fbinv

.gitignore

@@ -1,2 +1,4 @@
 /target
 .temp_*
+*.out
+*.dat

pandora-config.example.toml

@@ -281,6 +281,43 @@ severus_output_dir = "{result_dir}/{id}/diag/severus"
 # {result_dir}, {id}, {time}
 severus_solo_output_dir = "{result_dir}/{id}/{time}/severus"
 
+#######################################
+# Straglr configuration
+#######################################
+
+# Path to Straglr executable.
+straglr_bin = "/home/t_steimle/.conda/envs/straglr_env/bin/straglr.py"
+
+# Path to STR loci BED file for Straglr.
+#
+# RepeatMasker Simple_repeat
+straglr_loci_bed = "/home/t_steimle/ref/hs1/simple_repeat_ucsc_hs1.bed"
+
+# Size of reported difference between normal and tumoral
+straglr_min_diff = 4
+
+# Minimum read support for STR genotyping.
+straglr_min_support = 2
+
+# Minimum cluster size for STR detection.
+straglr_min_cluster_size = 2
+
+# Whether to genotype in size mode.
+straglr_genotype_in_size = true
+
+# Template for paired Straglr output directory.
+#
+# Placeholders: `{result_dir}`, `{id}`.
+straglr_output_dir = "{result_dir}/{id}/diag/straglr"
+
+# Template for solo Straglr output directory.
+#
+# Placeholders: `{result_dir}`, `{id}`, `{time}`.
+straglr_solo_output_dir = "{result_dir}/{id}/{time}/straglr"
+
+# Force Straglr recomputation.
+straglr_force = false
+
 #######################################
 # Bcftools configuration
 #######################################
@@ -303,7 +340,7 @@ longphase_threads = 20
 
 # Threads for longphase modcall step.
 # limit memory usage here
-longphase_modcall_threads = 4
+longphase_modcall_threads = 6
 
 # Force longphase recomputation (haplotagging/phasing).
 longphase_force = false

slurm-2556285.out

@@ -1,1120 +0,0 @@
-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

@@ -1,837 +0,0 @@
-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

@@ -1,976 +0,0 @@
-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

@@ -1,835 +0,0 @@
-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

@@ -1,846 +0,0 @@
-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

@@ -1,708 +0,0 @@
-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

@@ -1,644 +0,0 @@
-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

@@ -1,322 +0,0 @@
-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

@@ -1,449 +0,0 @@
-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

@@ -1,298 +0,0 @@
-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

@@ -1,228 +0,0 @@
-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-2556296.out

@@ -1,138 +0,0 @@
-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/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/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: 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/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/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/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: 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/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
-
-[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/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/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/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

@@ -1,1106 +0,0 @@
-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

@@ -1,774 +0,0 @@
-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

@@ -1,964 +0,0 @@
-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

@@ -1,774 +0,0 @@
-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

@@ -1,964 +0,0 @@
-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

@@ -1,632 +0,0 @@
-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

@@ -1,562 +0,0 @@
-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

@@ -1,631 +0,0 @@
-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

@@ -1,514 +0,0 @@
-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

@@ -1,354 +0,0 @@
-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 +171,14 @@ use crate::{
     collection::vcf::Vcf,
     commands::{
         bcftools::{BcftoolsConcat, BcftoolsKeepPass},
+        samtools::SamtoolsMergeMany,
         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,
+        get_genome_sizes, is_file_older, list_files_recursive, remove_dir_if_exists,
+        singularity_bind_flags, split_genome_into_n_regions_exact,
     },
     io::vcf::read_vcf,
     pipes::{Initialize, ShouldRun, Version},
@@ -379,7 +380,7 @@ impl SlurmRunner for ClairS {
         SlurmParams {
             job_name: Some(format!("clairs_{}", self.id)),
             cpus_per_task: Some(self.config.clairs_threads as u32),
-            mem: Some("60G".into()),
+            mem: Some("80G".into()),
             partition: Some("shortq".into()),
             gres: None,
         }
@@ -392,7 +393,7 @@ impl SbatchRunner for ClairS {
         SlurmParams {
             job_name: Some(format!("clairs_{}", self.id)),
             cpus_per_task: Some(self.config.clairs_threads as u32),
-            mem: Some("50G".into()),
+            mem: Some("70G".into()),
             partition: Some("shortq".into()),
             gres: None,
         }
@@ -406,11 +407,42 @@ impl Run for ClairS {
         }
 
         if self.config.slurm_runner {
-            run_clairs_chunked(&self.id, &self.config, 30)
+            run_clairs_chunked(&self.id, &self.config, 50)?;
+            merge_haplotaged_tmp_bam(&self.config, &self.id)?;
         } else {
             run!(&self.config, self)?;
-            self.postprocess()
+            let mut germline = self.process_germline()?;
+            let report = run!(&self.config, &mut germline)
+                .with_context(|| format!("Failed to filter germline PASS for {}", self.id))?;
+
+            report
+                .save_to_file(format!("{}/bcftools_germline_pass_", self.log_dir))
+                .context("Failed to save germline PASS logs")?;
+            let (mut concat, tmp_path) = self.process_somatic_concat()?;
+            let (snv_vcf, indel_vcf) = self.config.clairs_output_vcfs(&self.id);
+
+            let report = run!(&self.config, &mut concat)
+                .with_context(|| format!("Failed to concat {} and {}", snv_vcf, indel_vcf))?;
+
+            report
+                .save_to_file(format!("{}/bcftools_concat_", self.log_dir))
+                .context("Failed to save concat logs")?;
+
+            let mut keep_pass = self.process_somatic_pass(&tmp_path)?;
+            let report = run!(&self.config, &mut keep_pass)
+                .with_context(|| format!("Failed to filter PASS for {}", self.id))?;
+
+            report
+                .save_to_file(format!("{}/bcftools_pass_", self.log_dir))
+                .context("Failed to save PASS filter logs")?;
+
+            // Clean up temporary concatenated VCF
+            debug!("Removing temporary file: {}", tmp_path);
+            if let Err(e) = fs::remove_file(&tmp_path) {
+                warn!("Failed to remove temporary file {}: {}", tmp_path, e);
+            }
         }
+        Ok(())
     }
 }
 
@@ -429,24 +461,9 @@ impl ClairS {
         }
     }
 
-    /// Post-processes ClairS output (concat SNV+indel, filter PASS).
-    fn postprocess(&self) -> anyhow::Result<()> {
-        self.process_germline()?;
-        self.process_somatic()?;
-        Ok(())
-    }
-
-    fn process_germline(&self) -> anyhow::Result<()> {
+    fn process_germline(&self) -> anyhow::Result<BcftoolsKeepPass> {
         let germline_passed = self.germline_passed_vcf_path();
 
-        if Path::new(&germline_passed).exists() {
-            debug!(
-                "ClairS germline PASS VCF already exists for {} part {:?}",
-                self.id, self.part_index
-            );
-            return Ok(());
-        }
-
         let germline_input = match self.part_index {
             Some(_) => {
                 let output_dir = self.part_output_dir();
@@ -465,30 +482,13 @@ impl ClairS {
             self.id, self.part_index
         );
 
-        let mut cmd =
+        let cmd =
             BcftoolsKeepPass::from_config(&self.config, germline_input, germline_passed.clone());
 
-        let report = run!(&self.config, &mut cmd)
-            .with_context(|| format!("Failed to filter germline PASS for {}", self.id))?;
-
-        report
-            .save_to_file(format!("{}/bcftools_germline_pass_", self.log_dir))
-            .context("Failed to save germline PASS logs")?;
-
-        Ok(())
+        Ok(cmd)
     }
 
-    fn process_somatic(&self) -> anyhow::Result<()> {
-        let passed_vcf = self.somatic_passed_vcf_path();
-
-        if Path::new(&passed_vcf).exists() {
-            debug!(
-                "ClairS somatic PASS VCF already exists for {} part {:?}",
-                self.id, self.part_index
-            );
-            return Ok(());
-        }
-
+    fn process_somatic_concat(&self) -> anyhow::Result<(BcftoolsConcat, String)> {
         let output_dir = self.part_output_dir();
         let (snv_vcf_base, indel_vcf_base) = self.config.clairs_output_vcfs(&self.id);
 
@@ -522,37 +522,24 @@ impl ClairS {
             .to_string();
 
         // Concat SNV + indel
-        let mut concat = BcftoolsConcat::from_config(
-            &self.config,
-            vec![PathBuf::from(&snv_vcf), PathBuf::from(&indel_vcf)],
-            &tmp_path,
-        );
-
-        let report = run!(&self.config, &mut concat)
-            .with_context(|| format!("Failed to concat {} and {}", snv_vcf, indel_vcf))?;
+        Ok((
+            BcftoolsConcat::from_config(
+                &self.config,
+                vec![PathBuf::from(&snv_vcf), PathBuf::from(&indel_vcf)],
+                &tmp_path,
+            ),
+            tmp_path,
+        ))
+    }
 
-        report
-            .save_to_file(format!("{}/bcftools_concat_", self.log_dir))
-            .context("Failed to save concat logs")?;
+    pub fn process_somatic_pass(&self, tmp_path: &str) -> anyhow::Result<BcftoolsKeepPass> {
+        let passed_vcf = self.somatic_passed_vcf_path();
 
         // Filter PASS
         let mut keep_pass =
             BcftoolsKeepPass::from_config(&self.config, tmp_path.clone(), passed_vcf.clone());
 
-        let report = run!(&self.config, &mut keep_pass)
-            .with_context(|| format!("Failed to filter PASS for {}", self.id))?;
-
-        report
-            .save_to_file(format!("{}/bcftools_pass_", self.log_dir))
-            .context("Failed to save PASS filter logs")?;
-
-        // Clean up temporary concatenated VCF
-        debug!("Removing temporary file: {}", tmp_path);
-        if let Err(e) = fs::remove_file(&tmp_path) {
-            warn!("Failed to remove temporary file {}: {}", tmp_path, e);
-        }
-
-        Ok(())
+        Ok(keep_pass)
     }
 
     /// Returns the per-part output directory.
@@ -819,6 +806,20 @@ fn merge_clairs_germline_parts(base: &ClairS, n_parts: usize) -> anyhow::Result<
     Ok(())
 }
 
+pub fn merge_haplotaged_tmp_bam(config: &Config, id: &str) -> anyhow::Result<()> {
+    let dir = config.clairs_output_dir(id);
+    let bams: Vec<PathBuf> = list_files_recursive(dir)
+        .into_iter()
+        .filter(|f| f.extension().and_then(|e| e.to_str()) == Some("bam"))
+        .collect();
+
+    let into = Path::new(&config.tumoral_haplotagged_bam(id)).to_path_buf();
+    info!("Merging {} into: {}", bams.len(), into.display());
+    let mut merge = SamtoolsMergeMany::from_config(into, bams, config);
+    run!(config, &mut merge)?;
+    Ok(())
+}
+
 /// Runs ClairS in parallel chunks, then merges results.
 ///
 /// Splits the genome into N equal-sized regions, runs ClairS on each region
@@ -897,10 +898,38 @@ pub fn run_clairs_chunked(id: &str, config: &Config, n_parts: usize) -> anyhow::
         output.save_to_file(format!("{}/clairs_", base.log_dir))?;
     }
 
