+Total time elapsed: 73.92 s
+Calling variants ...
+Total processed positions in chr22 (chunk 5/15) : 10000
+Total time elapsed: 74.41 s
+Calling variants ...
+Total processed positions in chr22 (chunk 8/15) : 10000
+Total time elapsed: 74.48 s
+Calling variants ...
+Total processed positions in chr22 (chunk 9/15) : 10000
+Total time elapsed: 74.94 s
+Calling variants ...
+Total processed positions in chr22 (chunk 10/15) : 10000
+Total time elapsed: 75.68 s
+Calling variants ...
+Total processed positions in chr22 (chunk 11/15) : 10000
+Total time elapsed: 76.15 s
+Calling variants ...
+Total processed positions in chr22 (chunk 14/15) : 10000
+Total time elapsed: 76.72 s
+Calling variants ...
+Total processed positions in chr22 (chunk 1/15) : 10000
+Total time elapsed: 77.61 s
+Calling variants ...
+Total processed positions in chr22 (chunk 2/15) : 10000
+Total time elapsed: 78.09 s
+Calling variants ...
+Total processed positions in chr22 (chunk 6/15) : 10000
+Total time elapsed: 78.83 s
+Calling variants ...
+Total processed positions in chr22 (chunk 3/15) : 10000
+Total time elapsed: 79.62 s
+Calling variants ...
+Total processed positions in chr22 (chunk 15/15) : 9939
+Total time elapsed: 81.12 s
+Calling variants ...
+Total processed positions in chr22 (chunk 7/15) : 10000
+Total time elapsed: 88.00 s
+
+real	1m31.215s
+user	18m41.810s
+sys	1m11.725s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr22: 35275
+[INFO] Full-alignment variants processed in chr22: 85432
+
+real	0m2.993s
+user	0m3.163s
+sys	0m0.172s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	4m0.719s
+user	37m18.840s
+sys	2m2.204s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output --ctg_name=chr22 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr22
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr22 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr22
+[INFO] Chunk number for each contig: 11
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr22 (chunk 7/11) : 10394
+Total time elapsed: 45.47 s
+Calling variants ...
+Total processed positions in chr22 (chunk 9/11) : 10976
+Total time elapsed: 45.59 s
+Calling variants ...
+Total processed positions in chr22 (chunk 8/11) : 11033
+Total time elapsed: 45.89 s
+Calling variants ...
+Total processed positions in chr22 (chunk 6/11) : 11739
+Total time elapsed: 47.16 s
+Calling variants ...
+Total processed positions in chr22 (chunk 10/11) : 13612
+Total time elapsed: 49.61 s
+Calling variants ...
+Total processed positions in chr22 (chunk 11/11) : 13812
+Total time elapsed: 50.55 s
+Calling variants ...
+Total processed positions in chr22 (chunk 5/11) : 18299
+Total time elapsed: 54.44 s
+Calling variants ...
+Total processed positions in chr22 (chunk 3/11) : 33075
+Total time elapsed: 71.24 s
+Calling variants ...
+Total processed positions in chr22 (chunk 4/11) : 28574
+Total time elapsed: 73.72 s
+Calling variants ...
+Total processed positions in chr22 (chunk 2/11) : 26998
+Total time elapsed: 76.03 s
+Calling variants ...
+Total processed positions in chr22 (chunk 1/11) : 70814
+Total time elapsed: 137.65 s
+
+real	2m20.973s
+user	9m31.820s
+sys	0m35.384s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15
+[INFO] Total heterozygous SNP positions selected: chr22: 44110
+
+real	0m1.090s
+user	0m0.991s
+sys	0m0.091s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr22.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr22
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr22,18s)
+parsing total:  18s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 19s
+
+real	0m19.006s
+user	0m47.392s
+sys	0m2.952s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 8.0
+[INFO] Low quality reference calls to be processed in chr22: 12609
+[INFO] Low quality variants to be processed in chr22: 85928
+
+real	0m1.085s
+user	0m0.932s
+sys	0m0.136s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr22 (chunk 2/10) : 10000
+Total time elapsed: 81.37 s
+Calling variants ...
+Total processed positions in chr22 (chunk 1/10) : 10000
+Total time elapsed: 87.73 s
+Calling variants ...
+Total processed positions in chr22 (chunk 10/10) : 8537
+Total time elapsed: 91.82 s
+Calling variants ...
+Total processed positions in chr22 (chunk 4/10) : 10000
+Total time elapsed: 95.70 s
+Calling variants ...
+Total processed positions in chr22 (chunk 3/10) : 10000
+Total time elapsed: 97.11 s
+Calling variants ...
+Total processed positions in chr22 (chunk 5/10) : 10000
+Total time elapsed: 98.39 s
+Calling variants ...
+Total processed positions in chr22 (chunk 9/10) : 10000
+Total time elapsed: 98.82 s
+Calling variants ...
+Total processed positions in chr22 (chunk 8/10) : 10000
+Total time elapsed: 100.34 s
+Calling variants ...
+Total processed positions in chr22 (chunk 7/10) : 10000
+Total time elapsed: 103.07 s
+Calling variants ...
+Total processed positions in chr22 (chunk 6/10) : 10000
+Total time elapsed: 115.45 s
+
+real	1m58.631s
+user	15m21.575s
+sys	0m51.191s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr22: 37132
+[INFO] Full-alignment variants processed in chr22: 80741
+
+real	0m1.719s
+user	0m1.719s
+sys	0m0.142s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	4m48.800s
+user	25m49.863s
+sys	1m30.517s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr22: 61121, not found:919, not match:76, low_qual_count:0. Total normal:66656 Total tumor:62116, pro: 0.984
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/vcf/chr22.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_phased_chr22
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 1s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr22,39s)
+parsing total:  40s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 41s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/CONTIGS
+
+phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_phased_chr22.vcf.gz
+phased SV file:    
+phased MOD file:   
+input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
+output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/clair3_output/phased_output/tumor_chr22.bam
+number of threads: 1
+write log file:    false
+log file:          
+-------------------------------------------
+tag region:                    chr22
+filter mapping quality below:  1
+percentage threshold:          0.6
+tag supplementary:             false
+-------------------------------------------
+parsing SNP VCF ... 1s
+tag read start ...
+chr: chr22 ... 691s
+tag read 692s
+-------------------------------------------
+total process time:  693s
+total alignment:     1020895
+total supplementary: 24756
+total secondary:     0
+total unmapped:      0
+total tag alignment: 315339
+total untagged:      705556
+
+[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part25/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
+
+[INFO] chr22 chunk 0/11: Total snv candidates found: 14326, total indel candidates found: 1131