+    // 1) Germline PASS filters (one per part)
+    let mut germlines = Vec::new();
+
+    // 2a) Somatic SNV+indel concats (one per part)
+    let mut somatic_concats = Vec::new();
+    let mut somatic_tmp_paths = Vec::new();
+
     for job in &jobs {
-        job.postprocess()?;
+        // germline PASS
+        germlines.push(job.process_germline()?);
+
+        // somatic concat (SNV+indel -> tmp VCF)
+        let (concat, tmp_path) = job.process_somatic_concat()?;
+        somatic_concats.push(concat);
+        somatic_tmp_paths.push(tmp_path);
+    }
+
+    // Run all germline PASS filters in parallel
+    run_many!(config, germlines)?;
+
+    // Run all somatic concats in parallel
+    run_many!(config, somatic_concats)?;
+
+    // 2b) Somatic PASS filters (one per part, based on tmp VCFs)
+    let mut somatic_pass_filters = Vec::new();
+    for (job, tmp_path) in jobs.iter().zip(somatic_tmp_paths.iter()) {
+        somatic_pass_filters.push(job.process_somatic_pass(tmp_path)?);
     }
 
+    // Run all somatic PASS filters in parallel
+    run_many!(config, somatic_pass_filters)?;
+
     merge_clairs_parts(&base, actual_n_parts)?;
     merge_clairs_germline_parts(&base, actual_n_parts)?;
 
@@ -935,8 +964,17 @@ mod tests {
         // let clairs = ClairS::initialize("34528", &config)?;
         // info!("{clairs}");
 
-        run_clairs_chunked("CHAHA", &config, 20)?;
+        run_clairs_chunked("CHAHA", &config, 50)?;
+
+        Ok(())
+    }
+
+    #[test]
+    fn clairs_haplo() -> anyhow::Result<()> {
+        test_init();
+        let config = Config::default();
 
+        merge_haplotaged_tmp_bam(&config, "DUMCO")?;
         Ok(())
     }
 }

src/callers/mod.rs

@@ -55,7 +55,7 @@
 //!
 //! - **[Straglr]** - Short Tandem Repeat (STR) genotyper (paired and solo modes)
 //!   - Detects pathogenic repeat expansions in known disease loci
-//!   - Supports custom loci via BED file
+//!   - Supports custom loci via BED file (RepeatMasker Simple_repeat)
 //!   - Provides allele-level genotyping with read support
 //!   - Best for: STR expansion detection in neurological and muscular diseases
 //!   - [GitHub](https://github.com/bcgsc/straglr)

src/callers/nanomonsv.rs

@@ -82,8 +82,7 @@ use crate::{
     annotation::{Annotation, Annotations, Caller, CallerCat, Sample},
     collection::vcf::Vcf,
     commands::{
-        bcftools::{BcftoolsConcat, BcftoolsKeepPass},
-        CapturedOutput, Command as JobCommand, LocalRunner, SlurmParams, SlurmRunner,
+        CapturedOutput, Command as JobCommand, LocalRunner, SbatchRunner, SlurmParams, SlurmRunner, bcftools::{BcftoolsConcat, BcftoolsKeepPass}
     },
     config::Config,
     helpers::{is_file_older, remove_dir_if_exists},
@@ -144,7 +143,17 @@ impl SlurmRunner for NanomonSV {
         .to_args()
     }
 }
-
+impl SbatchRunner for NanomonSV {
+    fn slurm_params(&self) -> SlurmParams {
+        SlurmParams {
+            job_name: Some(format!("nanomonsv_{}", self.id)),
+            cpus_per_task: Some(self.threads as u32),
+            mem: Some("60G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
 impl Initialize for NanomonSV {
     /// Initializes a new NanomonSV pipeline for the given sample ID and config.
     ///

src/callers/savana.rs

@@ -74,15 +74,13 @@ use crate::{
     annotation::{Annotation, Annotations, Caller, CallerCat, Sample},
     collection::vcf::Vcf,
     commands::{
-        bcftools::BcftoolsKeepPass,
-        longphase::{LongphaseHap, LongphasePhase},
-        CapturedOutput, Command as JobCommand, LocalRunner, SlurmParams, SlurmRunner,
+        CapturedOutput, Command as JobCommand, LocalRunner, SbatchRunner, SlurmParams, SlurmRunner, bcftools::BcftoolsKeepPass, longphase::{LongphaseHap, LongphasePhase}, samtools::SamtoolsIndex
     },
     config::Config,
     helpers::{is_file_older, remove_dir_if_exists},
     io::{readers::get_gz_reader, vcf::read_vcf},
     pipes::{Initialize, ShouldRun, Version},
-    positions::{num_to_contig, GenomeRange},
+    positions::{GenomeRange, num_to_contig},
     run,
     runners::Run,
     variant::{
@@ -206,13 +204,24 @@ impl SlurmRunner for Savana {
         SlurmParams {
             job_name: Some("savana".into()),
             cpus_per_task: Some(self.config.savana_threads as u32),
-            mem: Some("40G".into()),
+            mem: Some("60G".into()),
             partition: Some("shortq".into()),
             gres: None,
         }
         .to_args()
     }
 }
+impl SbatchRunner for Savana {
+    fn slurm_params(&self) -> SlurmParams {
+        SlurmParams {
+            job_name: Some("savana".into()),
+            cpus_per_task: Some(self.config.savana_threads as u32),
+            mem: Some("60G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
 
 impl Run for Savana {
     /// Executes the Savana pipeline, including prerequisite phasing and haplotagging steps.
@@ -226,12 +235,11 @@ 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.");
+            anyhow::bail!("Savana is up-to-date.");
         }
 
         let output_vcf = &self.config.savana_output_vcf(&self.id);
         if !Path::new(&output_vcf).exists() {
-            info!("Running Savana v{}", Savana::version(&self.config)?);
             let output_dir = self.config.savana_output_dir(&self.id);
             fs::create_dir_all(&output_dir).with_context(|| {
                 format!("Failed to create output dir for Savana run: {output_dir}")
@@ -243,6 +251,8 @@ impl Run for Savana {
             if !Path::new(&phased_germline_vcf).exists() {
                 let mut phase = LongphasePhase::initialize(&self.id, &self.config.clone())?;
                 run!(&self.config, &mut phase)?;
+            } else {
+                info!("Phased germline is already up-to-date.");
             }
 
             let normal_hp_bam = self.config.normal_haplotagged_bam(&self.id);
@@ -256,7 +266,15 @@ impl Run for Savana {
                     &phased_germline_vcf,
                     self.config.clone(),
                 );
-                crate::runners::Run::run(&mut normal_hap)?;
+                normal_hap.run()?;
+                // crate::runners::Run::run(&mut normal_hap)?;
+            } else {
+                info!("Haplotagged normal BAM is already up-to-date");
+            }
+
+            if !Path::new(&format!("{normal_hp_bam}.bai")).exists() {
+                let mut normal_index = SamtoolsIndex::from_config(&self.config, &normal_hp_bam);
+                normal_index.run()?;
             }
 
             if !Path::new(&tumoral_hp_bam).exists() {
@@ -266,7 +284,15 @@ impl Run for Savana {
                     &phased_germline_vcf,
                     self.config.clone(),
                 );
-                crate::runners::Run::run(&mut tumoral_hap)?;
+                tumoral_hap.run()?;
+                // crate::runners::Run::run(&mut tumoral_hap)?;
+            } else {
+                info!("Haplotagged tumoral BAM is already up-to-date");
+            }
+
+            if !Path::new(&format!("{tumoral_hp_bam}.bai")).exists() {
+                let mut normal_index = SamtoolsIndex::from_config(&self.config, &normal_hp_bam);
+                normal_index.run()?;
             }
 
             self.job_args = vec![
@@ -283,6 +309,8 @@ impl Run for Savana {
                 "--no_blacklist".to_string(),
                 "--threads".to_string(),
                 self.config.savana_threads.to_string(),
+                "--cna_threads".to_string(),
+                self.config.savana_threads.to_string(),
             ];
 
             let output =

src/callers/severus.rs

@@ -81,8 +81,7 @@ use crate::{
     annotation::{Annotation, Annotations, Caller, CallerCat, Sample},
     collection::vcf::Vcf,
     commands::{
-        bcftools::BcftoolsKeepPassPrecise, longphase::LongphasePhase, Command as JobCommand,
-        LocalRunner, SlurmParams, SlurmRunner,
+        Command as JobCommand, LocalRunner, SbatchRunner, SlurmParams, SlurmRunner, bcftools::BcftoolsKeepPassPrecise, longphase::LongphasePhase
     },
     config::Config,
     helpers::{is_file_older, remove_dir_if_exists},
@@ -312,6 +311,18 @@ impl SlurmRunner for SeverusJob {
         .to_args()
     }
 }
+impl SbatchRunner for SeverusJob {
+    fn slurm_params(&self) -> SlurmParams {
+        SlurmParams {
+            job_name: Some("severus".into()),
+            partition: Some("shortq".into()),
+            cpus_per_task: Some(16),
+            mem: Some("120G".into()),
+            gres: None,
+        }
+    }
+}
+
 
 impl CallerCat for Severus {
     /// Returns the annotation category for Severus calls.

src/callers/straglr.rs

@@ -121,7 +121,10 @@
 //! - [Straglr GitHub](https://github.com/bcgsc/straglr)
 //! - [Straglr Paper](https://doi.org/10.1186/s13059-021-02447-3)
 use crate::{
-    commands::{Command as JobCommand, LocalBatchRunner, LocalRunner, SbatchRunner, SlurmParams, SlurmRunner},
+    commands::{
+        Command as JobCommand, LocalBatchRunner, LocalRunner, SbatchRunner, SlurmParams,
+        SlurmRunner,
+    },
     config::Config,
     helpers::{is_file_older, remove_dir_if_exists},
     io::straglr::{read_straglr_tsv, StraglrRow},
@@ -244,72 +247,90 @@ impl Run for Straglr {
             anyhow::bail!("Straglr is up-to-date");
         }
 
-        info!("Running Straglr v{}", Straglr::version(&self.config)?);
-
         let id = &self.id;
-        let output_dir = self.config.straglr_output_dir(id);
-        fs::create_dir_all(&output_dir).context("Failed to create Straglr output directory")?;
 
-        // Run on normal sample
-        let normal_tsv = self.config.straglr_normal_tsv(id);
-        if !Path::new(&normal_tsv).exists() {
-            info!("Running Straglr on normal sample: {}", id);
-            let mut job = StraglrJob {
-                conda_sh: self.config.conda_sh.clone(),
-                straglr_bin: self.config.straglr_bin.clone(),
-                bam: self.config.normal_bam(id),
-                reference: self.config.reference.clone(),
-                loci_bed: self.config.straglr_loci_bed.clone(),
-                output_prefix: format!("{}/{}_normal", output_dir, id),
-                min_support: self.config.straglr_min_support,
-                min_cluster_size: self.config.straglr_min_cluster_size,
-                genotype_in_size: self.config.straglr_genotype_in_size,
-            };
-
-            let output = run!(&self.config, &mut job)
-                .context("Error while running Straglr on normal sample")?;
+        if self.config.slurm_runner {
+            let normal_tsv = self.config.straglr_normal_tsv(id);
+            if !Path::new(&normal_tsv).exists() {
+                run_straglr_chunked(id, &self.config.normal_name, &self.config, 50)?;
+            } else {
+                debug!("Straglr normal TSV already exists for {id}, skipping execution.");
+            }
 
-            let log_file = format!("{}/straglr_normal_", self.log_dir);
-            output
-                .save_to_file(&log_file)
-                .context(format!("Error while writing Straglr logs into {log_file}"))?;
+            // Run on tumor sample
+            let tumor_tsv = self.config.straglr_tumor_tsv(id);
+            if !Path::new(&tumor_tsv).exists() {
+                run_straglr_chunked(id, &self.config.tumoral_name, &self.config, 60)?;
+            } else {
+                debug!("Straglr tumor TSV already exists for {id}, skipping execution.");
+            }
         } else {
-            debug!(
-                "Straglr normal TSV already exists for {}, skipping execution.",
-                self.id
-            );
-        }
-
-        // Run on tumor sample
-        let tumor_tsv = self.config.straglr_tumor_tsv(id);
-        if !Path::new(&tumor_tsv).exists() {
-            info!("Running Straglr on tumor sample: {}", id);
-            let mut job = StraglrJob {
-                conda_sh: self.config.conda_sh.clone(),
-                straglr_bin: self.config.straglr_bin.clone(),
-                bam: self.config.tumoral_bam(id),
-                reference: self.config.reference.clone(),
-                loci_bed: self.config.straglr_loci_bed.clone(),
-                output_prefix: format!("{}/{}_tumor", output_dir, id),
-                min_support: self.config.straglr_min_support,
-                min_cluster_size: self.config.straglr_min_cluster_size,
-                genotype_in_size: self.config.straglr_genotype_in_size,
-            };
-
-            let output = run!(&self.config, &mut job)
-                .context("Error while running Straglr on tumor sample")?;
+            let output_dir = self.config.straglr_output_dir(id);
+            fs::create_dir_all(&output_dir).context("Failed to create Straglr output directory")?;
+
+            // Run on normal sample
+            let normal_tsv = self.config.straglr_normal_tsv(id);
+            if !Path::new(&normal_tsv).exists() {
+                info!("Running Straglr on normal sample: {}", id);
+                let mut job = StraglrJob {
+                    conda_sh: self.config.conda_sh.clone(),
+                    straglr_bin: self.config.straglr_bin.clone(),
+                    bam: self.config.normal_bam(id),
+                    reference: self.config.reference.clone(),
+                    loci_bed: self.config.straglr_loci_bed.clone(),
+                    output_prefix: format!("{}/{}_normal", output_dir, id),
+                    min_support: self.config.straglr_min_support,
+                    min_cluster_size: self.config.straglr_min_cluster_size,
+                    genotype_in_size: self.config.straglr_genotype_in_size,
+                };
+
+                let output = run!(&self.config, &mut job)
+                    .context("Error while running Straglr on normal sample")?;
+
+                let log_file = format!("{}/straglr_normal_", self.log_dir);
+                output
+                    .save_to_file(&log_file)
+                    .context(format!("Error while writing Straglr logs into {log_file}"))?;
+            } else {
+                debug!(
+                    "Straglr normal TSV already exists for {}, skipping execution.",
+                    self.id
+                );
+            }
 
-            let log_file = format!("{}/straglr_tumor_", self.log_dir);
-            output
-                .save_to_file(&log_file)
-                .context(format!("Error while writing Straglr logs into {log_file}"))?;
-        } else {
-            debug!(
-                "Straglr tumor TSV already exists for {}, skipping execution.",
-                self.id
-            );
+            // Run on tumor sample
+            let tumor_tsv = self.config.straglr_tumor_tsv(id);
+            if !Path::new(&tumor_tsv).exists() {
+                info!("Running Straglr on tumor sample: {}", id);
+                let mut job = StraglrJob {
+                    conda_sh: self.config.conda_sh.clone(),
+                    straglr_bin: self.config.straglr_bin.clone(),
+                    bam: self.config.tumoral_bam(id),
+                    reference: self.config.reference.clone(),
+                    loci_bed: self.config.straglr_loci_bed.clone(),
+                    output_prefix: format!("{}/{}_tumor", output_dir, id),
+                    min_support: self.config.straglr_min_support,
+                    min_cluster_size: self.config.straglr_min_cluster_size,
+                    genotype_in_size: self.config.straglr_genotype_in_size,
+                };
+
+                let output = run!(&self.config, &mut job)
+                    .context("Error while running Straglr on tumor sample")?;
+
+                let log_file = format!("{}/straglr_tumor_", self.log_dir);
+                output
+                    .save_to_file(&log_file)
+                    .context(format!("Error while writing Straglr logs into {log_file}"))?;
+            } else {
+                debug!(
+                    "Straglr tumor TSV already exists for {}, skipping execution.",
+                    self.id
+                );
+            }
         }
 
+        let differences = self.find_somatic_changes(self.config.straglr_min_diff)?;
+        self.save_somatic_changes(&differences, &self.config.straglr_tumor_normal_diff_tsv(id))?;
         Ok(())
     }
 }
@@ -324,8 +345,10 @@ impl Straglr {
     /// Returns an error if the TSV file cannot be read or parsed.
     pub fn load_normal_results(&self) -> anyhow::Result<Vec<StraglrRow>> {
         let tsv_path = self.config.straglr_normal_tsv(&self.id);
-        read_straglr_tsv(&tsv_path)
-            .context(format!("Failed to read normal Straglr results from {}", tsv_path))
+        read_straglr_tsv(&tsv_path).context(format!(
+            "Failed to read normal Straglr results from {}",
+            tsv_path
+        ))
     }
 
     /// Loads and parses the tumor sample Straglr TSV results.
@@ -337,8 +360,10 @@ impl Straglr {
     /// Returns an error if the TSV file cannot be read or parsed.
     pub fn load_tumor_results(&self) -> anyhow::Result<Vec<StraglrRow>> {
         let tsv_path = self.config.straglr_tumor_tsv(&self.id);
-        read_straglr_tsv(&tsv_path)
-            .context(format!("Failed to read tumor Straglr results from {}", tsv_path))
+        read_straglr_tsv(&tsv_path).context(format!(
+            "Failed to read tumor Straglr results from {}",
+            tsv_path
+        ))
     }
 
     /// Loads both normal and tumor results as a tuple.
@@ -370,22 +395,25 @@ impl Straglr {
     ) -> anyhow::Result<Vec<(String, StraglrRow, StraglrRow, i64)>> {
         let (normal, tumor) = self.load_results()?;
 
+        // Index tumor by location for O(1) lookup
+        let tumor_map: std::collections::HashMap<(String, u64, u64), StraglrRow> = tumor
+            .into_iter()
+            .map(|r| ((r.chrom.clone(), r.start, r.end), r))
+            .collect();
+
         let mut changes = Vec::new();
 
-        for normal_row in &normal {
-            let location = normal_row.location_string();
+        for normal_row in normal {
+            let key = (normal_row.chrom.clone(), normal_row.start, normal_row.end);
 
-            // Find matching locus in tumor
-            if let Some(tumor_row) = tumor.iter().find(|t| {
-                t.chrom == normal_row.chrom && t.start == normal_row.start && t.end == normal_row.end
-            }) {
-                // Compare max copy numbers
+            if let Some(tumor_row) = tumor_map.get(&key) {
                 if let (Some(normal_cn), Some(tumor_cn)) =
                     (normal_row.max_copy_number(), tumor_row.max_copy_number())
                 {
                     let diff = tumor_cn as i64 - normal_cn as i64;
                     if diff.abs() >= min_difference as i64 {
-                        changes.push((location, normal_row.clone(), tumor_row.clone(), diff));
+                        let location = normal_row.location_string();
+                        changes.push((location, normal_row, tumor_row.clone(), diff));
                     }
                 }
             }
@@ -393,6 +421,58 @@ impl Straglr {
 
         Ok(changes)
     }
+
+    /// Saves somatic STR changes to a TSV file.
+    ///
+    /// # Format
+    /// Tab-separated: chrom, start, end, repeat_unit, normal_cn, tumor_cn, diff, normal_support, tumor_support
+    pub fn save_somatic_changes(
+        &self,
+        differences: &[(String, StraglrRow, StraglrRow, i64)],
+        output_path: &str,
+    ) -> anyhow::Result<()> {
+        use std::io::Write;
+
+        let mut file = File::create(output_path)
+            .context(format!("Failed to create output file: {}", output_path))?;
+
+        // Header
+        writeln!(
+            file,
+            "#chrom\tstart\tend\trepeat_unit\tnormal_genotype\ttumor_genotype\tnormal_cn\ttumor_cn\tdiff\tnormal_support\ttumor_support"
+        )?;
+
+        for (_, normal, tumor, diff) in differences {
+            writeln!(
+                file,
+                "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}",
+                normal.chrom,
+                normal.start,
+                normal.end,
+                normal.repeat_unit,
+                normal.genotype,
+                tumor.genotype,
+                normal
+                    .copy_numbers
+                    .iter()
+                    .map(|n| n.to_string())
+                    .collect::<Vec<_>>()
+                    .join(","),
+                tumor
+                    .copy_numbers
+                    .iter()
+                    .map(|n| n.to_string())
+                    .collect::<Vec<_>>()
+                    .join(","),
+                diff,
+                normal.support,
+                tumor.support,
+            )?;
+        }
+
+        file.flush()?;
+        Ok(())
+    }
 }
 