slurm-2557982.out

@@ -0,0 +1,631 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12 --region chr15:1-68861667 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr15
+[INFO] Number of chunks for each contig: 20
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr15:1-68861667
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output --ctg_name=chr15 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr15
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr15 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr15
+[INFO] Chunk number for each contig: 20
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr15 (chunk 2/20) : 12228
+Total time elapsed: 33.12 s
+Calling variants ...
+Total processed positions in chr15 (chunk 3/20) : 19201
+Total time elapsed: 43.93 s
+Calling variants ...
+Total processed positions in chr15 (chunk 1/20) : 17171
+Total time elapsed: 46.23 s
+Calling variants ...
+Total processed positions in chr15 (chunk 10/20) : 73614
+Total time elapsed: 120.45 s
+Calling variants ...
+Total processed positions in chr15 (chunk 9/20) : 75952
+Total time elapsed: 124.55 s
+Calling variants ...
+Total processed positions in chr15 (chunk 11/20) : 81432
+Total time elapsed: 125.32 s
+Calling variants ...
+Total processed positions in chr15 (chunk 7/20) : 78004
+Total time elapsed: 128.51 s
+Calling variants ...
+Total processed positions in chr15 (chunk 6/20) : 80932
+Total time elapsed: 128.80 s
+Calling variants ...
+Total processed positions in chr15 (chunk 15/20) : 82164
+Total time elapsed: 129.84 s
+Calling variants ...
+Total processed positions in chr15 (chunk 14/20) : 81844
+Total time elapsed: 133.74 s
+Calling variants ...
+Total processed positions in chr15 (chunk 16/20) : 85312
+Total time elapsed: 133.79 s
+Calling variants ...
+Total processed positions in chr15 (chunk 13/20) : 86377
+Total time elapsed: 135.44 s
+Calling variants ...
+Total processed positions in chr15 (chunk 8/20) : 83225
+Total time elapsed: 138.95 s
+Calling variants ...
+Total processed positions in chr15 (chunk 18/20) : 84823
+Total time elapsed: 140.47 s
+Calling variants ...
+Total processed positions in chr15 (chunk 17/20) : 87476
+Total time elapsed: 141.71 s
+Calling variants ...
+Total processed positions in chr15 (chunk 20/20) : 89114
+Total time elapsed: 141.91 s
+Calling variants ...
+Total processed positions in chr15 (chunk 4/20) : 76273
+Total time elapsed: 145.65 s
+Calling variants ...
+Total processed positions in chr15 (chunk 5/20) : 87326
+Total time elapsed: 146.23 s
+Calling variants ...
+Total processed positions in chr15 (chunk 19/20) : 87661
+Total time elapsed: 149.05 s
+Calling variants ...
+Total processed positions in chr15 (chunk 12/20) : 91236
+Total time elapsed: 153.70 s
+
+real	2m40.464s
+user	38m47.303s
+sys	1m49.544s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15
+[INFO] Total heterozygous SNP positions selected: chr15: 72128
+
+real	0m3.584s
+user	0m3.415s
+sys	0m0.145s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr15.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr15
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr15,7s)
+parsing total:  7s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 9s
+
+real	0m9.144s
+user	0m17.197s
+sys	0m1.117s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 13.0
+[INFO] Low quality reference calls to be processed in chr15: 127976
+[INFO] Low quality variants to be processed in chr15: 126873
+
+real	0m3.846s
+user	0m3.532s
+sys	0m0.253s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr15 (chunk 26/26) : 4849
+Total time elapsed: 54.76 s
+Calling variants ...
+Total processed positions in chr15 (chunk 1/26) : 10000
+Total time elapsed: 92.29 s
+Calling variants ...
+Total processed positions in chr15 (chunk 13/26) : 10000
+Total time elapsed: 92.40 s
+Calling variants ...
+Total processed positions in chr15 (chunk 18/26) : 10000
+Total time elapsed: 94.30 s
+Calling variants ...
+Total processed positions in chr15 (chunk 4/26) : 10000
+Total time elapsed: 94.58 s
+Calling variants ...
+Total processed positions in chr15 (chunk 20/26) : 10000
+Total time elapsed: 94.96 s
+Calling variants ...
+Total processed positions in chr15 (chunk 21/26) : 10000
+Total time elapsed: 95.44 s
+Calling variants ...
+Total processed positions in chr15 (chunk 23/26) : 10000
+Total time elapsed: 96.10 s
+Calling variants ...
+Total processed positions in chr15 (chunk 16/26) : 10000
+Total time elapsed: 96.44 s
+Calling variants ...
+Total processed positions in chr15 (chunk 24/26) : 10000
+Total time elapsed: 96.70 s
+Calling variants ...
+Total processed positions in chr15 (chunk 11/26) : 10000
+Total time elapsed: 96.71 s
+Calling variants ...
+Total processed positions in chr15 (chunk 8/26) : 10000
+Total time elapsed: 97.06 s
+Calling variants ...
+Total processed positions in chr15 (chunk 9/26) : 10000
+Total time elapsed: 96.80 s
+Calling variants ...
+Total processed positions in chr15 (chunk 15/26) : 10000
+Total time elapsed: 97.04 s
+Calling variants ...
+Total processed positions in chr15 (chunk 19/26) : 10000
+Total time elapsed: 98.37 s
+Calling variants ...
+Total processed positions in chr15 (chunk 12/26) : 10000
+Total time elapsed: 98.70 s
+Calling variants ...
+Total processed positions in chr15 (chunk 10/26) : 10000
+Total time elapsed: 99.01 s
+Calling variants ...
+Total processed positions in chr15 (chunk 3/26) : 10000
+Total time elapsed: 99.39 s
+Calling variants ...
+Total processed positions in chr15 (chunk 5/26) : 10000
+Total time elapsed: 99.54 s
+Calling variants ...
+Total processed positions in chr15 (chunk 22/26) : 10000
+Total time elapsed: 99.54 s
+Calling variants ...
+Total processed positions in chr15 (chunk 17/26) : 10000
+Total time elapsed: 99.98 s
+Calling variants ...
+Total processed positions in chr15 (chunk 25/26) : 10000
+Total time elapsed: 100.05 s
+Calling variants ...
+Total processed positions in chr15 (chunk 14/26) : 10000
+Total time elapsed: 100.80 s
+Calling variants ...
+Total processed positions in chr15 (chunk 7/26) : 10000
+Total time elapsed: 101.65 s
+Calling variants ...
+Total processed positions in chr15 (chunk 6/26) : 10000
+Total time elapsed: 101.48 s
+Calling variants ...
+Total processed positions in chr15 (chunk 2/26) : 10000
+Total time elapsed: 105.61 s
+
+real	1m49.098s
+user	40m10.751s
+sys	2m32.591s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr15: 54401
+[INFO] Full-alignment variants processed in chr15: 132191
+
+real	0m4.804s
+user	0m5.173s
+sys	0m0.250s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	5m10.002s
+user	79m45.187s
+sys	4m25.359s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output --ctg_name=chr15 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr15
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr15 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr15
+[INFO] Chunk number for each contig: 20
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr15 (chunk 9/20) : 7491
+Total time elapsed: 55.14 s
+Calling variants ...
+Total processed positions in chr15 (chunk 14/20) : 9361
+Total time elapsed: 55.72 s
+Calling variants ...
+Total processed positions in chr15 (chunk 15/20) : 9383
+Total time elapsed: 56.59 s
+Calling variants ...
+Total processed positions in chr15 (chunk 12/20) : 11544
+Total time elapsed: 59.13 s
+Calling variants ...
+Total processed positions in chr15 (chunk 10/20) : 9656
+Total time elapsed: 59.74 s
+Calling variants ...
+Total processed positions in chr15 (chunk 18/20) : 11760
+Total time elapsed: 60.49 s
+Calling variants ...
+Total processed positions in chr15 (chunk 11/20) : 10978
+Total time elapsed: 60.82 s
+Calling variants ...
+Total processed positions in chr15 (chunk 13/20) : 10162
+Total time elapsed: 61.12 s
+Calling variants ...
+Total processed positions in chr15 (chunk 19/20) : 11914
+Total time elapsed: 62.92 s
+Calling variants ...
+Total processed positions in chr15 (chunk 16/20) : 12177
+Total time elapsed: 64.27 s
+Calling variants ...
+Total processed positions in chr15 (chunk 8/20) : 10118
+Total time elapsed: 64.25 s
+Calling variants ...
+Total processed positions in chr15 (chunk 7/20) : 13907
+Total time elapsed: 64.83 s
+Calling variants ...
+Total processed positions in chr15 (chunk 20/20) : 14539
+Total time elapsed: 64.93 s
+Calling variants ...
+Total processed positions in chr15 (chunk 3/20) : 18253
+Total time elapsed: 65.98 s
+Calling variants ...
+Total processed positions in chr15 (chunk 6/20) : 14360
+Total time elapsed: 66.49 s
+Calling variants ...
+Total processed positions in chr15 (chunk 17/20) : 14148
+Total time elapsed: 66.93 s
+Calling variants ...
+Total processed positions in chr15 (chunk 5/20) : 19401
+Total time elapsed: 69.04 s
+Calling variants ...
+Total processed positions in chr15 (chunk 2/20) : 22300
+Total time elapsed: 72.61 s
+Calling variants ...
+Total processed positions in chr15 (chunk 1/20) : 32347
+Total time elapsed: 93.54 s
+Calling variants ...
+Total processed positions in chr15 (chunk 4/20) : 60396
+Total time elapsed: 129.60 s
+
+real	2m13.325s
+user	15m52.912s
+sys	1m8.409s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19
+[INFO] Total heterozygous SNP positions selected: chr15: 76778
+
+real	0m1.391s
+user	0m1.235s
+sys	0m0.141s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr15.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr15
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr15,29s)
+parsing total:  29s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 31s
+
+real	0m30.940s
+user	1m14.730s
+sys	0m4.743s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 8.0
+[INFO] Low quality reference calls to be processed in chr15: 13158
+[INFO] Low quality variants to be processed in chr15: 134520
+
+real	0m1.391s
+user	0m1.198s
+sys	0m0.164s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr15 (chunk 15/15) : 7678
+Total time elapsed: 81.87 s
+Calling variants ...
+Total processed positions in chr15 (chunk 1/15) : 10000
+Total time elapsed: 85.06 s
+Calling variants ...
+Total processed positions in chr15 (chunk 4/15) : 10000
+Total time elapsed: 85.15 s
+Calling variants ...
+Total processed positions in chr15 (chunk 5/15) : 10000
+Total time elapsed: 96.87 s
+Calling variants ...
+Total processed positions in chr15 (chunk 6/15) : 10000
+Total time elapsed: 99.58 s
+Calling variants ...
+Total processed positions in chr15 (chunk 3/15) : 10000
+Total time elapsed: 101.27 s
+Calling variants ...
+Total processed positions in chr15 (chunk 2/15) : 10000
+Total time elapsed: 103.28 s
+Calling variants ...
+Total processed positions in chr15 (chunk 10/15) : 10000
+Total time elapsed: 104.61 s
+Calling variants ...
+Total processed positions in chr15 (chunk 14/15) : 10000
+Total time elapsed: 106.73 s
+Calling variants ...
+Total processed positions in chr15 (chunk 13/15) : 10000
+Total time elapsed: 108.63 s
+Calling variants ...
+Total processed positions in chr15 (chunk 8/15) : 10000
+Total time elapsed: 111.70 s
+Calling variants ...
+Total processed positions in chr15 (chunk 9/15) : 10000
+Total time elapsed: 112.92 s
+Calling variants ...
+Total processed positions in chr15 (chunk 11/15) : 10000
+Total time elapsed: 113.13 s
+Calling variants ...
+Total processed positions in chr15 (chunk 7/15) : 10000
+Total time elapsed: 113.21 s
+Calling variants ...
+Total processed positions in chr15 (chunk 12/15) : 10000
+Total time elapsed: 116.27 s
+
+real	1m59.555s
+user	24m15.192s
+sys	1m22.459s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr15: 58048
+[INFO] Full-alignment variants processed in chr15: 125321
+
+real	0m2.269s
+user	0m2.312s
+sys	0m0.150s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	4m56.856s
+user	41m34.648s
+sys	2m36.843s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr15: 102605, not found:921, not match:89, low_qual_count:0. Total normal:101744 Total tumor:103615, pro: 0.9903
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/vcf/chr15.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/phased_output/tumor_phased_chr15
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 1s
+(chr15,48s)
+parsing total:  48s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 50s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part12/tmp/CONTIGS
+

slurm-2557983.out

@@ -0,0 +1,514 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24 --region chr21:1-45090682 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr21
+[INFO] Number of chunks for each contig: 10
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr21:1-45090682
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output --ctg_name=chr21 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr21
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr21 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr21
+[INFO] Chunk number for each contig: 10
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr21 (chunk 1/10) : 21247
+Total time elapsed: 41.35 s
+Calling variants ...
+Total processed positions in chr21 (chunk 2/10) : 55447
+Total time elapsed: 92.05 s
+Calling variants ...
+Total processed positions in chr21 (chunk 5/10) : 65383
+Total time elapsed: 103.81 s
+Calling variants ...
+Total processed positions in chr21 (chunk 6/10) : 71156
+Total time elapsed: 106.40 s
+Calling variants ...
+Total processed positions in chr21 (chunk 3/10) : 71284
+Total time elapsed: 108.33 s
+Calling variants ...
+Total processed positions in chr21 (chunk 4/10) : 73057
+Total time elapsed: 115.65 s
+Calling variants ...
+Total processed positions in chr21 (chunk 7/10) : 75897
+Total time elapsed: 120.81 s
+Calling variants ...
+Total processed positions in chr21 (chunk 9/10) : 81308
+Total time elapsed: 120.97 s
+Calling variants ...
+Total processed positions in chr21 (chunk 8/10) : 78139
+Total time elapsed: 124.79 s
+Calling variants ...
+Total processed positions in chr21 (chunk 10/10) : 86992
+Total time elapsed: 134.60 s
+
+real	2m21.035s
+user	17m6.093s
+sys	0m58.159s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
+[INFO] Total heterozygous SNP positions selected: chr21: 38730
+
+real	0m1.266s
+user	0m1.125s
+sys	0m0.103s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr21.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr21
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr21,4s)
+parsing total:  4s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 5s
+
+real	0m4.675s
+user	0m10.375s
+sys	0m0.761s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 19.0
+[INFO] Set reference calls quality cutoff 13.0
+[INFO] Low quality reference calls to be processed in chr21: 57899
+[INFO] Low quality variants to be processed in chr21: 69711
+
+real	0m1.477s
+user	0m1.179s
+sys	0m0.155s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr21 (chunk 13/13) : 7610
+Total time elapsed: 77.34 s
+Calling variants ...
+Total processed positions in chr21 (chunk 10/13) : 10000
+Total time elapsed: 93.29 s
+Calling variants ...
+Total processed positions in chr21 (chunk 9/13) : 10000
+Total time elapsed: 93.47 s
+Calling variants ...
+Total processed positions in chr21 (chunk 8/13) : 10000
+Total time elapsed: 93.64 s
+Calling variants ...
+Total processed positions in chr21 (chunk 6/13) : 10000
+Total time elapsed: 94.19 s
+Calling variants ...
+Total processed positions in chr21 (chunk 3/13) : 10000
+Total time elapsed: 93.99 s
+Calling variants ...
+Total processed positions in chr21 (chunk 4/13) : 10000
+Total time elapsed: 94.03 s
+Calling variants ...
+Total processed positions in chr21 (chunk 12/13) : 10000
+Total time elapsed: 94.45 s
+Calling variants ...
+Total processed positions in chr21 (chunk 7/13) : 10000
+Total time elapsed: 95.22 s
+Calling variants ...
+Total processed positions in chr21 (chunk 11/13) : 10000
+Total time elapsed: 95.42 s
+Calling variants ...
+Total processed positions in chr21 (chunk 5/13) : 10000
+Total time elapsed: 95.72 s
+Calling variants ...
+Total processed positions in chr21 (chunk 2/13) : 10000
+Total time elapsed: 95.91 s
+Calling variants ...
+Total processed positions in chr21 (chunk 1/13) : 10000
+Total time elapsed: 96.01 s
+
+real	1m38.621s
+user	19m32.131s
+sys	1m4.775s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr21: 29908
+[INFO] Full-alignment variants processed in chr21: 74068
+
+real	0m1.761s
+user	0m1.912s
+sys	0m0.145s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
+
+real	4m16.843s
+user	36m59.599s
+sys	2m5.097s
+
+[INFO] Call Germline Variant in Tumor BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output --ctg_name=chr21 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/2_CLAIR3_TUMOR.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr21
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr21 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr21
+[INFO] Chunk number for each contig: 10
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr21 (chunk 7/10) : 9368
+Total time elapsed: 44.16 s
+Calling variants ...
+Total processed positions in chr21 (chunk 6/10) : 10461
+Total time elapsed: 44.92 s
+Calling variants ...
+Total processed positions in chr21 (chunk 4/10) : 10732
+Total time elapsed: 46.14 s
+Calling variants ...
+Total processed positions in chr21 (chunk 5/10) : 11068
+Total time elapsed: 46.09 s
+Calling variants ...
+Total processed positions in chr21 (chunk 8/10) : 11175
+Total time elapsed: 47.12 s
+Calling variants ...
+Total processed positions in chr21 (chunk 9/10) : 11777
+Total time elapsed: 47.74 s
+Calling variants ...
+Total processed positions in chr21 (chunk 10/10) : 15430
+Total time elapsed: 53.78 s
+Calling variants ...
+Total processed positions in chr21 (chunk 1/10) : 36882
+Total time elapsed: 83.76 s
+Calling variants ...
+Total processed positions in chr21 (chunk 3/10) : 32029
+Total time elapsed: 93.36 s
+Calling variants ...
+Total processed positions in chr21 (chunk 2/10) : 75635
+Total time elapsed: 140.71 s
+
+real	2m23.464s
+user	8m51.533s
+sys	0m36.386s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 17
+[INFO] Total heterozygous SNP positions selected: chr21: 39429
+
+real	0m0.724s
+user	0m0.608s
+sys	0m0.088s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr21.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr21
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr21,17s)
+parsing total:  17s
+merge results ... 0s
+writeResult SNP ... 0s
+
+total process: 17s
+
+real	0m17.072s
+user	0m51.072s
+sys	0m3.322s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 21.0
+[INFO] Set reference calls quality cutoff 9.0
+[INFO] Low quality reference calls to be processed in chr21: 11425
+[INFO] Low quality variants to be processed in chr21: 77112
+
+real	0m0.771s
+user	0m0.589s
+sys	0m0.114s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr21 (chunk 9/9) : 8537
+Total time elapsed: 100.99 s
+Calling variants ...
+Total processed positions in chr21 (chunk 1/9) : 10000
+Total time elapsed: 101.80 s
+Calling variants ...
+Total processed positions in chr21 (chunk 3/9) : 10000
+Total time elapsed: 105.89 s
+Calling variants ...
+Total processed positions in chr21 (chunk 4/9) : 10000
+Total time elapsed: 108.09 s
+Calling variants ...
+Total processed positions in chr21 (chunk 2/9) : 10000
+Total time elapsed: 111.57 s
+Calling variants ...
+Total processed positions in chr21 (chunk 6/9) : 10000
+Total time elapsed: 113.03 s
+Calling variants ...
+Total processed positions in chr21 (chunk 7/9) : 10000
+Total time elapsed: 117.18 s
+Calling variants ...
+Total processed positions in chr21 (chunk 5/9) : 10000
+Total time elapsed: 120.80 s
+Calling variants ...
+Total processed positions in chr21 (chunk 8/9) : 10000
+Total time elapsed: 120.76 s
+
+real	2m3.456s
+user	15m42.135s
+sys	0m48.676s
+
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
+[INFO] Pileup variants processed in chr21: 33077
+[INFO] Full-alignment variants processed in chr21: 73272
+
+real	0m1.099s
+user	0m1.102s
+sys	0m0.113s
+
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
+
+real	4m51.155s
+user	25m30.754s
+sys	1m29.337s
+
+[INFO] Select Heterozygous SNP for Phasing
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/1_select_hetero_snp_for_phasing.log
+
+[INFO] Total HET SNP calls selected: chr21: 54974, not found:1251, not match:50, low_qual_count:0. Total normal:57735 Total tumor:56275, pro: 0.9769
+
+[INFO] Phase the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS
+
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf/chr21.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_chr21
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 0s
+(chr21,31s)
+parsing total:  31s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 32s
+
+[INFO] Haplotag the Tumor BAM
+[INFO] RUN THE FOLLOWING COMMAND:
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS
+