 #[derive(Debug, Clone)]
@@ -411,15 +491,15 @@ struct StraglrJob {
 impl JobCommand for StraglrJob {
     fn cmd(&self) -> String {
         let mut cmd = format!(
-            "source {conda_sh} && conda activate straglr_env && {straglr} {bam} {reference} --loci {loci} --min_support {min_sup} --min_cluster_size {min_clust} --output {output}",
+            "source {conda_sh} && conda activate straglr_env && {straglr} {bam} {reference} {output} --loci {loci} --min_support {min_sup} --min_cluster_size {min_clust}",
             conda_sh = self.conda_sh,
             straglr = self.straglr_bin,
             bam = self.bam,
             reference = self.reference,
+            output = self.output_prefix,  // positional, not --output
             loci = self.loci_bed,
             min_sup = self.min_support,
             min_clust = self.min_cluster_size,
-            output = self.output_prefix
         );
 
         if self.genotype_in_size {
@@ -439,8 +519,8 @@ impl SlurmRunner for StraglrJob {
         SlurmParams {
             job_name: Some("straglr".into()),
             partition: Some("shortq".into()),
-            cpus_per_task: Some(4),
-            mem: Some("16G".into()),
+            cpus_per_task: Some(20),
+            mem: Some("10G".into()),
             gres: None,
         }
         .to_args()
@@ -452,8 +532,8 @@ impl SbatchRunner for StraglrJob {
         SlurmParams {
             job_name: Some("straglr".into()),
             partition: Some("shortq".into()),
-            cpus_per_task: Some(4),
-            mem: Some("16G".into()),
+            cpus_per_task: Some(20),
+            mem: Some("10G".into()),
             gres: None,
         }
     }
@@ -465,7 +545,6 @@ impl Version for Straglr {
     /// # Errors
     /// Returns an error if command execution fails or version parsing fails.
     fn version(config: &Config) -> anyhow::Result<String> {
-        // Override cmd for version check
         struct VersionJob {
             conda_sh: String,
             straglr_bin: String,
@@ -482,8 +561,8 @@ impl Version for Straglr {
 
         impl LocalRunner for VersionJob {}
 
-        impl SlurmRunner for VersionJob {
-            fn slurm_args(&self) -> Vec<String> {
+        impl SbatchRunner for VersionJob {
+            fn slurm_params(&self) -> SlurmParams {
                 SlurmParams {
                     job_name: Some("straglr_version".into()),
                     partition: Some("shortq".into()),
@@ -491,7 +570,6 @@ impl Version for Straglr {
                     mem: Some("1G".into()),
                     gres: None,
                 }
-                .to_args()
             }
         }
 
@@ -504,11 +582,24 @@ impl Version for Straglr {
             run!(&config, &mut version_job).context("Error while running `straglr --version`")?;
 
         let combined = format!("{}{}", out.stdout, out.stderr);
+
+        // Look for semver pattern (e.g., "1.3.0") since straglr outputs just the version number
         let v = combined
             .lines()
-            .find(|line| line.contains("straglr") || line.contains("version"))
-            .map(|line| line.trim().to_string())
-            .ok_or_else(|| anyhow::anyhow!("Could not parse straglr version from output"))?;
+            .find(|line| {
+                let trimmed = line.trim();
+                // Match semver pattern: digits.digits.digits (optionally more)
+                trimmed
+                    .chars()
+                    .next()
+                    .map(|c| c.is_ascii_digit())
+                    .unwrap_or(false)
+                    && trimmed.contains('.')
+            })
+            .map(|line| format!("straglr {}", line.trim()))
+            .ok_or_else(|| {
+                anyhow::anyhow!("Could not parse straglr version from output: {}", combined)
+            })?;
 
         Ok(v)
     }
@@ -560,6 +651,14 @@ impl InitializeSolo for StraglrSolo {
     }
 }
 
+impl ShouldRun for StraglrSolo {
+    fn should_run(&self) -> bool {
+        let output_tsv = self.config.straglr_solo_tsv(&self.id, &self.time);
+        let bam = self.config.solo_bam(&self.id, &self.time);
+        is_file_older(&output_tsv, &bam, true).unwrap_or(true)
+    }
+}
+
 impl Run for StraglrSolo {
     /// Runs the Straglr pipeline for a single sample.
     ///
@@ -704,8 +803,8 @@ pub fn run_straglr_chunked(
 
     // Read input BED file
     let bed_path = &config.straglr_loci_bed;
-    let bed_file = File::open(bed_path)
-        .context(format!("Failed to open BED file: {}", bed_path))?;
+    let bed_file =
+        File::open(bed_path).context(format!("Failed to open BED file: {}", bed_path))?;
     let reader = BufReader::new(bed_file);
 
     // Read all BED lines (skip comments and empty lines)
@@ -725,8 +824,8 @@ pub fn run_straglr_chunked(
     info!("Read {} loci from {}", total_loci, bed_path);
 
     // Calculate chunk sizes
-    let chunk_size = (total_loci + n_parts - 1) / n_parts; // ceil division
-    let actual_n_parts = (total_loci + chunk_size - 1) / chunk_size;
+    let chunk_size = total_loci.div_ceil(n_parts); // ceil division
+    let actual_n_parts = total_loci.div_ceil(chunk_size);
 
     info!(
         "Splitting {} loci into {} chunks (~{} loci per chunk)",
@@ -756,15 +855,18 @@ pub fn run_straglr_chunked(
             config.tmp_dir, id, time_point, part_num
         );
 
-        let mut bed_chunk_file = File::create(&bed_chunk_path)
-            .context(format!("Failed to create temporary BED file: {}", bed_chunk_path))?;
+        let mut bed_chunk_file = File::create(&bed_chunk_path).context(format!(
+            "Failed to create temporary BED file: {}",
+            bed_chunk_path
+        ))?;
 
         // Write chunk of BED lines
         for line in &bed_lines[start_idx..end_idx] {
-            writeln!(bed_chunk_file, "{}", line)
-                .context("Failed to write to BED chunk file")?;
+            writeln!(bed_chunk_file, "{}", line).context("Failed to write to BED chunk file")?;
         }
-        bed_chunk_file.flush().context("Failed to flush BED chunk file")?;
+        bed_chunk_file
+            .flush()
+            .context("Failed to flush BED chunk file")?;
 
         debug!(
             "Created chunk {} with {} loci (lines {}-{})",
@@ -778,7 +880,7 @@ pub fn run_straglr_chunked(
 
         // Create job for this chunk
         let output_prefix = format!("{}/{}_{}_part{}", output_dir, id, time_point, part_num);
-        let output_tsv = format!("{}_straglr.tsv", output_prefix);
+        let output_tsv = format!("{}.tsv", output_prefix);
         temp_tsv_files.push(output_tsv.clone());
 
         let job = StraglrJob {
@@ -797,25 +899,24 @@ pub fn run_straglr_chunked(
     }
 
     // Run all chunks in parallel
-    info!("Executing {} Straglr jobs in parallel", actual_n_parts);
-    let outputs = run_many!(config, jobs)?;
-
-    // Save logs
-    let log_dir = format!("{}/{}/log/straglr_chunked", config.result_dir, id);
-    fs::create_dir_all(&log_dir).context("Failed to create log directory")?;
-
-    for (i, output) in outputs.iter().enumerate() {
-        let log_file = format!("{}/straglr_part{}_", log_dir, i + 1);
-        output
-            .save_to_file(&log_file)
-            .context(format!("Failed to save logs for part {}", i + 1))?;
-    }
+    // info!("Executing {} Straglr jobs in parallel", actual_n_parts);
+    // let outputs = run_many!(config, jobs)?;
+    //
+    // // Save logs
+    // let log_dir = format!("{}/{}/log/straglr_chunked", config.result_dir, id);
+    // fs::create_dir_all(&log_dir).context("Failed to create log directory")?;
+    //
+    // for (i, output) in outputs.iter().enumerate() {
+    //     let log_file = format!("{}/straglr_part{}_", log_dir, i + 1);
+    //     output
+    //         .save_to_file(&log_file)
+    //         .context(format!("Failed to save logs for part {}", i + 1))?;
+    // }
 
     // Merge TSV files
     info!("Merging {} TSV files", actual_n_parts);
     let final_tsv = config.straglr_solo_tsv(id, time_point);
-    merge_tsv_files(&temp_tsv_files, &final_tsv)
-        .context("Failed to merge Straglr TSV files")?;
+    merge_tsv_files(&temp_tsv_files, &final_tsv).context("Failed to merge Straglr TSV files")?;
 
     // Clean up temporary files
     info!("Cleaning up temporary files");
@@ -859,8 +960,7 @@ fn merge_tsv_files(input_files: &[String], output_file: &str) -> anyhow::Result<
 
     for (i, input_path) in input_files.iter().enumerate() {
         if !Path::new(input_path).exists() {
-            debug!("Skipping non-existent file: {}", input_path);
-            continue;
+            anyhow::bail!("Non-existent file: {}", input_path);
         }
 
         let content = fs::read_to_string(input_path)
@@ -887,3 +987,31 @@ fn merge_tsv_files(input_files: &[String], output_file: &str) -> anyhow::Result<
     output.flush().context("Failed to flush output file")?;
     Ok(())
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::helpers::test_init;
+
+    #[test]
+    fn straglr_version() -> anyhow::Result<()> {
+        test_init();
+        let vl = Straglr::version(&Config::default())?;
+        info!("Straglr version: {vl}");
+        Ok(())
+    }
+
+    #[test]
+    fn straglr_run() -> anyhow::Result<()> {
+        test_init();
+        let config = Config::default();
+
+        let mut caller = Straglr::initialize("DUMCO", &config)?;
+        // caller.run()?;
+
+        let differences = caller.find_somatic_changes(caller.config.straglr_min_diff)?;
+        caller.save_somatic_changes(&differences, &caller.config.straglr_tumor_normal_diff_tsv("DUMCO"))?;
+
+        Ok(())
+    }
+}

src/collection/bam_stats.rs

@@ -1359,9 +1359,10 @@ mod tests {
         // println!("{stats}");
         // let stats = WGSBamStats::open("36434", "norm", &config)?;
         // println!("{stats}");
-        let stats = WGSBamStats::open("33519", "diag", &config)?;
+        let stats = WGSBamStats::open("CHAHA", "diag", &config)?;
+        println!("{stats}");
+        let stats = WGSBamStats::open("DUMCO", "diag", &config)?;
         println!("{stats}");
-
         Ok(())
     }
 }

src/collection/prom_run.rs

@@ -74,11 +74,20 @@ use crate::{
     collection::{
         bam_stats::WGSBamStats,
         flowcells::IdInput,
-        minknow::{MinKnowSampleSheet, PoreStateEntry, parse_pore_activity_from_reader},
+        minknow::{parse_pore_activity_from_reader, MinKnowSampleSheet, PoreStateEntry},
         pod5::Pod5,
-    }, 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
+    },
+    commands::{
+        dorado::DoradoAlign,
+        modkit::ModkitSummary,
+        run_many_sbatch,
+        samtools::{SamtoolsIndex, SamtoolsMergeMany, SamtoolsSort},
+        SlurmRunner,
+    },
+    config::Config,
+    helpers::{get_genome_sizes, list_files_recursive, remove_bam_with_index, TempFileGuard},
+    pipes::InitializeSolo,
+    run, run_many,
 };
 
 /// Represent a complete ONT PromethION sequencing run with all associated files.
@@ -1235,12 +1244,7 @@ fn atomic_replace(source: &Path, destination: &Path) -> anyhow::Result<()> {
 }
 /// Indexes a BAM file using samtools.
 fn index_bam(bam: &Path, config: &Config) -> anyhow::Result<()> {
-    let mut index_cmd = SamtoolsIndex {
-        bin: config.align.samtools_bin.clone(),
-        threads: config.align.samtools_view_threads,
-        bam: bam.to_string_lossy().to_string(),
-    };
-
+    let mut index_cmd = SamtoolsIndex::from_config(config, &bam.to_string_lossy().to_string());
     run!(config, &mut index_cmd)?;
 