slurm-2557984.out

@@ -0,0 +1,354 @@
+WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6': destination is already in the mount point list
+
+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6 --region chr11:84448351-135127769 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
+
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/logs
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/split_beds
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/candidates
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/pileup_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/fa_tensor_can
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/tmp_vcf_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/logs/clair3_log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/phased_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/vcf
+[INFO] --include_all_ctgs enabled
+[INFO] Call variants in contigs: chr11
+[INFO] Number of chunks for each contig: 28
+
+[INFO] CALLER VERSION: 0.4.4
+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
+[INFO] THREADS: 40
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6
+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/output.vcf.gz
+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/region.bed
+[INFO] GENOTYPING MODE VCF FILE PATH: None
+[INFO] HYBRID MODE VCF FILE PATH: None
+[INFO] REGION FOR CALLING: chr11:84448351-135127769
+[INFO] CONTIGS FOR CALLING: None
+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
+[INFO] SAMTOOLS BINARY PATH: samtools
+[INFO] PYTHON BINARY PATH: python3
+[INFO] PYPY BINARY PATH: pypy3
+[INFO] PARALLEL BINARY PATH: parallel
+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] SNV MINIMUM AF: 0.05
+[INFO] SNV MINIMUM QUAL: 8
+[INFO] INDEL MINIMUM AF: 0.1
+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
+[INFO] INDEL MINIMUM QUAL: 8
+[INFO] NORMAL VCF FILE PATH: None
+[INFO] DISABLE PHASING: False
+[INFO] ENABLE DRY RUN: False
+[INFO] ENABLE INDEL CALLING: True
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE PRINTING GERMLINE CALLS: True
+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+
+[INFO] Call Germline Variants in Normal BAM using Clair3
+[INFO] RUN THE FOLLOWING COMMAND:
+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output --ctg_name=chr11 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/logs/clair3_log/1_CLAIR3_NORMAL.log
+
+[INFO] CLAIR3 VERSION: v1.0.8
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output
+[INFO] PLATFORM: ont
+[INFO] THREADS: 40
+[INFO] BED FILE PATH: EMPTY
+[INFO] VCF FILE PATH: EMPTY
+[INFO] CONTIGS: chr11
+[INFO] CONDA PREFIX: 
+[INFO] SAMTOOLS PATH: samtools
+[INFO] PYTHON PATH: python3
+[INFO] PYPY PATH: pypy3
+[INFO] PARALLEL PATH: parallel
+[INFO] WHATSHAP PATH: whatshap
+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
+[INFO] CHUNK SIZE: 5000000
+[INFO] FULL ALIGN PROPORTION: 0.7
+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
+[INFO] PHASING PROPORTION: 0.7
+[INFO] MINIMUM MQ: 5
+[INFO] MINIMUM COVERAGE: 4
+[INFO] SNP AF THRESHOLD: 0.08
+[INFO] INDEL AF THRESHOLD: 0.15
+[INFO] BASE ERROR IN GVCF: 0.001
+[INFO] GQ BIN SIZE IN GVCF: 5
+[INFO] ENABLE FILEUP ONLY CALLING: False
+[INFO] ENABLE FAST MODE CALLING: False
+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
+[INFO] ENABLE PRINTING REFERENCE CALLS: False
+[INFO] ENABLE OUTPUT GVCF: False
+[INFO] ENABLE HAPLOID PRECISE MODE: False
+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
+[INFO] ENABLE LONG INDEL CALLING: False
+[INFO] ENABLE C_IMPLEMENT: True
+
++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr11 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
+
+[INFO] Check environment variables
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/log
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/merge_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
+[INFO] Call variant in contigs: chr11
+[INFO] Chunk number for each contig: 28
+[INFO] 1/7 Call variants using pileup model
+Calling variants ...
+Total processed positions in chr11 (chunk 11/28) : 49165
+Total time elapsed: 178.48 s
+Calling variants ...
+Total processed positions in chr11 (chunk 12/28) : 56920
+Total time elapsed: 181.36 s
+Calling variants ...
+Total processed positions in chr11 (chunk 22/28) : 75977
+Total time elapsed: 209.99 s
+Calling variants ...
+Total processed positions in chr11 (chunk 19/28) : 71613
+Total time elapsed: 214.42 s
+Calling variants ...
+Total processed positions in chr11 (chunk 9/28) : 70940
+Total time elapsed: 222.08 s
+Calling variants ...
+Total processed positions in chr11 (chunk 6/28) : 73742
+Total time elapsed: 222.47 s
+Calling variants ...
+Total processed positions in chr11 (chunk 5/28) : 75204
+Total time elapsed: 224.15 s
+Calling variants ...
+Total processed positions in chr11 (chunk 21/28) : 71045
+Total time elapsed: 224.79 s
+Calling variants ...
+Total processed positions in chr11 (chunk 7/28) : 73918
+Total time elapsed: 227.41 s
+Calling variants ...
+Total processed positions in chr11 (chunk 17/28) : 78578
+Total time elapsed: 229.56 s
+Calling variants ...
+Total processed positions in chr11 (chunk 18/28) : 73703
+Total time elapsed: 234.10 s
+Calling variants ...
+Total processed positions in chr11 (chunk 4/28) : 81512
+Total time elapsed: 236.81 s
+Calling variants ...
+Total processed positions in chr11 (chunk 14/28) : 83931
+Total time elapsed: 237.93 s
+Calling variants ...
+Total processed positions in chr11 (chunk 16/28) : 82083
+Total time elapsed: 240.35 s
+Calling variants ...
+Total processed positions in chr11 (chunk 3/28) : 82458
+Total time elapsed: 241.23 s
+Calling variants ...
+Total processed positions in chr11 (chunk 13/28) : 79284
+Total time elapsed: 243.04 s
+Calling variants ...
+Total processed positions in chr11 (chunk 2/28) : 79749
+Total time elapsed: 243.40 s
+Calling variants ...
+Total processed positions in chr11 (chunk 15/28) : 84644
+Total time elapsed: 247.06 s
+Calling variants ...
+Total processed positions in chr11 (chunk 20/28) : 78075
+Total time elapsed: 249.18 s
+Calling variants ...
+Total processed positions in chr11 (chunk 26/28) : 89044
+Total time elapsed: 249.72 s
+Calling variants ...
+Total processed positions in chr11 (chunk 24/28) : 84661
+Total time elapsed: 253.22 s
+Calling variants ...
+Total processed positions in chr11 (chunk 10/28) : 85066
+Total time elapsed: 253.66 s
+Calling variants ...
+Total processed positions in chr11 (chunk 28/28) : 83894
+Total time elapsed: 253.82 s
+Calling variants ...
+Total processed positions in chr11 (chunk 23/28) : 77217
+Total time elapsed: 229.34 s
+Calling variants ...
+Total processed positions in chr11 (chunk 8/28) : 83397
+Total time elapsed: 256.16 s
+Calling variants ...
+Total processed positions in chr11 (chunk 25/28) : 85368
+Total time elapsed: 235.94 s
+Calling variants ...
+Total processed positions in chr11 (chunk 1/28) : 94486
+Total time elapsed: 265.61 s
+Calling variants ...
+Total processed positions in chr11 (chunk 27/28) : 84745
+Total time elapsed: 246.95 s
+
+real	4m41.889s
+user	104m58.241s
+sys	4m37.088s
+
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16
+[INFO] Total heterozygous SNP positions selected: chr11: 85688
+
+real	0m4.179s
+user	0m3.753s
+sys	0m0.321s
+
+[INFO] 3/7 Phase VCF file using LongPhase
+LongPhase Ver 1.7
+
+--- File Parameter --- 
+SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr11.vcf
+SV  File      : 
+MOD File      : 
+REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr11
+Generate Dot  : False
+BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
+
+--- Phasing Parameter --- 
+Seq Platform       : ONT
+Phase Indel        : False
+Distance Threshold : 300000
+Connect Adjacent   : 20
+Edge Threshold     : 0.7
+Mapping Quality    : 1
+Variant Confidence : 0.75
+ReadTag Confidence : 0.65
+
+parsing VCF ... 0s
+parsing SV VCF ... 0s
+parsing Meth VCF ... 0s
+reading reference ... 2s
+(chr11,10s)
+parsing total:  10s
+merge results ... 0s
+writeResult SNP ... 1s
+
+total process: 13s
+
+real	0m13.103s
+user	0m44.278s
+sys	0m3.402s
+
+[INFO] 5/7 Select candidates for full-alignment calling
+[INFO] Set variants quality cutoff 20.0
+[INFO] Set reference calls quality cutoff 14.0
+[INFO] Low quality reference calls to be processed in chr11: 195328
+[INFO] Low quality variants to be processed in chr11: 162732
+
+real	0m4.471s
+user	0m4.035s
+sys	0m0.344s
+
+[INFO] 6/7 Call low-quality variants using full-alignment model
+Calling variants ...
+Total processed positions in chr11 (chunk 4/36) : 10000
+Total time elapsed: 143.44 s
+Calling variants ...
+Total processed positions in chr11 (chunk 22/36) : 10000
+Total time elapsed: 143.91 s
+Calling variants ...
+Total processed positions in chr11 (chunk 2/36) : 10000
+Total time elapsed: 145.31 s
+Calling variants ...
+Total processed positions in chr11 (chunk 10/36) : 10000
+Total time elapsed: 148.91 s
+Calling variants ...
+Total processed positions in chr11 (chunk 9/36) : 10000
+Total time elapsed: 158.77 s
+Calling variants ...
+Total processed positions in chr11 (chunk 16/36) : 10000
+Total time elapsed: 160.86 s
+Calling variants ...
+Total processed positions in chr11 (chunk 13/36) : 10000
+Total time elapsed: 161.73 s
+Calling variants ...
+Total processed positions in chr11 (chunk 26/36) : 10000
+Total time elapsed: 162.70 s
+Calling variants ...
+Total processed positions in chr11 (chunk 5/36) : 10000
+Total time elapsed: 163.82 s
+Calling variants ...
+Total processed positions in chr11 (chunk 25/36) : 10000
+Total time elapsed: 164.25 s
+Calling variants ...
+Total processed positions in chr11 (chunk 21/36) : 10000
+Total time elapsed: 165.81 s
+Calling variants ...
+Total processed positions in chr11 (chunk 19/36) : 10000
+Total time elapsed: 166.75 s
+Calling variants ...
+Total processed positions in chr11 (chunk 7/36) : 10000
+Total time elapsed: 172.07 s
+Calling variants ...
+Total processed positions in chr11 (chunk 18/36) : 10000
+Total time elapsed: 172.46 s
+Calling variants ...
+Total processed positions in chr11 (chunk 30/36) : 10000
+Total time elapsed: 178.30 s
+Calling variants ...
+Total processed positions in chr11 (chunk 1/36) : 10000
+Total time elapsed: 179.50 s
+Calling variants ...
+Total processed positions in chr11 (chunk 15/36) : 10000
+Total time elapsed: 179.65 s
+Calling variants ...
+Total processed positions in chr11 (chunk 24/36) : 10000
+Total time elapsed: 179.97 s
+Calling variants ...
+Total processed positions in chr11 (chunk 12/36) : 10000
+Total time elapsed: 179.65 s
+Calling variants ...
+Total processed positions in chr11 (chunk 8/36) : 10000
+Total time elapsed: 181.87 s
+Calling variants ...
+Total processed positions in chr11 (chunk 3/36) : 10000
+Total time elapsed: 182.80 s
+Calling variants ...
+Total processed positions in chr11 (chunk 29/36) : 10000
+Total time elapsed: 183.85 s
+Calling variants ...
+Total processed positions in chr11 (chunk 27/36) : 10000
+Total time elapsed: 183.49 s
+Calling variants ...
+Total processed positions in chr11 (chunk 17/36) : 10000
+Total time elapsed: 184.91 s
+Calling variants ...
+Total processed positions in chr11 (chunk 11/36) : 10000
+Total time elapsed: 185.82 s
+Calling variants ...
+Total processed positions in chr11 (chunk 28/36) : 10000
+Total time elapsed: 186.43 s
+Calling variants ...
+Total processed positions in chr11 (chunk 6/36) : 10000
+Total time elapsed: 187.85 s
+Calling variants ...
+Total processed positions in chr11 (chunk 14/36) : 10000
+Total time elapsed: 188.97 s
+Calling variants ...
+Total processed positions in chr11 (chunk 23/36) : 10000
+Total time elapsed: 189.86 s
+Calling variants ...
+Total processed positions in chr11 (chunk 20/36) : 10000
+Total time elapsed: 191.75 s

src/callers/clairs.rs

@@ -171,13 +171,13 @@ use crate::{
     collection::vcf::Vcf,
     commands::{
         bcftools::{BcftoolsConcat, BcftoolsKeepPass},
-        CapturedOutput, Command as JobCommand, LocalBatchRunner, LocalRunner, SbatchRunner,
-        SlurmParams, SlurmRunner,
+        Command as JobCommand, LocalBatchRunner, LocalRunner, SbatchRunner, SlurmParams,
+        SlurmRunner,
     },
     config::Config,
     helpers::{
         get_genome_sizes, is_file_older, remove_dir_if_exists, singularity_bind_flags,
-        split_genome_into_n_regions_exact, temp_file_path,
+        split_genome_into_n_regions_exact,
     },
     io::vcf::read_vcf,
     pipes::{Initialize, ShouldRun, Version},
@@ -199,6 +199,7 @@ use std::{
     path::{Path, PathBuf},
     process::{Command as ProcessCommand, Stdio},
 };
+use uuid::Uuid;
 
 /// ClairS haplotype-aware somatic variant caller runner.
 ///
@@ -378,7 +379,7 @@ impl SlurmRunner for ClairS {
         SlurmParams {
             job_name: Some(format!("clairs_{}", self.id)),
             cpus_per_task: Some(self.config.clairs_threads as u32),
-            mem: Some("40G".into()),
+            mem: Some("60G".into()),
             partition: Some("shortq".into()),
             gres: None,
         }
@@ -391,7 +392,7 @@ impl SbatchRunner for ClairS {
         SlurmParams {
             job_name: Some(format!("clairs_{}", self.id)),
             cpus_per_task: Some(self.config.clairs_threads as u32),
-            mem: Some("40G".into()),
+            mem: Some("50G".into()),
             partition: Some("shortq".into()),
             gres: None,
         }
@@ -400,8 +401,16 @@ impl SbatchRunner for ClairS {
 
 impl Run for ClairS {
     fn run(&mut self) -> anyhow::Result<()> {
-        run!(&self.config, self)?;
-        Ok(())
+        if !self.should_run() {
+            anyhow::bail!("ClairS is up-to-data.");
+        }
+
+        if self.config.slurm_runner {
+            run_clairs_chunked(&self.id, &self.config, 30)
+        } else {
+            run!(&self.config, self)?;
+            self.postprocess()
+        }
     }
 }
 
@@ -505,7 +514,8 @@ impl ClairS {
             self.id, self.part_index
         );
 
-        let tmp_file = temp_file_path(".vcf.gz")?;
+        let tmp_file =
+            Path::new(&self.config.tmp_dir).join(format!("pandora-temp-{}.vcf.gz", Uuid::new_v4()));
         let tmp_path = tmp_file
             .to_str()
             .context("Temp path not valid UTF-8")?
@@ -692,7 +702,8 @@ impl Version for ClairS {
         }
 
         let mut job = ClairSVersionJob { config };
-        let out = SlurmRunner::run(&mut job).context("Failed to run ClairS --version via Slurm")?;
+        let out =
+            SlurmRunner::exec(&mut job).context("Failed to run ClairS --version via Slurm")?;
 
         let mut combined = out.stdout.clone();
         if let Some(epilog) = &out.slurm_epilog {
@@ -811,18 +822,14 @@ fn merge_clairs_germline_parts(base: &ClairS, n_parts: usize) -> anyhow::Result<
 /// Runs ClairS in parallel chunks, then merges results.
 ///
 /// Execution mode (local vs Slurm) is determined by `config.slurm_runner`.
-pub fn run_clairs_chunked_with_merge(
-    id: &str,
-    config: &Config,
-    n_parts: usize,
-) -> anyhow::Result<Vec<CapturedOutput>> {
+pub fn run_clairs_chunked(id: &str, config: &Config, n_parts: usize) -> anyhow::Result<()> {
     anyhow::ensure!(n_parts > 0, "n_parts must be > 0");
 
     let base = ClairS::initialize(id, config)?;
 
     if !base.should_run() {
         debug!("ClairS PASS VCF already up-to-date for {id}, skipping.");
-        return Ok(Vec::new());
+        return Ok(());
     }
 
     let normal_bam = config.normal_bam(id);
@@ -854,6 +861,10 @@ pub fn run_clairs_chunked_with_merge(
 
     let outputs = run_many!(config, jobs.clone())?;
 
+    for output in outputs.iter() {
+        output.save_to_file(format!("{}/clairs_", base.log_dir))?;
+    }
+
     for job in &jobs {
         job.postprocess()?;
     }
@@ -866,7 +877,7 @@ pub fn run_clairs_chunked_with_merge(
         id, actual_n_parts
     );
 
-    Ok(outputs)
+    Ok(())
 }
 
 #[cfg(test)]
@@ -892,8 +903,7 @@ mod tests {
         // let clairs = ClairS::initialize("34528", &config)?;
         // info!("{clairs}");
 
-        let outputs = run_clairs_chunked_with_merge("DUMCO", &config, 20)?;
-        info!("Completed with {} job outputs", outputs.len());
+        run_clairs_chunked("CHAHA", &config, 20)?;
 
         Ok(())
     }

src/callers/deep_somatic.rs

@@ -97,7 +97,9 @@ use crate::{
     annotation::{Annotation, Annotations, Caller, CallerCat, Sample},
     collection::vcf::Vcf,
     commands::{
-        CapturedOutput, Command as JobCommand, LocalBatchRunner, LocalRunner, SbatchRunner, SlurmParams, SlurmRunner, bcftools::{BcftoolsConcat, BcftoolsKeepPass}
+        bcftools::{BcftoolsConcat, BcftoolsKeepPass},
+        Command as JobCommand, LocalBatchRunner, LocalRunner, SbatchRunner, SlurmParams,
+        SlurmRunner,
     },
     config::Config,
     helpers::{
@@ -286,7 +288,8 @@ impl SlurmRunner for DeepSomatic {
             mem: Some("60G".into()),
             partition: Some("batch".into()),
             gres: None,
-        }.to_args()
+        }
+        .to_args()
     }
 }
 
@@ -354,9 +357,16 @@ impl DeepSomatic {
 
 impl Run for DeepSomatic {
     fn run(&mut self) -> anyhow::Result<()> {
-        run!(&self.config, self)?;
-        self.filter_pass()?;
-        Ok(())
+        if !self.should_run() {
+            anyhow::bail!("DeepSomatic is up-to-data.");
+        }
+
+        if self.config.slurm_runner {
+            run_deepsomatic_chunked(&self.id, &self.config, 30)
+        } else {
+            run!(&self.config, self)?;
+            self.filter_pass()
+        }
     }
 }
 
@@ -453,12 +463,13 @@ impl Version for DeepSomatic {
                     cpus_per_task: Some(1),
                     mem: Some("10G".into()),
                     gres: None,
-                }.to_args()
+                }
+                .to_args()
             }
         }
 
         let mut job = DeepSomaticVersionJob { config };
-        let out = crate::commands::SlurmRunner::run(&mut job)
+        let out = crate::commands::SlurmRunner::exec(&mut job)
             .context("Failed to run DeepSomatic --version via Slurm")?;
 
         let mut combined = out.stdout.clone();
@@ -531,18 +542,14 @@ fn merge_deepsomatic_parts(base: &DeepSomatic, n_parts: usize) -> anyhow::Result
 /// Runs DeepSomatic in parallel chunks, then merges results.
 ///
 /// Execution mode (local vs Slurm) is determined by `config.slurm_runner`.
-pub fn run_deepsomatic_chunked_with_merge(
-    id: &str,
-    config: &Config,
-    n_parts: usize,
-) -> anyhow::Result<Vec<CapturedOutput>> {
+pub fn run_deepsomatic_chunked(id: &str, config: &Config, n_parts: usize) -> anyhow::Result<()> {
     anyhow::ensure!(n_parts > 0, "n_parts must be > 0");
 
     let base = DeepSomatic::initialize(id, config)?;
 
     if !base.should_run() {
         debug!("DeepSomatic PASS VCF already up-to-date for {id}, skipping.");
-        return Ok(Vec::new());
+        return Ok(());
     }
 
     // Get genome sizes from tumor BAM header
@@ -576,6 +583,9 @@ pub fn run_deepsomatic_chunked_with_merge(
 