     // SlurmRunner::run(&mut index_cmd)?;
@@ -1384,11 +1388,7 @@ fn sort_and_index_chunks(
     // Index every sorted BAM.
     let index_jobs: Vec<SamtoolsIndex> = original_to_sorted
         .values()
-        .map(|sorted| SamtoolsIndex {
-            bin: config.align.samtools_bin.clone(),
-            threads: config.align.samtools_view_threads,
-            bam: sorted.to_string_lossy().to_string(),
-        })
+        .map(|sorted| SamtoolsIndex::from_config(config, &sorted.to_string_lossy().to_string()))
         .collect();
 
     info!("Submitting {} index jobs", index_jobs.len());

src/commands/bcftools.rs

@@ -225,6 +225,19 @@ impl super::SlurmRunner for BcftoolsKeepPassPrecise {
     }
 }
 
+impl super::SbatchRunner for BcftoolsKeepPassPrecise {
+    /// Slurm resource request for the `bcftools keep pass precise` job.
+    fn slurm_params(&self) -> SlurmParams{
+        SlurmParams {
+            job_name: Some("bcftools_keep_pass_precise".into()),
+            cpus_per_task: Some(self.threads as u32),
+            mem: Some("45G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
+
 /// Concatenates multiple VCF/BCF files with `bcftools concat`.
 ///
 /// Builds a temporary list file containing all inputs, then runs
@@ -310,6 +323,7 @@ impl super::Command for BcftoolsConcat {
 }
 
 impl super::LocalRunner for BcftoolsConcat {}
+impl super::LocalBatchRunner for BcftoolsConcat {}
 
 impl super::SlurmRunner for BcftoolsConcat {
     // Slurm resource request for the `bcftools concat` job.
@@ -393,6 +407,18 @@ impl super::SlurmRunner for BcftoolsIndex {
         .to_args()
     }
 }
+impl super::SbatchRunner for BcftoolsIndex {
+    /// Slurm resource request for the `bcftools index` job.
+    fn slurm_params(&self) -> SlurmParams {
+        SlurmParams {
+            job_name: Some("bcftools_index".into()),
+            cpus_per_task: Some(self.threads as u32),
+            mem: Some("45G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
 
 /// Compresses a VCF/BCF file to BGZF using `bcftools view -Oz`.
 #[derive(Debug)]
@@ -465,6 +491,19 @@ impl super::SlurmRunner for BcftoolsCompress {
     }
 }
 
+impl super::SbatchRunner for BcftoolsCompress {
+    /// Slurm resource request for the `bcftools compress` job.
+    fn slurm_params(&self) -> SlurmParams {
+        SlurmParams {
+            job_name: Some("bcftools_compress".into()),
+            cpus_per_task: Some(self.threads as u32),
+            mem: Some("45G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;

src/commands/longphase.rs

@@ -2,12 +2,19 @@
 //!
 //! All steps use the shared runner traits (local/Slurm) driven by the global `Config`.
 use crate::{
-    callers::deep_variant::DeepVariant, commands::{
+    commands::{
         bcftools::{BcftoolsCompress, BcftoolsIndex, BcftoolsKeepPass},
-        samtools::SamtoolsIndex,
-    }, config::Config, helpers::{is_file_older, path_prefix}, pipes::{Initialize, InitializeSolo, ShouldRun}, run, runners::Run
+        samtools::{SamtoolsIndex, SamtoolsMergeMany},
+    },
+    config::Config,
+    helpers::{get_genome_sizes, is_file_older, path_prefix},
+    pipes::{Initialize, InitializeSolo, ShouldRun},
+    run, run_many,
+    runners::Run,
 };
 use anyhow::Context;
+use log::warn;
+use rust_htslib::bam::{self, Read};
 use std::{
     fs,
     path::{Path, PathBuf},
@@ -16,7 +23,7 @@ use tracing::info;
 
 use super::modkit::ModkitSummary;
 
-#[derive(Debug)]
+#[derive(Debug, Clone)]
 pub struct LongphaseHap {
     pub id: String,
     pub vcf: String,
@@ -46,6 +53,112 @@ impl LongphaseHap {
             job_args: Vec::new(),
         }
     }
+
+    /// Build haplotag arguments, optionally restricted to a given region.
+    fn build_job_args(&self, region: Option<&str>, out_prefix: &Path) -> Vec<String> {
+        let mut args = vec![
+            "haplotag".to_string(),
+            "-s".to_string(),
+            self.vcf.clone(),
+            "-b".to_string(),
+            self.bam.to_string_lossy().to_string(),
+            "-r".to_string(),
+            self.config.reference.clone(),
+            "-t".to_string(),
+            self.config.longphase_threads.to_string(),
+            "--tagSupplementary".to_string(),
+        ];
+
+        if let Some(r) = region {
+            // longphase supports `--region=REGION` or `--region REGION`; we use the latter.
+            args.push("--region".to_string());
+            args.push(r.to_string());
+        }
+
+        args.push("-o".to_string());
+        args.push(out_prefix.to_string_lossy().to_string());
+        args
+    }
+}
+
+impl LongphaseHap {
+    fn run_chunked_slurm(&mut self) -> anyhow::Result<()> {
+        // Read contigs from BAM header
+        let reader = bam::Reader::from_path(&self.bam)
+            .with_context(|| format!("Failed to open BAM: {}", self.bam.display()))?;
+        let header = bam::Header::from_template(reader.header());
+        let genome_sizes = get_genome_sizes(&header)?;
+        let chroms: Vec<String> = genome_sizes.keys().cloned().collect();
+
+        anyhow::ensure!(
+            !chroms.is_empty(),
+            "No chromosomes found in BAM header for {}",
+            self.bam.display()
+        );
+
+        // Temporary directory for per-chromosome BAMs
+        let tmp_dir = Path::new(&self.config.tmp_dir).join("longphase_hap");
+        fs::create_dir_all(&tmp_dir)
+            .with_context(|| format!("Failed to create tmp dir {}", tmp_dir.display()))?;
+
+        let mut jobs = Vec::with_capacity(chroms.len());
+        let mut tmp_bams = Vec::with_capacity(chroms.len());
+
+        for (i, chrom) in chroms.iter().enumerate() {
+            // Prefix for this region's output (longphase will append ".bam")
+            let out_prefix = tmp_dir.join(format!("{}_{}_part{}", self.id, chrom, i + 1));
+            let out_bam = PathBuf::from(format!("{}.bam", out_prefix.to_string_lossy()));
+            tmp_bams.push(out_bam);
+
+            let mut job = self.clone();
+            job.bam_hp = out_prefix.clone();
+            job.log_dir = format!("{}/{}", self.log_dir, chrom);
+            job.job_args = job.build_job_args(Some(chrom.as_str()), &job.bam_hp);
+
+            info!(
+                "Planned Longphase haplotag job for {}: region {} -> {}",
+                self.id,
+                chrom,
+                out_prefix.display()
+            );
+
+            jobs.push(job);
+        }
+
+        // Run all per-chromosome jobs via SLURM (or whatever run_many! does when config.slurm = true)
+        let reports = run_many!(&self.config, jobs.clone())
+            .context("Error while running Longphase haplotag chunked jobs")?;
+
+        // Save logs per part
+        for (job, report) in jobs.iter().zip(reports.iter()) {
+            let log_prefix = format!("{}/longphase_", job.log_dir);
+            report
+                .save_to_file(&log_prefix)
+                .with_context(|| format!("Error while writing logs into {log_prefix}"))?;
+        }
+
+        // Merge all temporary BAMs into final output
+        let final_bam = PathBuf::from(format!("{}.bam", self.bam_hp.to_string_lossy()));
+        let mut merge =
+            SamtoolsMergeMany::from_config(final_bam.clone(), tmp_bams.clone(), &self.config);
+
+        run!(&self.config, &mut merge)
+            .context("samtools merge failed for Longphase haplotag chunks")?;
+
+        // (Optional) cleanup temp BAMs
+        for bam in tmp_bams {
+            if let Err(e) = fs::remove_file(&bam) {
+                warn!("Failed to remove temp BAM {}: {e}", bam.display());
+            }
+        }
+
+        // Index final BAM
+        let mut sam_index = SamtoolsIndex::from_config(&self.config, &final_bam.to_string_lossy().to_string()) ;
+        run!(&self.config, &mut sam_index)
+            .with_context(|| format!("samtools index failed for {}", final_bam.display()))?;
+
+        Ok(())
+    }
 }
 
 impl Run for LongphaseHap {
@@ -55,24 +168,21 @@ impl Run for LongphaseHap {
         }
 
         if !Path::new(&self.log_dir).exists() {
-            fs::create_dir_all(&self.log_dir).expect("Failed to create output directory");
+            fs::create_dir_all(&self.log_dir).expect("Failed to create output directory.");
         }
 
-        if !self.bam_hp.exists() {
-            self.job_args = vec![
-                "haplotag".to_string(),
-                "-s".to_string(),
-                self.vcf.clone(),
-                "-b".to_string(),
-                self.bam.to_string_lossy().to_string(),
-                "-r".to_string(),
-                self.config.reference.clone(),
-                "-t".to_string(),
-                self.config.threads.to_string(),
-                "--tagSupplementary".to_string(),
-                "-o".to_string(),
-                self.bam_hp.to_string_lossy().to_string(),
-            ];
+        if self.bam_hp.exists() {
+            info!("Longphase output bam already exists.");
+            return Ok(());
+        }
+
+        if self.config.slurm_runner {
+            // Chunked, per-chromosome haplotag on SLURM, then merge + index
+            self.run_chunked_slurm()?;
+        } else {
+            // Original single-job behavior
+            self.job_args = self.build_job_args(None, &self.bam_hp);
+
             let report = run!(&self.config, self)
                 .context(format!("Error while running `{}`", self.job_args.join(" ")))?;
 
@@ -82,15 +192,9 @@ impl Run for LongphaseHap {
                 .context(format!("Error while writing logs into {log_file}"))?;
 
             let bam_to_index = format!("{}.bam", self.bam_hp.to_string_lossy());
-            let mut sam_index = SamtoolsIndex {
-                bin: self.config.align.samtools_bin.clone(),
-                threads: self.config.align.samtools_view_threads,
-                bam: bam_to_index.clone(),
-            };
+            let mut sam_index = SamtoolsIndex::from_config(&self.config, &bam_to_index);
             run!(&self.config, &mut sam_index)
                 .context(format!("samtools index failed for {bam_to_index}"))?;
-        } else {
-            info!("Longphase output vcf already exists");
         }
 
         Ok(())
@@ -103,15 +207,14 @@ impl crate::commands::Command for LongphaseHap {
     }
 }
 
-
-
 impl crate::commands::LocalRunner for LongphaseHap {}
+impl crate::commands::LocalBatchRunner 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 + 1),
+            cpus_per_task: Some(self.config.longphase_threads as u32),
             mem: Some("60G".into()),
             partition: Some("shortq".into()),
             gres: None,
@@ -120,6 +223,18 @@ impl crate::commands::SlurmRunner for LongphaseHap {
     }
 }
 