     // Run DeepSomatic jobs
     let outputs = run_many!(config, jobs.clone())?;
+    for output in outputs.iter() {
+        output.save_to_file(format!("{}/deepsomatic_", base.log_dir))?;
+    }
 
     // Filter PASS variants for each part in parallel
     info!(
@@ -598,7 +608,7 @@ pub fn run_deepsomatic_chunked_with_merge(
         id, actual_n_parts
     );
 
-    Ok(outputs)
+    Ok(())
 }
 
 #[cfg(test)]
@@ -621,8 +631,6 @@ mod tests {
     fn deepsomatic_run() -> anyhow::Result<()> {
         test_init();
         let config = Config::default();
-        let outputs = run_deepsomatic_chunked_with_merge("34528", &config, 30)?;
-        info!("Completed with {} job outputs", outputs.len());
-        Ok(())
+        run_deepsomatic_chunked("34528", &config, 30)
     }
 }

src/callers/deep_variant.rs

@@ -119,7 +119,6 @@ use crate::{
 };
 
 use crate::commands::{
-    CapturedOutput,
     Command as JobCommand, // your trait
     LocalRunner,
     SbatchRunner,
@@ -482,9 +481,16 @@ impl DeepVariant {
 
 impl Run for DeepVariant {
     fn run(&mut self) -> anyhow::Result<()> {
-        run!(&self.config, self)?;
-        self.filter_pass()?;
-        Ok(())
+        if !self.should_run() {
+            anyhow::bail!("DeepVariant is up-to-data.");
+        }
+
+        if self.config.slurm_runner {
+            run_deepvariant_chunked(&self.id, &self.time_point, &self.config, 30)
+        } else {
+            run!(&self.config, self)?;
+            self.filter_pass()
+        }
     }
 }
 
@@ -645,7 +651,7 @@ impl Version for DeepVariant {
 
         let mut job = DeepVariantVersionJob { config };
         let out =
-            SlurmRunner::run(&mut job).context("failed to run DeepVariant --version via Slurm")?;
+            SlurmRunner::exec(&mut job).context("failed to run DeepVariant --version via Slurm")?;
 
         // Combine stdout, Slurm epilog (if any), and stderr for parsing
         let mut combined = out.stdout.clone();
@@ -717,7 +723,8 @@ fn merge_deepvariant_parts(base: &DeepVariant, n_parts: usize) -> anyhow::Result
 
     let mut concat = BcftoolsConcat::from_config(&base.config, part_pass_paths, &final_tmp);
     run!(&base.config, &mut concat)
-        .context("Failed to run bcftools concat for DeepVariant parts")?;
+        .context("Failed to run bcftools concat for DeepVariant parts")?
+        .save_to_file(format!("{}/bcftools_concat", base.log_dir))?;
 
     fs::rename(&final_tmp, &final_passed_vcf)
         .context("Failed to rename merged DeepVariant PASS VCF")?;
@@ -733,19 +740,19 @@ fn merge_deepvariant_parts(base: &DeepVariant, n_parts: usize) -> anyhow::Result
 /// Runs DeepVariant in parallel chunks, then merges results.
 ///
 /// Execution mode (local vs Slurm) is determined by `config.slurm_runner`.
-pub fn run_deepvariant_chunked_with_merge(
+pub fn run_deepvariant_chunked(
     id: &str,
     time_point: &str,
     config: &Config,
     n_parts: usize,
-) -> anyhow::Result<Vec<CapturedOutput>> {
+) -> anyhow::Result<()> {
     anyhow::ensure!(n_parts > 0, "n_parts must be > 0");
 
     let base = DeepVariant::initialize(id, time_point, config)?;
 
     if !base.should_run() {
         debug!("DeepVariant PASS VCF already up-to-date for {id} {time_point}, skipping.");
-        return Ok(Vec::new());
+        return Ok(());
     }
 
     let bam_path = config.solo_bam(id, time_point);
@@ -778,6 +785,9 @@ pub fn run_deepvariant_chunked_with_merge(
 
     // Run all DeepVariant jobs
     let outputs = run_many!(config, jobs.clone())?;
+    for output in outputs.iter() {
+        output.save_to_file(format!("{}/deepvariant_", base.log_dir))?;
+    }
 
     // Filter PASS variants for each part
     info!(
@@ -800,7 +810,7 @@ pub fn run_deepvariant_chunked_with_merge(
         id, time_point, actual_n_parts
     );
 
-    Ok(outputs)
+    Ok(())
 }
 
 #[cfg(test)]
@@ -826,7 +836,7 @@ mod tests {
         let config = Config::default();
 
         for id in ["DUMCO", "CHAHA"] {
-            let _ = run_deepvariant_chunked_with_merge(id, "diag", &config, 30)?;
+            run_deepvariant_chunked(id, "diag", &config, 30)?;
         }
         Ok(())
     }

src/callers/mod.rs

@@ -5,9 +5,47 @@
 //! - Savana — <https://github.com/cortes-ciriano-lab/savana>
 //! - Severus — <https://github.com/genome-nexus/severus> (structural variants)
 //! - NanomonSV — <https://github.com/friend1ws/nanomonsv>
+
+use crate::{
+    callers::{clairs::ClairS, deep_somatic::DeepSomatic, deep_variant::DeepVariant, nanomonsv::NanomonSV, savana::Savana, severus::Severus},
+    config::Config,
+    pipes::{Initialize, InitializeSolo},
+    runners::Run,
+};
+
 pub mod clairs;
-pub mod deep_variant;
 pub mod deep_somatic;
+pub mod deep_variant;
+pub mod nanomonsv;
 pub mod savana;
 pub mod severus;
-pub mod nanomonsv;
+
+pub fn run_somatic_callers(id: &str, config: &Config) -> anyhow::Result<()> {
+    // DeepVariant
+    DeepVariant::initialize(id, &config.normal_name, config)?.run()?;
+    DeepVariant::initialize(id, &config.tumoral_name, config)?.run()?;
+    // ClairS
+    ClairS::initialize(id, config)?.run()?;
+    // Severus
+    Severus::initialize(id, config)?.run()?;
+    // Savana
+    Savana::initialize(id, config)?.run()?;
+    // Savana
+    NanomonSV::initialize(id, config)?.run()?;
+    // DeepSomatic
+    DeepSomatic::initialize(id, config)?.run()?;
+    Ok(())
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::helpers::test_init;
+
+    #[test]
+    fn callers_run_all() -> anyhow::Result<()> {
+        test_init();
+        let config = Config::default();
+        run_somatic_callers("DUMCO", &config)
+    }
+}

src/callers/nanomonsv.rs

@@ -219,6 +219,10 @@ impl Run for NanomonSV {
     /// 2. Running NanomonSV `get` for both samples.
     /// 3. Filtering final VCF to retain PASS variants only.
     fn run(&mut self) -> anyhow::Result<()> {
+        if !self.should_run() {
+            anyhow::bail!("NanomonSV is up-to-data.");
+        }
+
         let diag_bam = self.config.tumoral_bam(&self.id);
         let mrd_bam = self.config.normal_bam(&self.id);
 

src/callers/savana.rs

@@ -22,7 +22,7 @@
 //! Before running Savana, ensure:
 //! - Tumor and normal BAMs are indexed
 //! - Reference genome is accessible
-//! - Conda environment with Savana is configured (`config.conda_sh`)
+//! - Conda environment with Savana is configured (environment name: savana_env)
 //!
 //! ## Output Files
 //!
@@ -185,7 +185,7 @@ impl ShouldRun for Savana {
 impl JobCommand for Savana {
     fn cmd(&self) -> String {
         format!(
-            "source {conda_sh} && conda activate savana && {bin} {args}",
+            "source {conda_sh} && conda activate savana_env && {bin} {args}",
             conda_sh = self.config.conda_sh,
             bin = self.config.savana_bin,
             args = self.job_args.join(" ")
@@ -200,7 +200,7 @@ impl SlurmRunner for Savana {
         SlurmParams {
             job_name: Some("savana".into()),
             cpus_per_task: Some(self.config.savana_threads as u32),
-            mem: Some("120G".into()),
+            mem: Some("40G".into()),
             partition: Some("shortq".into()),
             gres: None,
         }
@@ -219,6 +219,10 @@ impl Run for Savana {
     ///
     /// `Ok(())` if the run completes successfully, or an error otherwise.
     fn run(&mut self) -> anyhow::Result<()> {
+        if !self.should_run() {
+            anyhow::bail!("Savana is up-to-data.");
+        }
+
         let output_vcf = &self.config.savana_output_vcf(&self.id);
         if !Path::new(&output_vcf).exists() {
             info!("Running Savana v{}", Savana::version(&self.config)?);
@@ -246,7 +250,7 @@ impl Run for Savana {
                     &phased_germline_vcf,
                     self.config.clone(),
                 );
-                run!(&self.config, &mut normal_hap)?;
+                crate::runners::Run::run(&mut normal_hap)?;
             }
 
             if !Path::new(&tumoral_hp_bam).exists() {
@@ -256,7 +260,7 @@ impl Run for Savana {
                     &phased_germline_vcf,
                     self.config.clone(),
                 );
-                run!(&self.config, &mut tumoral_hap)?;
+                crate::runners::Run::run(&mut tumoral_hap)?;
             }
 
             self.job_args = vec![
@@ -306,6 +310,16 @@ impl Run for Savana {
     }
 }
 
+impl Savana {
+    pub fn run(&mut self) -> anyhow::Result<()> {
+        if self.should_run() {
+            <Self as crate::runners::Run>::run(self)
+        } else {
+            anyhow::bail!("Savana is up-to-date.")
+        }
+    }
+}
+
 impl Version for Savana {
     /// Retrieves the Savana version by running `savana --version` in its conda environment.
     ///
@@ -322,17 +336,6 @@ impl Version for Savana {
             run!(&config, &mut job).context("Error while running `savana --version` (local)")?;
         parse_savana_version(&out)
     }
-
-    fn version_slurm(config: &Config) -> anyhow::Result<String> {
-        let mut job = Savana {
-            id: "version".into(),
-            config: config.clone(),
-            log_dir: config.tmp_dir.clone(),
-            job_args: vec!["--version".to_string()],
-        };
-        let out = SlurmRunner::run(&mut job).context("Failed to run Savana --version via Slurm")?;
-        parse_savana_version(&out)
-    }
 }
 
 fn parse_savana_version(out: &CapturedOutput) -> anyhow::Result<String> {
@@ -816,3 +819,28 @@ impl SavanaCN {
         Ok(Self { segments })
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::helpers::test_init;
+
+    #[test]
+    fn savana_version() -> anyhow::Result<()> {
+        test_init();
+        let vl = Savana::version(&Config::default())?;
+        info!("Savana version: {vl}");
+        Ok(())
+    }
+
+    #[test]
+    fn savana_run() -> anyhow::Result<()> {
+        test_init();
+        let config = Config::default();
+
+        let mut caller = Savana::initialize("DUMCO", &config)?;
+        caller.run()?;
+        // crate::runners::Run::run(&mut caller)?;
+        Ok(())
+    }
+}

src/callers/severus.rs

@@ -24,7 +24,7 @@
 //! - Tumor and normal BAMs (paired mode) or single BAM (solo mode)
 //! - VNTR annotation BED file (`config.vntrs_bed`)
 //! - Phased germline VCF (automatically generated via LongPhase if missing)
-//! - Conda environment with Severus configured
+//! - Conda environment with Severus configured (environment name: severus_env)
 //!
 //! ## Output Files
 //!
@@ -81,8 +81,8 @@ use crate::{
     annotation::{Annotation, Annotations, Caller, CallerCat, Sample},
     collection::vcf::Vcf,
     commands::{
-        bcftools::BcftoolsKeepPassPrecise, longphase::LongphasePhase,
-        Command as JobCommand, LocalRunner, SlurmParams, SlurmRunner,
+        bcftools::BcftoolsKeepPassPrecise, longphase::LongphasePhase, Command as JobCommand,
+        LocalRunner, SlurmParams, SlurmRunner,
     },
     config::Config,
     helpers::{is_file_older, remove_dir_if_exists},
@@ -181,7 +181,9 @@ impl Run for Severus {
     ///
     /// `Ok(())` if everything runs successfully; otherwise, an error with context.
     fn run(&mut self) -> anyhow::Result<()> {
-        info!("Running Severus v{}", Severus::version(&self.config)?);
+        if !self.should_run() {
+            anyhow::bail!("Severus is up-to-date");
+        }
 
         let id = &self.id;
         let output_vcf = &self.config.severus_output_vcf(id);
@@ -193,7 +195,8 @@ impl Run for Severus {
             // Run Longphase if necessary
             if !Path::new(constit_phased_vcf).exists() {
                 let mut phase = LongphasePhase::initialize(&self.id, &self.config)?;
-                run!(&self.config, &mut phase)?;
+                crate::runners::Run::run(&mut phase)?;
+                // run!(&self.config, &mut phase)?;
             }
 
             fs::create_dir_all(self.config.severus_output_dir(id))
@@ -244,7 +247,7 @@ impl Run for Severus {
             let report = run!(&self.config, &mut keep).context(format!(
                 "Error while running bcftools keep PASS for {output_vcf}"
             ))?;
-            let log_file = format!("{}/bcftools_pass", self.log_dir);
+            let log_file = format!("{}/severus_bcftools_pass", self.log_dir);
             report
                 .save_to_file(&log_file)
                 .context(format!("Error while writing logs into {log_file}"))?;
@@ -367,10 +370,19 @@ impl Version for Severus {
         };
         let out = run!(&config, &mut job).context("Error while running `severus --version`")?;
         let combined = format!("{}{}", out.stdout, out.stderr);
-        let v = combined
-            .split_once(':')
-            .map(|(_, value)| value.trim().to_string())
-            .ok_or_else(|| anyhow::anyhow!("Error while parsing `severus --version`"))?;
+        // Take first non-empty trimmed line
+        let line = combined
+            .lines()
+            .map(str::trim)
+            .find(|l| !l.is_empty())
+            .ok_or_else(|| anyhow::anyhow!("No output from `severus --version`"))?;
+
+        // Accept either "1.6" or "Severus version: 1.6"
+        let v = if let Some((_, value)) = line.split_once(':') {
+            value.trim().to_string()
+        } else {
+            line.to_string()
+        };
         Ok(v)
     }
 }
@@ -482,3 +494,31 @@ impl Run for SeverusSolo {
         Ok(())
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::helpers::test_init;
+
+    #[test]
+    fn severus_version() -> anyhow::Result<()> {
+        test_init();
+        let vl = Severus::version(&Config::default())?;
+        info!("Severus version: {vl}");
+        Ok(())
+    }
+
+    #[test]
+    fn severus_run() -> anyhow::Result<()> {
+        test_init();
+        let config = Config::default();
+        // let clairs = ClairS::initialize("34528", &config)?;
+        // info!("{clairs}");
+
+        let mut caller = Severus::initialize("DUMCO", &config)?;
+        caller.run()?;
+
+
+        Ok(())
+    }
+}

src/collection/prom_run.rs

@@ -74,18 +74,11 @@ use crate::{
     collection::{
         bam_stats::WGSBamStats,
         flowcells::IdInput,
-        minknow::{parse_pore_activity_from_reader, MinKnowSampleSheet, PoreStateEntry},
+        minknow::{MinKnowSampleSheet, PoreStateEntry, parse_pore_activity_from_reader},
         pod5::Pod5,
-    },
-    commands::{
-        dorado::DoradoAlign,
-        run_many_sbatch,
-        samtools::{SamtoolsIndex, SamtoolsMergeMany, SamtoolsSort},
-        SlurmRunner,
-    },
-    config::Config,
-    helpers::{get_genome_sizes, list_files_recursive, remove_bam_with_index, TempFileGuard},
-    run, run_many,
+    }, commands::{
+        SlurmRunner, dorado::DoradoAlign, modkit::ModkitSummary, run_many_sbatch, samtools::{SamtoolsIndex, SamtoolsMergeMany, SamtoolsSort}
+    }, config::Config, helpers::{TempFileGuard, get_genome_sizes, list_files_recursive, remove_bam_with_index}, pipes::InitializeSolo, run, run_many
 };
 
 /// Represent a complete ONT PromethION sequencing run with all associated files.
@@ -1174,7 +1167,7 @@ fn merge_chunk_bams(
     let mut merge_cmd =
         SamtoolsMergeMany::from_config(merged_path.clone(), chunk_bams.to_vec(), config);
 
-    SlurmRunner::run(&mut merge_cmd).with_context(|| {
+    SlurmRunner::exec(&mut merge_cmd).with_context(|| {
         format!(
             "Failed to merge {} chunk BAMs for case {}",
             chunk_bams.len(),
@@ -1486,6 +1479,7 @@ fn finalize_case_bams(
         }
 
         let stats = WGSBamStats::open(&case.case_id, &case.sample_type, config)?;
+        ModkitSummary::initialize(&case.case_id, &case.sample_type, config)?.run()?;
         info!("✅ Output: {}\n{stats}", final_bam_path.display());
         finalized.push(final_bam_path);
     }

src/commands/bcftools.rs

@@ -6,7 +6,7 @@
 //! or Slurm execution.
 
 use anyhow::Context;
-use log::info;
+use log::{debug, info};
 use std::{
     fs,
     path::{Path, PathBuf},
@@ -287,6 +287,8 @@ impl super::Command for BcftoolsConcat {
             .collect::<Vec<_>>()
             .join("\n");
 
+        debug!("Concatening:\n{list}");
+
         info!("Writing bcftools concat list: {}", self.tmp_list.display());
         fs::write(&self.tmp_list, list)?;
         Ok(())
@@ -516,7 +518,7 @@ mod tests {
 
         // 1) compress raw.vcf -> raw.vcf.gz
         let mut compress = BcftoolsCompress::from_config(&config, &raw, &raw_gz);
-        let out_compress = SlurmRunner::run(&mut compress)?;
+        let out_compress = SlurmRunner::exec(&mut compress)?;
         println!("{out_compress}");
         assert!(
             raw_gz.exists(),
@@ -525,7 +527,7 @@ mod tests {
 
         // 2) index raw.vcf.gz
         let mut index = BcftoolsIndex::from_config(&config, &raw_gz);
-        let out_index = SlurmRunner::run(&mut index)?;
+        let out_index = SlurmRunner::exec(&mut index)?;
         println!("{out_index}");
 
         let tbi = PathBuf::from(format!("{}.tbi", raw_gz.display()));
@@ -554,7 +556,7 @@ mod tests {
 
         // 1) compress raw.vcf -> raw.vcf.gz
         let mut compress = BcftoolsCompress::from_config(&config, &raw, &raw_gz);
-        let out_compress = SlurmRunner::run(&mut compress)?;
+        let out_compress = SlurmRunner::exec(&mut compress)?;
         println!("{out_compress}");
         assert!(
             raw_gz.exists(),
@@ -563,7 +565,7 @@ mod tests {
 
         // 2) index raw.vcf.gz
         let mut index = BcftoolsIndex::from_config(&config, &raw_gz);
-        let out_index = SlurmRunner::run(&mut index)?;
+        let out_index = SlurmRunner::exec(&mut index)?;
         println!("{out_index}");
 
         let raw_tbi = PathBuf::from(format!("{}.tbi", raw_gz.display()));
@@ -575,7 +577,7 @@ mod tests {
 
         // 3) keep only FILTER=PASS from raw.vcf.gz -> pass.vcf.gz (with index)
         let mut keep = BcftoolsKeepPass::from_config(&config, &raw_gz, &pass_vcf_gz);
-        let out_keep = SlurmRunner::run(&mut keep)?;
+        let out_keep = SlurmRunner::exec(&mut keep)?;
         println!("{out_keep}");
 
         assert!(
@@ -608,7 +610,7 @@ mod tests {
 
         // 1) compress raw.vcf -> raw.vcf.gz
         let mut compress = BcftoolsCompress::from_config(&config, &raw, &raw_gz);
-        let out_compress = SlurmRunner::run(&mut compress)?;
+        let out_compress = SlurmRunner::exec(&mut compress)?;
         println!("{out_compress}");
         assert!(
             raw_gz.exists(),
@@ -617,7 +619,7 @@ mod tests {
 
         // 2) index raw.vcf.gz
         let mut index = BcftoolsIndex::from_config(&config, &raw_gz);
-        let out_index = SlurmRunner::run(&mut index)?;
+        let out_index = SlurmRunner::exec(&mut index)?;
         println!("{out_index}");
 
         let tbi = PathBuf::from(format!("{}.tbi", raw_gz.display()));
@@ -630,7 +632,7 @@ mod tests {
         // 3) keep only precise FILTER=PASS from raw.vcf.gz
         let mut keep_precise =
             BcftoolsKeepPassPrecise::from_config(&config, &raw_gz, &pass_precise_vcf_gz);
-        let out_keep_precise = SlurmRunner::run(&mut keep_precise)?;
+        let out_keep_precise = SlurmRunner::exec(&mut keep_precise)?;
         println!("{out_keep_precise}");
         assert!(pass_precise_vcf_gz.exists());
         let pp_tbi = PathBuf::from(format!("{}.tbi", pass_precise_vcf_gz.display()));
@@ -665,9 +667,9 @@ mod tests {
         let mut c1 = BcftoolsCompress::from_config(&config, &raw1, &gz1);
         let mut c2 = BcftoolsCompress::from_config(&config, &raw2, &gz2);
         let mut c3 = BcftoolsCompress::from_config(&config, &raw3, &gz3);
-        SlurmRunner::run(&mut c1)?;
-        SlurmRunner::run(&mut c2)?;
-        SlurmRunner::run(&mut c3)?;
+        SlurmRunner::exec(&mut c1)?;
+        SlurmRunner::exec(&mut c2)?;
+        SlurmRunner::exec(&mut c3)?;
         assert!(
             gz1.exists() && gz2.exists() && gz3.exists(),
             "all compressed VCFs should exist"
@@ -677,9 +679,9 @@ mod tests {
         let mut i1 = BcftoolsIndex::from_config(&config, &gz1);
         let mut i2 = BcftoolsIndex::from_config(&config, &gz2);
         let mut i3 = BcftoolsIndex::from_config(&config, &gz3);
-        SlurmRunner::run(&mut i1)?;
-        SlurmRunner::run(&mut i2)?;
-        SlurmRunner::run(&mut i3)?;
+        SlurmRunner::exec(&mut i1)?;
+        SlurmRunner::exec(&mut i2)?;
+        SlurmRunner::exec(&mut i3)?;
         // just basic existence checks; index suffix may be .tbi or .csi
         assert!(
             gz1.with_extension("vcf.gz.tbi").exists()
@@ -690,7 +692,7 @@ mod tests {
 
         // 3) concat compressed VCFs (bcftools can concat bgzip VCFs)
         let mut concat = BcftoolsConcat::from_config(&config, vec![&gz1, &gz2, &gz3], &concat_gz);
-        let out_concat = SlurmRunner::run(&mut concat)?;
+        let out_concat = SlurmRunner::exec(&mut concat)?;
         println!("{out_concat}");
         assert!(concat_gz.exists(), "concatenated BGZF VCF should exist");
 

src/commands/dorado.rs

@@ -291,7 +291,7 @@ mod tests {
         );
 
         info!("Basecalling");
-        let out = SlurmRunner::run(&mut dca)?;
+        let out = SlurmRunner::exec(&mut dca)?;
 
         println!("{out:#?}");
 
@@ -311,7 +311,7 @@ mod tests {
         );
 
         info!("Basecalling");
-        let _out = SlurmRunner::run(&mut dca)?;
+        let _out = SlurmRunner::exec(&mut dca)?;
 