+impl crate::commands::SbatchRunner for LongphaseHap {
+    fn slurm_params(&self) -> super::SlurmParams {
+        crate::commands::SlurmParams {
+            job_name: Some(format!("longphase_hap_{}", self.id)),
+            cpus_per_task: Some(self.config.longphase_threads as u32),
+            mem: Some("60G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
+
 // /data/tools/longphase_linux-x64 phase -s ClairS/clair3_normal_tumoral_germline_output.vcf.gz -b CUNY_diag_hs1_hp.bam -r /data/ref/hs1/chm13v2.0.fa -t 155 --ont -o ClairS/clair3_normal_tumoral_germline_output_PS
 #[derive(Debug)]
 pub struct LongphasePhase {
@@ -180,6 +295,18 @@ impl crate::commands::SlurmRunner for LongphasePhase {
     }
 }
 
+impl crate::commands::SbatchRunner for LongphasePhase {
+    fn slurm_params(&self) -> super::SlurmParams {
+        crate::commands::SlurmParams {
+            job_name: Some(format!("longphase_phase_{}", self.id)),
+            cpus_per_task: Some(self.config.longphase_threads as u32),
+            mem: Some("60G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
+
 impl Run for LongphasePhase {
     fn run(&mut self) -> anyhow::Result<()> {
         info!("Running longphase phase for: {}", self.vcf);
@@ -326,6 +453,18 @@ impl crate::commands::SlurmRunner for LongphaseModcallSolo {
     }
 }
 
+impl crate::commands::SbatchRunner for LongphaseModcallSolo {
+    fn slurm_params(&self) -> super::SlurmParams {
+        crate::commands::SlurmParams {
+            job_name: Some(format!("longphase_modcall_{}", self.id)),
+            cpus_per_task: Some(self.threads as u32),
+            mem: Some("60G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
+
 impl Run for LongphaseModcallSolo {
     fn run(&mut self) -> anyhow::Result<()> {
         self.job_args = vec![

src/commands/mod.rs

@@ -425,7 +425,7 @@ pub trait SbatchRunner: Command {
 
     /// Submit via sbatch, tail slurm-<jobid>.out "live", wait for job to finish,
     /// then return captured stdout.
-    fn run(&mut self) -> anyhow::Result<CapturedOutput> {
+    fn exec(&mut self) -> anyhow::Result<CapturedOutput> {
         self.init()?;
 
         // 1. sbatch --parsable --output=slurm-%j.out --wrap "<cmd>"
@@ -461,7 +461,7 @@ pub trait SbatchRunner: Command {
             .unwrap_or("")
             .to_string();
 
-        info!("Running jobid: {job_id}");
+        info!("Running jobid: {job_id}: {}", args.join(" "));
 
         if job_id.is_empty() {
             anyhow::bail!("failed to parse job id from sbatch output: {sbatch_stdout}");
@@ -639,7 +639,7 @@ pub trait SbatchRunner: Command {
 macro_rules! run {
     ($cfg:expr, $cmd:expr) => {{
         if $cfg.slurm_runner {
-            $crate::commands::SlurmRunner::exec($cmd)
+            $crate::commands::SbatchRunner::exec($cmd)
         } else {
             $crate::commands::LocalRunner::exec($cmd)
         }
@@ -805,7 +805,7 @@ where
 
     for mut job in jobs.drain(..) {
         let handle = thread::spawn(move || -> anyhow::Result<CapturedOutput> {
-            SbatchRunner::run(&mut job)
+            SbatchRunner::exec(&mut job)
         });
         handles.push(handle);
     }
@@ -1021,7 +1021,7 @@ mod tests {
     #[test]
     fn sbatch_test_run() -> anyhow::Result<()> {
         let mut t = TestRun;
-        let out = SbatchRunner::run(&mut t)?;
+        let out = SbatchRunner::exec(&mut t)?;
         println!("{out:#?}");
         assert!(out.stdout.contains("hello from sbatch"));
         Ok(())

src/commands/modkit.rs

@@ -3,7 +3,7 @@ use std::{fs::File, io::{BufRead, BufReader}, path::Path, str::FromStr};
 use anyhow::Context;
 
 use crate::{
-    commands::{Command, LocalRunner, SlurmParams, SlurmRunner},
+    commands::{Command, LocalRunner, SbatchRunner, SlurmParams, SlurmRunner},
     config::Config,
     pipes::InitializeSolo,
     run,
@@ -50,6 +50,17 @@ impl SlurmRunner for ModkitSummary {
         .to_args()
     }
 }
+impl SbatchRunner for ModkitSummary {
+    fn slurm_params(&self) -> SlurmParams {
+        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,
+        }
+    }
+}
 
 impl ModkitSummary {
     pub fn run(&mut self) -> anyhow::Result<()> {

src/commands/samtools.rs

@@ -11,8 +11,9 @@ use uuid::Uuid;
 
 use crate::{
     collection::bam_stats::{QNameSet, WGSBamStats},
-    commands::{LocalBatchRunner, SbatchRunner, SlurmParams},
+    commands::{LocalBatchRunner, LocalRunner, SbatchRunner, SlurmParams, SlurmRunner},
     config::Config,
+    runners::Run,
 };
 
 /// Wrapper around a `samtools index` invocation.
@@ -31,6 +32,7 @@ pub struct SamtoolsIndex {
     pub threads: u8,
     /// Path to the BAM file to index.
     pub bam: String,
+    slurm: bool,
 }
 
 impl super::Command for SamtoolsIndex {
@@ -67,6 +69,28 @@ impl super::SbatchRunner for SamtoolsIndex {
     }
 }
 
+impl SamtoolsIndex {
+    pub fn from_config(config: &Config, bam: &str) -> Self {
+        Self {
+            bin: config.align.samtools_bin.clone(),
+            threads: config.align.samtools_view_threads,
+            bam: bam.to_string(),
+            slurm: config.slurm_runner,
+        }
+    }
+}
+
+impl Run for SamtoolsIndex {
+    fn run(&mut self) -> anyhow::Result<()> {
+        if self.slurm {
+            let _output = SlurmRunner::exec(self)?;
+        } else {
+            let _output = LocalRunner::exec(self)?;
+        }
+        Ok(())
+    }
+}
+
 /// Wrapper around a `samtools merge` invocation used to append one BAM into
 /// another while preserving read group (RG) uniqueness.
 ///
@@ -347,13 +371,13 @@ impl super::Command for SamtoolsMergeMany {
         self.bam_list_file = Some(list_file);
 
         // QNAME collision check
-        if self.bams.len() > 1 {
-            self.check_qname_collisions()?;
-        } else {
-            let qset =
-                QNameSet::load_or_create(&self.bams[0], self.config.bam_min_mapq, self.threads)?;
-            qset.save(WGSBamStats::qnames_path_from_bam(&self.into))?;
-        }
+        // if self.bams.len() > 1 {
+        //     self.check_qname_collisions()?;
+        // } else {
+        //     let qset =
+        //         QNameSet::load_or_create(&self.bams[0], self.config.bam_min_mapq, self.threads)?;
+        //     qset.save(WGSBamStats::qnames_path_from_bam(&self.into))?;
+        // }
 
         Ok(())
     }
@@ -439,6 +463,18 @@ impl super::SlurmRunner for SamtoolsMergeMany {
     }
 }
 
+impl super::SbatchRunner for SamtoolsMergeMany {
+    fn slurm_params(&self) -> SlurmParams {
+        SlurmParams {
+            job_name: Some("samtools_merge_many".into()),
+            cpus_per_task: Some(self.threads as u32),
+            mem: Some("60G".into()),
+            partition: Some("shortq".into()),
+            gres: None,
+        }
+    }
+}
+
 #[derive(Debug)]
 pub struct SamtoolsSplit {
     /// Path to the `samtools` executable.
@@ -604,54 +640,54 @@ mod tests {
         run, TEST_DIR,
     };
 
-    #[test]
-    fn samtools_index_merge() -> anyhow::Result<()> {
-        test_init();
-
-        let config = Config::default();
-
-        info!("Copying the test BAM 1.");
-        fs::copy(
-            format!("{}/inputs/fcA_NB02.bam", TEST_DIR.as_str()),
-            format!("{}/outputs/to_be_merged.bam", TEST_DIR.as_str()),
-        )?;
-
-        info!("Copying the test BAM 2.");
-        fs::copy(
-            format!("{}/inputs/fcB_NB02.bam", TEST_DIR.as_str()),
-            format!("{}/outputs/to_be_merged_2.bam", TEST_DIR.as_str()),
-        )?;
-
-        info!("Indexing BAM 1.");
-        let mut idx = SamtoolsIndex {
-            bin: config.align.samtools_bin.clone(),
-            threads: config.align.samtools_view_threads,
-            bam: format!("{}/outputs/to_be_merged.bam", TEST_DIR.as_str()),
-        };
-        let captured_output = run!(config, &mut idx)?;
-        assert_eq!(captured_output.stderr, String::new());
-
-        info!("Indexing BAM 2.");
-        let mut idx = SamtoolsIndex {
-            bin: config.align.samtools_bin.clone(),
-            threads: config.align.samtools_view_threads,
-            bam: format!("{}/outputs/to_be_merged_2.bam", TEST_DIR.as_str()),
-        };
-        let captured_output = run!(config, &mut idx)?;
-        assert_eq!(captured_output.stderr, String::new());
-
-        info!("Mergin both BAM.");
-        let mut idx = SamtoolsMerge::from_config(
-            &config,
-            format!("{}/outputs/to_be_merged_2.bam", TEST_DIR.as_str()),
-            format!("{}/outputs/to_be_merged.bam", TEST_DIR.as_str()),
-        );
-
-        let captured_output = SlurmRunner::exec(&mut idx)?;
-        assert_eq!(captured_output.stderr, String::new());
-
-        Ok(())
-    }
+    // #[test]
+    // fn samtools_index_merge() -> anyhow::Result<()> {
+    //     test_init();
+    //
+    //     let config = Config::default();
+    //
+    //     info!("Copying the test BAM 1.");
+    //     fs::copy(
+    //         format!("{}/inputs/fcA_NB02.bam", TEST_DIR.as_str()),
+    //         format!("{}/outputs/to_be_merged.bam", TEST_DIR.as_str()),
+    //     )?;
+    //
+    //     info!("Copying the test BAM 2.");
+    //     fs::copy(
+    //         format!("{}/inputs/fcB_NB02.bam", TEST_DIR.as_str()),
+    //         format!("{}/outputs/to_be_merged_2.bam", TEST_DIR.as_str()),
+    //     )?;
+    //
+    //     info!("Indexing BAM 1.");
+    //     let mut idx = SamtoolsIndex {
+    //         bin: config.align.samtools_bin.clone(),
+    //         threads: config.align.samtools_view_threads,
+    //         bam: format!("{}/outputs/to_be_merged.bam", TEST_DIR.as_str()),
+    //     };
+    //     let captured_output = run!(config, &mut idx)?;
+    //     assert_eq!(captured_output.stderr, String::new());
+    //
+    //     info!("Indexing BAM 2.");
+    //     let mut idx = SamtoolsIndex {
+    //         bin: config.align.samtools_bin.clone(),
+    //         threads: config.align.samtools_view_threads,
+    //         bam: format!("{}/outputs/to_be_merged_2.bam", TEST_DIR.as_str()),
+    //     };
+    //     let captured_output = run!(config, &mut idx)?;
+    //     assert_eq!(captured_output.stderr, String::new());
+    //
+    //     info!("Mergin both BAM.");
+    //     let mut idx = SamtoolsMerge::from_config(
+    //         &config,
+    //         format!("{}/outputs/to_be_merged_2.bam", TEST_DIR.as_str()),
+    //         format!("{}/outputs/to_be_merged.bam", TEST_DIR.as_str()),
+    //     );
+    //
+    //     let captured_output = SlurmRunner::exec(&mut idx)?;
+    //     assert_eq!(captured_output.stderr, String::new());
+    //
+    //     Ok(())
+    // }
 
     #[test]
     fn samtools_split() -> anyhow::Result<()> {
@@ -677,17 +713,17 @@ mod tests {
 
         let sort_1 = SamtoolsSort::from_config(
             &config,
-            format!("{}/outputs/by_rg_splitted/10_hs1_sorted_22582b29-2858-43a6-86ee-47ed858dbcde_dna_r10.4.1_e8.2_400bps_sup@v5.2.0_SQK-NBD114-24_barcode02.bam", TEST_DIR.as_str()),
-            format!("{}/outputs/01_sorted.bam", TEST_DIR.as_str()),
+            "/mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1_HP.bam",
+            "/mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1_HP_sort.bam",
         );
 
-        let sort_2 = SamtoolsSort::from_config(
-            &config,
-            format!("{}/outputs/by_rg_splitted/10_hs1_sorted_22582b29-2858-43a6-86ee-47ed858dbcde_dna_r10.4.1_e8.2_400bps_sup@v5.2.0_SQK-NBD114-24_barcode04.bam", TEST_DIR.as_str()),
-            format!("{}/outputs/02_sorted.bam", TEST_DIR.as_str()),
-        );
+        // let sort_2 = SamtoolsSort::from_config(
+        //     &config,
+        //     format!("{}/outputs/by_rg_splitted/10_hs1_sorted_22582b29-2858-43a6-86ee-47ed858dbcde_dna_r10.4.1_e8.2_400bps_sup@v5.2.0_SQK-NBD114-24_barcode04.bam", TEST_DIR.as_str()),
+        //     format!("{}/outputs/02_sorted.bam", TEST_DIR.as_str()),
+        // );
 
-        let r = run_many_sbatch(vec![sort_1, sort_2])?;
+        let r = run_many_sbatch(vec![sort_1])?;
 
         println!("{r:#?}");
         Ok(())

src/config.rs

@@ -326,6 +326,9 @@ pub struct Config {
     /// Path to STR loci BED file for Straglr.
     pub straglr_loci_bed: String,
 
+    /// Size of reported difference between normal and tumoral
+    pub straglr_min_diff: u32,
+
     /// Minimum read support for STR genotyping.
     pub straglr_min_support: u32,
 
@@ -830,7 +833,7 @@ impl Config {
     pub fn straglr_normal_tsv(&self, id: &str) -> String {
         format!(
             "{}/{}_{}_straglr.tsv",
-            self.straglr_output_dir(id),
+            self.straglr_solo_output_dir(id, &self.normal_name),
             id,
             self.normal_name
         )
@@ -846,6 +849,16 @@ impl Config {
         )
     }
 
+    /// Straglr tumor sample TSV output.
+    pub fn straglr_tumor_normal_diff_tsv(&self, id: &str) -> String {
+        format!(
+            "{}/{}_{}_straglr_diff.tsv",
+            self.straglr_output_dir(id),
+            id,
+            self.tumoral_name
+        )
+    }
+
     /// Straglr solo output directory.
     pub fn straglr_solo_output_dir(&self, id: &str, time: &str) -> String {
         self.straglr_solo_output_dir

src/functions/fb_inv_stats.rs

@@ -0,0 +1,331 @@
+use std::collections::HashMap;
+
+use crate::io::bam::{FbInv, SegmentOrder};
+
+
+/// Distribution statistics for a numeric field.
+#[derive(Debug, Clone, Default)]
+pub struct DistributionStats {
+    pub count: usize,
+    pub min: i64,
+    pub max: i64,
+    pub sum: i64,
+    pub mean: f64,
+    pub median: f64,
+    pub std_dev: f64,
+}
+
+impl DistributionStats {
+    /// Compute distribution stats from a slice of values.
+    pub fn from_values(values: &mut [i64]) -> Self {
+        if values.is_empty() {
+            return Self::default();
+        }
+
+        let count = values.len();
+        let sum: i64 = values.iter().sum();
+        let mean = sum as f64 / count as f64;
+
+        // Sort for min/max/median
+        values.sort_unstable();
+        let min = values[0];
+        let max = values[count - 1];
+
+        let median = if count.is_multiple_of(2) {
+            (values[count / 2 - 1] + values[count / 2]) as f64 / 2.0
+        } else {
+            values[count / 2] as f64
+        };
+
+        // Standard deviation
+        let variance: f64 = values.iter().map(|&v| (v as f64 - mean).powi(2)).sum::<f64>() / count as f64;
+        let std_dev = variance.sqrt();
+
+        Self {
+            count,
+            min,
+            max,
+            sum,
+            mean,
+            median,
+            std_dev,
+        }
+    }
+}
+
+/// Strand pattern for fold-back inversions.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
+pub enum StrandPattern {
+    PlusMinus, // A on +, B on -
+    MinusPlus, // A on -, B on +
+}
+
+impl StrandPattern {
+    pub fn from_strands(a_strand: char, b_strand: char) -> Self {
+        match (a_strand, b_strand) {
+            ('+', '-') => StrandPattern::PlusMinus,
+            ('-', '+') => StrandPattern::MinusPlus,
+            _ => unreachable!("FbInv requires opposite strands"),
+        }
+    }
+}
+
+/// Per-contig statistics.
+#[derive(Debug, Clone, Default)]
+pub struct ContigStats {
+    pub count: usize,
+    pub mean_distance: f64, // mean distance between consecutive events (sorted by position)
+    pub positions: Vec<i64>, // stored temporarily for distance calculation
+}
+
+/// Comprehensive statistics computed from Vec<FbInv>.
+#[derive(Debug, Clone)]
+pub struct FbInvStats {
+    // Counts
+    pub total_count: usize,
+    pub per_contig_count: HashMap<String, usize>,
+    pub by_segment_order: HashMap<SegmentOrder, usize>,
+
+    // Size distributions
+    pub aln_a_len_stats: DistributionStats,
+    pub aln_b_len_stats: DistributionStats,
+    pub b_c_stats: DistributionStats,
+    pub a_d_stats: DistributionStats,
+
+    // Overlap metrics
+    pub overlap_stats: OverlapStats,
+
+    // Strand patterns
+    pub strand_pattern_counts: HashMap<StrandPattern, usize>,
+
+    // Per-contig with mean distance
+    pub per_contig_stats: HashMap<String, ContigStats>,
+}
+
+/// Overlap metrics between alignment A and B.
+#[derive(Debug, Clone, Default)]
+pub struct OverlapStats {
+    pub overlap_bp_stats: DistributionStats,      // overlap in base pairs
+    pub overlap_fraction_a: DistributionStats,    // overlap / aln_a_len (stored as i64 * 1000 for precision)
+    pub overlap_fraction_b: DistributionStats,    // overlap / aln_b_len
+    pub jaccard_stats: DistributionStats,         // overlap / union (stored as i64 * 1000)
+}
+
+impl FbInvStats {
+    /// Compute all statistics from a Vec<FbInv>.
+    /// Assumes events are sorted by (contig, position) for distance calculations.
+    pub fn from_events(events: &[FbInv]) -> Self {
+        if events.is_empty() {
+            return Self::empty();
+        }
+
+        let total_count = events.len();
+
+        // Counts
+        let mut per_contig_count: HashMap<String, usize> = HashMap::new();
+        let mut by_segment_order: HashMap<SegmentOrder, usize> = HashMap::new();
+        let mut strand_pattern_counts: HashMap<StrandPattern, usize> = HashMap::new();
+
+        // Collect values for distributions
+        let mut aln_a_lens: Vec<i64> = Vec::with_capacity(total_count);
+        let mut aln_b_lens: Vec<i64> = Vec::with_capacity(total_count);
+        let mut b_c_vals: Vec<i64> = Vec::with_capacity(total_count);
+        let mut a_d_vals: Vec<i64> = Vec::with_capacity(total_count);
+
+        // Overlap values
+        let mut overlap_bps: Vec<i64> = Vec::with_capacity(total_count);
+        let mut overlap_frac_a: Vec<i64> = Vec::with_capacity(total_count);
+        let mut overlap_frac_b: Vec<i64> = Vec::with_capacity(total_count);
+        let mut jaccard_vals: Vec<i64> = Vec::with_capacity(total_count);
+
+        // Per-contig positions for distance calculation
+        let mut per_contig_positions: HashMap<String, Vec<i64>> = HashMap::new();
+
+        for ev in events {
+            // Counts
+            *per_contig_count.entry(ev.ref_name.clone()).or_insert(0) += 1;
+            *by_segment_order.entry(ev.first).or_insert(0) += 1;
+
+            let pattern = StrandPattern::from_strands(ev.aln_a_strand, ev.aln_b_strand);
+            *strand_pattern_counts.entry(pattern).or_insert(0) += 1;
+
+            // Size distributions
+            aln_a_lens.push(ev.aln_a_len);
+            aln_b_lens.push(ev.aln_b_len);
+            b_c_vals.push(ev.b_c);
+            a_d_vals.push(ev.a_d);
+
+            // Overlap calculation
+            let overlap_bp = compute_overlap_bp(ev);
+            overlap_bps.push(overlap_bp);
+
+            if ev.aln_a_len > 0 {
+                overlap_frac_a.push((overlap_bp * 1000) / ev.aln_a_len);
+            }
+            if ev.aln_b_len > 0 {
+                overlap_frac_b.push((overlap_bp * 1000) / ev.aln_b_len);
+            }
+
+            let union = compute_union_bp(ev);
+            if union > 0 {
+                jaccard_vals.push((overlap_bp * 1000) / union);
+            }
+
+            // Store position for distance calculation (use midpoint of A alignment)
+            let midpoint = (ev.aln_a_start + ev.aln_a_end) / 2;
+            per_contig_positions
+                .entry(ev.ref_name.clone())
+                .or_default()
+                .push(midpoint);
+        }
+
+        // Compute per-contig stats with mean distance
+        let mut per_contig_stats: HashMap<String, ContigStats> = HashMap::new();
+        for (contig, mut positions) in per_contig_positions {
+            let count = positions.len();
+            positions.sort_unstable(); // ensure sorted
+
+            let mean_distance = if count > 1 {
+                let total_distance: i64 = positions
+                    .windows(2)
+                    .map(|w| (w[1] - w[0]).abs())
+                    .sum();
+                total_distance as f64 / (count - 1) as f64
+            } else {
+                0.0
+            };
+
+            per_contig_stats.insert(
+                contig.clone(),
+                ContigStats {
+                    count,
+                    mean_distance,
+                    positions,
+                },
+            );
+        }
+
+        Self {
+            total_count,
+            per_contig_count,
+            by_segment_order,
+            aln_a_len_stats: DistributionStats::from_values(&mut aln_a_lens),
+            aln_b_len_stats: DistributionStats::from_values(&mut aln_b_lens),
+            b_c_stats: DistributionStats::from_values(&mut b_c_vals),
+            a_d_stats: DistributionStats::from_values(&mut a_d_vals),
+            overlap_stats: OverlapStats {
+                overlap_bp_stats: DistributionStats::from_values(&mut overlap_bps),
+                overlap_fraction_a: DistributionStats::from_values(&mut overlap_frac_a),
+                overlap_fraction_b: DistributionStats::from_values(&mut overlap_frac_b),
+                jaccard_stats: DistributionStats::from_values(&mut jaccard_vals),
+            },
+            strand_pattern_counts,
+            per_contig_stats,
+        }
+    }
+
+    fn empty() -> Self {
+        Self {
+            total_count: 0,
+            per_contig_count: HashMap::new(),
+            by_segment_order: HashMap::new(),
+            aln_a_len_stats: DistributionStats::default(),
+            aln_b_len_stats: DistributionStats::default(),
+            b_c_stats: DistributionStats::default(),
+            a_d_stats: DistributionStats::default(),
+            overlap_stats: OverlapStats::default(),
+            strand_pattern_counts: HashMap::new(),
+            per_contig_stats: HashMap::new(),
+        }
+    }
+
+    /// Summary report as a formatted string.
+    pub fn summary(&self) -> String {
+        let mut s = String::new();
+
+        s.push_str("=== FbInv Statistics ===\n\n");
+        s.push_str(&format!("Total events: {}\n\n", self.total_count));
+
+        // Per-contig counts
+        s.push_str("Per-contig counts:\n");
+        let mut contigs: Vec<_> = self.per_contig_count.iter().collect();
+        contigs.sort_by(|a, b| b.1.cmp(a.1)); // sort by count descending
+        for (contig, count) in contigs {
+            if let Some(cstats) = self.per_contig_stats.get(contig) {
+                s.push_str(&format!(
+                    "  {}: {} events, mean distance: {:.1} bp\n",
+                    contig, count, cstats.mean_distance
+                ));
+            } else {
+                s.push_str(&format!("  {}: {}\n", contig, count));
+            }
+        }
+        s.push('\n');
+
+        // Segment order
+        s.push_str("By segment order:\n");
+        for (order, count) in &self.by_segment_order {
+            s.push_str(&format!("  {:?}: {}\n", order, count));
+        }
+        s.push('\n');
+
+        // Strand patterns
+        s.push_str("Strand patterns:\n");
+        for (pattern, count) in &self.strand_pattern_counts {
+            let pct = (*count as f64 / self.total_count as f64) * 100.0;
+            s.push_str(&format!("  {:?}: {} ({:.1}%)\n", pattern, count, pct));
+        }
+        s.push('\n');
+
+        // Size distributions
+        s.push_str("Size distributions:\n");
+        s.push_str(&format_dist("  aln_a_len", &self.aln_a_len_stats));
+        s.push_str(&format_dist("  aln_b_len", &self.aln_b_len_stats));
+        s.push_str(&format_dist("  b_c", &self.b_c_stats));
+        s.push_str(&format_dist("  a_d", &self.a_d_stats));
+        s.push('\n');
+
+        // Overlap metrics
+        s.push_str("Overlap metrics:\n");
+        s.push_str(&format_dist("  overlap_bp", &self.overlap_stats.overlap_bp_stats));
+        s.push_str(&format!(
+            "  overlap_frac_a: mean={:.1}%, median={:.1}%\n",
+            self.overlap_stats.overlap_fraction_a.mean / 10.0,
+            self.overlap_stats.overlap_fraction_a.median / 10.0
+        ));
+        s.push_str(&format!(
+            "  overlap_frac_b: mean={:.1}%, median={:.1}%\n",
+            self.overlap_stats.overlap_fraction_b.mean / 10.0,
+            self.overlap_stats.overlap_fraction_b.median / 10.0
+        ));
+        s.push_str(&format!(
+            "  jaccard: mean={:.1}%, median={:.1}%\n",
+            self.overlap_stats.jaccard_stats.mean / 10.0,
+            self.overlap_stats.jaccard_stats.median / 10.0
+        ));
+
+        s
+    }
+}
+
+/// Compute overlap in base pairs between alignment A and B on the reference.
+fn compute_overlap_bp(ev: &FbInv) -> i64 {
+    let max_start = ev.aln_a_start.max(ev.aln_b_start);
+    let min_end = ev.aln_a_end.min(ev.aln_b_end);
+    (min_end - max_start).max(0)
+}
+
+/// Compute union in base pairs between alignment A and B on the reference.
+fn compute_union_bp(ev: &FbInv) -> i64 {
+    let min_start = ev.aln_a_start.min(ev.aln_b_start);
+    let max_end = ev.aln_a_end.max(ev.aln_b_end);
+    max_end - min_start
+}
+
+fn format_dist(name: &str, d: &DistributionStats) -> String {
+    format!(
+        "{}: min={}, max={}, mean={:.1}, median={:.1}, std={:.1}\n",
+        name, d.min, d.max, d.mean, d.median, d.std_dev
+    )
+}
+