         Ok(())
     }

src/commands/longphase.rs

@@ -2,13 +2,10 @@
 //!
 //! All steps use the shared runner traits (local/Slurm) driven by the global `Config`.
 use crate::{
-    commands::bcftools::{BcftoolsCompress, BcftoolsIndex, BcftoolsKeepPass},
-    commands::samtools::SamtoolsIndex,
-    config::Config,
-    helpers::path_prefix,
-    pipes::{Initialize, InitializeSolo},
-    run,
-    runners::Run,
+    callers::deep_variant::DeepVariant, commands::{
+        bcftools::{BcftoolsCompress, BcftoolsIndex, BcftoolsKeepPass},
+        samtools::SamtoolsIndex,
+    }, config::Config, helpers::{is_file_older, path_prefix}, pipes::{Initialize, InitializeSolo, ShouldRun}, run, runners::Run
 };
 use anyhow::Context;
 use std::{
@@ -49,8 +46,10 @@ impl LongphaseHap {
             job_args: Vec::new(),
         }
     }
+}
 
-    pub fn run(&mut self) -> anyhow::Result<()> {
+impl Run for LongphaseHap {
+    fn run(&mut self) -> anyhow::Result<()> {
         if self.config.longphase_force && self.bam_hp.exists() {
             fs::remove_file(&self.bam_hp)?;
         }
@@ -84,8 +83,8 @@ impl LongphaseHap {
 
             let bam_to_index = format!("{}.bam", self.bam_hp.to_string_lossy());
             let mut sam_index = SamtoolsIndex {
-                bin: self.config.longphase_bin.clone(),
-                threads: self.config.longphase_threads,
+                bin: self.config.align.samtools_bin.clone(),
+                threads: self.config.align.samtools_view_threads,
                 bam: bam_to_index.clone(),
             };
             run!(&self.config, &mut sam_index)
@@ -104,13 +103,15 @@ impl crate::commands::Command for LongphaseHap {
     }
 }
 
+
+
 impl crate::commands::LocalRunner for LongphaseHap {}
 
 impl crate::commands::SlurmRunner for LongphaseHap {
     fn slurm_args(&self) -> Vec<String> {
         crate::commands::SlurmParams {
             job_name: Some(format!("longphase_hap_{}", self.id)),
-            cpus_per_task: Some(self.config.longphase_threads as u32),
+            cpus_per_task: Some(self.config.longphase_threads as u32 + 1),
             mem: Some("60G".into()),
             partition: Some("shortq".into()),
             gres: None,
@@ -134,15 +135,16 @@ pub struct LongphasePhase {
 
 impl Initialize for LongphasePhase {
     fn initialize(id: &str, config: &crate::config::Config) -> anyhow::Result<Self> {
+        info!("Initializing longphase phase for germline variants of: {id}");
         let log_dir = format!("{}/{}/log/longphase_phase", config.result_dir, id);
         if !Path::new(&log_dir).exists() {
             fs::create_dir_all(&log_dir)
                 .context(format!("Failed  to create {log_dir} directory"))?;
         }
         let vcf = config.constit_vcf(id);
-        let bam = config.tumoral_bam(id);
+        let bam = config.normal_bam(id);
         let out_prefix = path_prefix(&config.constit_phased_vcf(id))?;
-        let modcall_vcf = config.longphase_modcall_vcf(id, "diag");
+        let modcall_vcf = config.longphase_modcall_vcf(id, &config.normal_name);
 
         Ok(LongphasePhase {
             id: id.to_string(),
@@ -183,6 +185,12 @@ impl Run for LongphasePhase {
         info!("Running longphase phase for: {}", self.vcf);
         info!("Saving longphase phase results in: {}", self.out_prefix);
 
+        let mut modcall =
+            LongphaseModcallSolo::initialize(&self.id, &self.config.normal_name, &self.config)?;
+        if modcall.should_run() {
+            modcall.run()?;
+        }
+
         let final_vcf = self.config.constit_phased_vcf(&self.id);
         if !Path::new(&final_vcf).exists() {
             self.job_args = vec![
@@ -259,10 +267,9 @@ impl InitializeSolo for LongphaseModcallSolo {
         }
 
         let mut modkit_summary = ModkitSummary::initialize(&id, &time, config)?;
-        modkit_summary.load()?;
         let mod_threshold = modkit_summary
-            .result
-            .ok_or_else(|| anyhow::anyhow!("Error no ModkitSummary for {id} {time}"))?
+            .load()
+            .context(format!("Error no ModkitSummary for {id} {time}"))?
             .pass_threshold;
 
         let out_vcf = config.longphase_modcall_vcf(&id, &time);
@@ -287,6 +294,17 @@ impl InitializeSolo for LongphaseModcallSolo {
     }
 }
 
+impl ShouldRun for LongphaseModcallSolo {
+    fn should_run(&self) -> bool {
+        is_file_older(
+            &self.config.longphase_modcall_vcf(&self.id, &self.time),
+            &self.config.solo_bam(&self.id, &self.time),
+            true,
+        )
+        .unwrap_or(true)
+    }
+}
+
 impl crate::commands::Command for LongphaseModcallSolo {
     fn cmd(&self) -> String {
         format!("{} {}", self.config.longphase_bin, self.job_args.join(" "))
@@ -320,6 +338,9 @@ impl Run for LongphaseModcallSolo {
             self.reference.clone(),
             "-m".to_string(),
             self.mod_threshold.to_string(),
+            "-s".to_string(),
+            self.config.clairs_germline_passed_vcf(&self.id),
+            "--all".to_string(),
             "-o".to_string(),
             self.prefix.clone(),
         ];

src/commands/mod.rs

@@ -50,7 +50,7 @@ pub trait LocalRunner: Command {
 
     /// Run locally with:
     ///     <shell> -c "<cmd()>"
-    fn run(&mut self) -> anyhow::Result<CapturedOutput> {
+    fn exec(&mut self) -> anyhow::Result<CapturedOutput> {
         self.init()?;
         let mut cmd = ProcessCommand::new(self.shell());
         cmd.arg("-c")
@@ -256,7 +256,7 @@ pub trait SlurmRunner: Command {
     /// ```text
     /// <slurm_bin> <slurm_args...> bash -lc "<cmd()>"
     /// ```
-    fn run(&mut self) -> anyhow::Result<CapturedOutput> {
+    fn exec(&mut self) -> anyhow::Result<CapturedOutput> {
         self.init()?;
 
         let mut cmd = ProcessCommand::new(self.slurm_bin());
@@ -639,9 +639,9 @@ pub trait SbatchRunner: Command {
 macro_rules! run {
     ($cfg:expr, $cmd:expr) => {{
         if $cfg.slurm_runner {
-            $crate::commands::SlurmRunner::run($cmd)
+            $crate::commands::SlurmRunner::exec($cmd)
         } else {
-            $crate::commands::LocalRunner::run($cmd)
+            $crate::commands::LocalRunner::exec($cmd)
         }
     }};
 }

src/commands/modkit.rs

@@ -1,214 +1,74 @@
-use std::{
-    fs::{self, File}, io::{BufRead, BufReader}, path::{Path, PathBuf}, str::FromStr
-};
+use std::{fs::File, io::{BufRead, BufReader}, path::Path, str::FromStr};
 
 use anyhow::Context;
 
 use crate::{
+    commands::{Command, LocalRunner, SlurmParams, SlurmRunner},
+    config::Config,
     pipes::InitializeSolo,
-    runners::{run_wait, CommandRun, Run},
+    run,
 };
 
-#[derive(Debug, Clone)]
-pub struct ModkitConfig {
-    pub bin: String,
-    pub crabz_bin: String,
-    pub tabix_bin: String,
-    pub reference: String,
-    pub cgi: String,
-    pub threads: u8,
-    pub result_dir: String,
+pub struct ModkitSummary {
+    id: String,
+    time: String,
+    config: Config,
 }
+impl InitializeSolo for ModkitSummary {
+    fn initialize(id: &str, time: &str, config: &Config) -> anyhow::Result<Self> {
+        Ok(Self {
+            id: id.to_string(),
+            time: time.to_string(),
 
-impl Default for ModkitConfig {
-    fn default() -> Self {
-        Self {
-            bin: "modkit".to_string(),
-            crabz_bin: "crabz".to_string(),
-            tabix_bin: "tabix".to_string(),
-            reference: "/data/ref/hs1/chm13v2.0.fa".to_string(),
-            cgi: "/data/ref/hs1/chm13v2.0_CGI_corrected.bed".to_string(),
-            threads: 155,
-            result_dir: "/data/longreads_basic_pipe".to_string(),
-        }
+            config: config.clone(),
+        })
     }
 }
 
-pub fn bed_methyl(bam: PathBuf, config: &ModkitConfig) -> anyhow::Result<()> {
-    let dir = bam
-        .parent()
-        .context(format!("No parent dir for {}", bam.display()))?;
-    let meth_dir = dir.join("5mC_5hmC");
-
-    // create modified base dir
-    if !meth_dir.exists() {
-        fs::create_dir(&meth_dir).context(format!("Can't create {}", meth_dir.display()))?;
+impl Command for ModkitSummary {
+    fn cmd(&self) -> String {
+        format!(
+            "{} summary -t {} {} > {}",
+            self.config.modkit_bin,
+            self.config.modkit_summary_threads,
+            self.config.solo_bam(&self.id, &self.time),
+            self.config.modkit_summary_file(&self.id, &self.time)
+        )
     }
-    // let time_point_dir = dir
-    //     .parent()
-    //     .context(format!("No parent dir for {}", dir.display()))?;
-    let time_point = dir.file_name().unwrap().to_str().unwrap();
-
-    let id_dir = dir
-        .parent()
-        .context(format!("No parent dir for {}", dir.display()))?;
-    let id = id_dir.file_name().unwrap().to_str().unwrap();
-
-    let pileup_bed = meth_dir.join(format!("{id}_{time_point}_5mC_5hmC_modPileup.bed"));
-
-    let pileup_bed_str = pileup_bed.to_str().unwrap();
-    let mut cmd_run = CommandRun::new(
-        &config.bin,
-        &[
-            "pileup",
-            "-t",
-            &config.threads.to_string(),
-            bam.to_str().unwrap(),
-            pileup_bed_str,
-            "--log-filepath",
-            meth_dir.join("pileup.log").to_str().unwrap(),
-        ],
-    );
-    let _ = run_wait(&mut cmd_run)?;
-
-    let mut cmd_compress =
-        CommandRun::new(&config.crabz_bin, &["-I", "-f", "bgzf", pileup_bed_str]);
-    let _ = run_wait(&mut cmd_compress).context(format!(
-        "Error while runnig crabz for {}",
-        pileup_bed.display()
-    ))?;
-
-    let final_bed = format!("{pileup_bed_str}.gz");
-    let mut cmd_tabix = CommandRun::new(&config.tabix_bin, &[&final_bed]);
-    let _ =
-        run_wait(&mut cmd_tabix).context(format!("Error while runnig tabix for {final_bed}"))?;
-
-    Ok(())
-}
-
-pub fn modkit_dmr(
-    a: &str,
-    b: &str,
-    out: &str,
-    base: &str,
-    config: &ModkitConfig,
-) -> anyhow::Result<()> {
-    let args = [
-        "dmr",
-        "pair",
-        "-m",
-        base,
-        "--ref",
-        &config.reference,
-        "-r",
-        &config.cgi,
-        "-t",
-        &config.threads.to_string(),
-        "-a",
-        a,
-        "-b",
-        b,
-        "-o",
-        out,
-    ];
-    let mut cmd_run = CommandRun::new(&config.bin, &args);
-    run_wait(&mut cmd_run).context(format!("Error while running modkit {}", args.join(" ")))?;
-
-    let mut cmd_tabix = CommandRun::new(&config.tabix_bin, &[out]);
-    let _ = run_wait(&mut cmd_tabix).context(format!("Error while runnig tabix for {out}"))?;
-    Ok(())
-}
-
-pub fn dmr_c_mrd_diag(id: &str, config: &ModkitConfig) -> anyhow::Result<()> {
-    let mrd = format!(
-        "{}/{id}/mrd/5mC_5hmC/{id}_mrd_5mC_5hmC_modPileup.bed.gz",
-        config.result_dir
-    );
-    let diag = format!(
-        "{}/{id}/diag/5mC_5hmC/{id}_diag_5mC_5hmC_modPileup.bed.gz",
-        config.result_dir
-    );
-    let out = format!(
-        "{}/{id}/diag/5mC_5hmC/{id}_diag_5mC_5hmC_DMR_C_mrd.bed.gz",
-        config.result_dir
-    );
-
-    modkit_dmr(&mrd, &diag, &out, "C", config)
-}
-
-pub struct ModkitSummary {
-    pub id: String,
-    pub time: String,
-    pub bam: String,
-    pub threads: u8,
-    pub log_dir: String,
-    pub summary_file: String,
-    pub result: Option<ModkitSummaryResult>,
 }
 
-impl InitializeSolo for ModkitSummary {
-    fn initialize(id: &str, time: &str, config: &crate::config::Config) -> anyhow::Result<Self> {
-        let id = id.to_string();
-        let time = time.to_string();
-        let log_dir = format!("{}/{}/log/modkit_summary", config.result_dir, id);
-        if !Path::new(&log_dir).exists() {
-            fs::create_dir_all(&log_dir)
-                .context(format!("Failed  to create {log_dir} directory"))?;
+impl LocalRunner for ModkitSummary {}
+impl SlurmRunner for ModkitSummary {
+    fn slurm_args(&self) -> Vec<String> {
+        SlurmParams {
+            job_name: Some(format!("modkit_summary_{}_{}", self.id, self.time)),
+            cpus_per_task: Some(self.config.modkit_summary_threads.into()),
+            mem: Some("40G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
         }
-
-        let bam = config.solo_bam(&id, &time);
-        if !Path::new(&bam).exists() {
-            anyhow::bail!("Required bam file doesn't exist: {bam}");
-        }
-
-        let summary_file = config.modkit_summary_file(&id, &time);
-        Ok(ModkitSummary {
-            id,
-            time,
-            bam,
-            log_dir,
-            result: None,
-            summary_file,
-            threads: config.modkit_summary_threads,
-        })
+        .to_args()
     }
 }
 
-impl Run for ModkitSummary {
-    fn run(&mut self) -> anyhow::Result<()> {
-        let modkit_args = [
-            "summary",
-            "-t",
-            &self.threads.to_string(),
-            &self.bam,
-            ">",
-            &self.summary_file
-        ];
-        let args = [
-            "-c",
-            &modkit_args.join(" ")
-        ];
-        let mut cmd_run = CommandRun::new("bash", &args);
-        let report = run_wait(&mut cmd_run).context(format!(
-            "Error while running `modkit summary {}`",
-            args.join(" ")
+impl ModkitSummary {
+    pub fn run(&mut self) -> anyhow::Result<()> {
+        let report = run!(&self.config, self)?;
+        let log_prefix = format!("{}/{}/log/modkit", self.config.result_dir, self.id);
+        report.save_to_file(&log_prefix).context(format!(
+            "Error while writing Severus logs into {log_prefix}"
         ))?;
-
-        let log_file = format!("{}/modkit_summary_", self.log_dir);
-        report
-            .save_to_file(&log_file)
-            .context(format!("Error while writing logs into {log_file}"))?;
         Ok(())
     }
 }
 
 impl ModkitSummary {
-    pub fn load(&mut self) -> anyhow::Result<()> {
-        if !Path::new(&self.summary_file).exists() {
+    pub fn load(&mut self) -> anyhow::Result<ModkitSummaryResult> {
+        let summary_file = self.config.modkit_summary_file(&self.id, &self.time);
+        if !Path::new(&summary_file).exists() {
             self.run()?;
         }
-        self.result = Some(ModkitSummaryResult::parse_file(&self.summary_file)?);
-        Ok(())
+        ModkitSummaryResult::parse_file(&summary_file)
     }
 }
 
@@ -297,3 +157,29 @@ where
         .context(format!("Invalid {} line", key))?;
     T::from_str(value).context(format!("Failed to parse {} value", key))
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::helpers::test_init;
+
+    #[test]
+    fn modkit_version() -> anyhow::Result<()> {
+        test_init();
+        // let vl = Severus::version(&Config::default())?;
+        // info!("Severus version: {vl}");
+        Ok(())
+    }
+
+    #[test]
+    fn modkit_summary() -> anyhow::Result<()> {
+        test_init();
+        let config = Config::default();
+
+        let mut caller = ModkitSummary::initialize("DUMCO", "diag", &config)?;
+        caller.run()?;
+
+
+        Ok(())
+    }
+}

src/commands/samtools.rs

@@ -647,7 +647,7 @@ mod tests {
             format!("{}/outputs/to_be_merged.bam", TEST_DIR.as_str()),
         );
 
-        let captured_output = SlurmRunner::run(&mut idx)?;
+        let captured_output = SlurmRunner::exec(&mut idx)?;
         assert_eq!(captured_output.stderr, String::new());
 
         Ok(())
@@ -664,7 +664,7 @@ mod tests {
             format!("{}/outputs/by_rg_splitted", TEST_DIR.as_str()),
         );
 
-        let captured_output = SlurmRunner::run(&mut cmd)?;
+        let captured_output = SlurmRunner::exec(&mut cmd)?;
         assert_eq!(captured_output.stderr, String::new());
 
         Ok(())

src/helpers.rs

@@ -764,7 +764,7 @@ pub fn detect_repetition(s: &str) -> Repeat {
 }
 
 pub fn test_init() {
-    let _ = env_logger::Builder::from_env(env_logger::Env::default().default_filter_or("info"))
+    let _ = env_logger::Builder::from_env(env_logger::Env::default().default_filter_or("debug"))
         .try_init();
 }
 

src/lib.rs

@@ -141,7 +141,6 @@ pub mod functions;
 pub mod helpers;
 pub mod io;
 pub mod math;
-pub mod modkit;
 pub mod pipes;
 pub mod positions;
 pub mod runners;

src/modkit.rs

@@ -1,74 +0,0 @@
-use std::{
-    io::{BufRead, BufReader},
-    process::Command,
-};
-
-pub fn modkit(bam_path: &str) {
-    // Command to execute your installed CLI application
-    let mut cmd = Command::new("modkit");
-
-    // Optionally, you can add arguments to the command
-    cmd.arg("summary").arg(bam_path);
-
-    // Spawn the command and obtain a handle to its output
-    let mut child = cmd
-        .stdout(std::process::Stdio::piped())
-        .spawn()
-        .expect("Failed to start command");
-
-    if let Some(stdout) = child.stdout.take() {
-        print_stdout(stdout);
-    }
-
-    // let stdout = child.stdout.take().expect("Failed to open stdout");
-
-    // Create a buffer to store the output
-    // let mut reader = std::io::BufReader::new(stdout);
-    // let mut output = String::new();
-    //
-    // loop {
-    //     // Read the output of the command
-    //     match reader.read_line(&mut output) {
-    //         Ok(0) => break, // End of output
-    //         Ok(_) => {
-    //             // Print or process the output here
-    //             print!("{}", output);
-    //             io::stdout().flush().unwrap();
-    //             // print!("{}[2J", 27 as char);
-    //             print!("\x1B[2J\x1B[1;1H");
-    //
-    //             output.clear();
-    //         }
-    //         Err(err) => {
-    //             eprintln!("Error reading from stdout: {}", err);
-    //             break;
-    //         }
-    //     }
-    //
-    //     // Optionally, you can add a delay to control refresh rate
-    //     std::thread::sleep(Duration::from_millis(100));
-    // }
-
-    // Wait for the command to finish
-    child.wait().expect("Command didn't finish");
-}
-
-// fn print_stderr(stderr: std::process::ChildStderr) {
-//     let stderr_reader = BufReader::new(stderr);
-//     for line in stderr_reader.lines() {
-//         match line {
-//             Ok(line) => eprintln!("{}", line),
-//             Err(err) => eprintln!("Error reading stderr: {}", err),
-//         }
-//     }
-// }
-//
-fn print_stdout(stdout: std::process::ChildStdout) {
-    let stdout_reader = BufReader::new(stdout);
-    for line in stdout_reader.lines() {
-        match line {
-            Ok(line) => eprintln!("{}", line),
-            Err(err) => eprintln!("Error reading stderr: {}", err),
-        }
-    }
-}

src/pipes/somatic_slurm.rs

@@ -305,7 +305,7 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
         // DoradoBasecall must accept a directory of POD5s here
         let mut cmd =
             DoradoBasecall::from_config(config, local_pod5_dir.clone(), tmp_basecalled_bam.clone());
-        let _out = SlurmRunner::run(&mut cmd)?;
+        let _out = SlurmRunner::exec(&mut cmd)?;
         info!("Basecalled ✅ (run: {})", run.run_id);
 
         // Split by read group
@@ -317,7 +317,7 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
 
         let mut cmd =
             SamtoolsSplit::from_config(config, &tmp_basecalled_bam, local_split_dir.clone());
-        let _out = SlurmRunner::run(&mut cmd)?;
+        let _out = SlurmRunner::exec(&mut cmd)?;
         fs::remove_file(&tmp_basecalled_bam).context(format!(
             "Failed to remove temporary basecalled BAM: {}",
             tmp_basecalled_bam.display()
@@ -455,7 +455,7 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
             );
 
             let mut sort_cmd = SamtoolsSort::from_config(config, &bam, &sorted_bam);
-            SlurmRunner::run(&mut sort_cmd)?;
+            SlurmRunner::exec(&mut sort_cmd)?;
 
             // remove unsorted chunk
             fs::remove_file(&bam)?;
@@ -465,7 +465,7 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
                 threads: config.align.samtools_view_threads,
                 bam: sorted_bam.to_string_lossy().to_string(),
             };
-            SlurmRunner::run(&mut index_cmd)?;
+            SlurmRunner::exec(&mut index_cmd)?;
 
             // replace path in case_bam_map with sorted version
             *bam = sorted_bam;
@@ -531,7 +531,7 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
 
             let mut merge_many_cmd =
                 SamtoolsMergeMany::from_config(tmp_merged.clone(), aligned_bams.clone(), config);
-            SlurmRunner::run(&mut merge_many_cmd)?;
+            SlurmRunner::exec(&mut merge_many_cmd)?;
 
             // Remove chunk BAMs and their indices
             for bam in aligned_bams {
@@ -561,19 +561,19 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
                 threads: config.align.samtools_view_threads,
                 bam: case_merged_bam.to_string_lossy().to_string(),
             };
-            SlurmRunner::run(&mut index_cmd)?;
+            SlurmRunner::exec(&mut index_cmd)?;
 
             let mut index_cmd = SamtoolsIndex {
                 bin: config.align.samtools_bin.clone(),
                 threads: config.align.samtools_view_threads,
                 bam: final_bam_path.to_string_lossy().to_string(),
             };
-            SlurmRunner::run(&mut index_cmd)?;
+            SlurmRunner::exec(&mut index_cmd)?;
 
             // Merge into existing final BAM.
             let mut merge_cmd =
                 SamtoolsMerge::from_config(config, &case_merged_bam, &final_bam_path);
-            SlurmRunner::run(&mut merge_cmd)?;
+            SlurmRunner::exec(&mut merge_cmd)?;
         } else {
             info!(
                 "  Creating new final BAM for case {} → {}",
@@ -598,7 +598,7 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
         );
 
         let mut sort_cmd = SamtoolsSort::from_config(config, &final_bam_path, &sorted_tmp);
-        SlurmRunner::run(&mut sort_cmd)?;
+        SlurmRunner::exec(&mut sort_cmd)?;
 
         // Replace unsorted BAM with sorted BAM
         fs::rename(&sorted_tmp, &final_bam_path)?;
@@ -609,7 +609,7 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
             threads: config.align.samtools_view_threads,
             bam: final_bam_path.to_string_lossy().to_string(),
         };
-        SlurmRunner::run(&mut index_cmd)?;
+        SlurmRunner::exec(&mut index_cmd)?;
 
         info!("  Output: {}", final_bam_path.display());