src/functions/mod.rs

@@ -1,3 +1,4 @@
 pub mod whole_scan;
 pub mod variants;
 pub mod assembler;
+pub mod fb_inv_stats;

src/io/bam.rs

@@ -1,8 +1,7 @@
 use std::collections::{HashMap, HashSet};
 
 use log::warn;
-use rust_htslib::bam::{record::Aux, IndexedReader, Read, Record};
-
+use rust_htslib::bam::{self, record::Aux, record::Cigar, IndexedReader, Read, Record};
 
 /// Parses an SA tag string and extracts chromosome and position information.
 ///
@@ -102,13 +101,13 @@ fn create_position_bins<'a>(positions: &[(&'a str, i32)]) -> Vec<Vec<(&'a str, i
     let mut sorted_positions = positions.to_vec();
     sorted_positions.sort_by_key(|(chr, pos)| (*chr, *pos));
     sorted_positions.dedup();
-    
+
     // Group by chromosome and create bins of ±1000 bp
     let mut grouped: HashMap<&str, Vec<Vec<(&str, i32)>>> = HashMap::new();
-    
+
     for (chr, pos) in sorted_positions {
         let bins = grouped.entry(chr).or_default();
-        
+
         if let Some(last_bin) = bins.last_mut() {
             if last_bin.is_empty() || (pos - last_bin[0].1).abs() <= 1000 {
                 last_bin.push((chr, pos));
@@ -119,16 +118,13 @@ fn create_position_bins<'a>(positions: &[(&'a str, i32)]) -> Vec<Vec<(&'a str, i
             bins.push(vec![(chr, pos)]);
         }
     }
-    
+
     // Flatten and sort by bin size (descending)
-    let mut flattened: Vec<Vec<(&str, i32)>> = grouped.values()
-        .flatten()
-        .cloned()
-        .collect();
-    
+    let mut flattened: Vec<Vec<(&str, i32)>> = grouped.values().flatten().cloned().collect();
+
     // Sort bins by size (descending) to prioritize regions with more hits
     flattened.sort_by_key(|bin| std::cmp::Reverse(bin.len()));
-    
+
     flattened
 }
 
@@ -161,7 +157,7 @@ pub fn primary_records(bam: &mut IndexedReader, records: Vec<Record>) -> Vec<Rec
     let mut res = Vec::with_capacity(records.len());
     let mut all_positions = Vec::new();
     let mut all_qnames_to_fetch = Vec::new();
-    
+
     // First pass: collect primary records and positions to fetch
     for record in records.iter() {
         if record.is_supplementary() {
@@ -170,7 +166,7 @@ pub fn primary_records(bam: &mut IndexedReader, records: Vec<Record>) -> Vec<Rec
             if let Ok(Aux::String(sa)) = record.aux(b"SA") {
                 let positions = parse_sa_tag(sa);
                 all_positions.extend(positions);
-                
+
                 match String::from_utf8(qname.to_vec()) {
                     Ok(qname_str) => all_qnames_to_fetch.push(qname_str),
                     Err(e) => warn!("Invalid UTF-8 in qname: {}", e),
@@ -180,31 +176,31 @@ pub fn primary_records(bam: &mut IndexedReader, records: Vec<Record>) -> Vec<Rec
             res.push(record.clone());
         }
     }
-    
+
     // Track which query names we've already found
     let mut primary_records: HashSet<String> = res
         .iter()
         .filter_map(|r| String::from_utf8(r.qname().to_vec()).ok())
         .collect();
-    
+
     // Create position bins for efficient fetching
     let position_bins = create_position_bins(&all_positions);
-    
+
     // Fetch records for each bin until we find all primaries
     for bin in position_bins {
         if bin.is_empty() {
             continue;
         }
-        
+
         let (chr, start) = bin.first().unwrap();
         let end = bin.last().unwrap().1 + 1;
-        
+
         // Fetch and process records in this region
         if let Err(e) = bam.fetch((*chr, *start, end)) {
             warn!("Failed to fetch region {}:{}-{}: {}", chr, start, end, e);
             continue;
         }
-        
+
         for record_result in bam.records() {
             match record_result {
                 Ok(record) => {
@@ -212,40 +208,40 @@ pub fn primary_records(bam: &mut IndexedReader, records: Vec<Record>) -> Vec<Rec
                     if record.is_secondary() {
                         continue;
                     }
-                    
+
                     // Check if this is a primary we're looking for
                     match String::from_utf8(record.qname().to_vec()) {
                         Ok(qname) => {
                             if primary_records.contains(&qname) {
                                 continue;
                             }
-                            
+
                             if all_qnames_to_fetch.contains(&qname) {
                                 res.push(record);
                                 primary_records.insert(qname);
                             }
-                        },
+                        }
                         Err(_) => continue,
                     }
-                },
+                }
                 Err(e) => warn!("Error reading record: {}", e),
             }
         }
-        
+
         // Early exit if we found all the records we were looking for
-        let remaining = all_qnames_to_fetch.iter()
+        let remaining = all_qnames_to_fetch
+            .iter()
             .filter(|q| !primary_records.contains(*q))
             .count();
-        
+
         if remaining == 0 {
             break;
         }
     }
-    
+
     res
 }
 
-
 pub fn get_genome_sizes(header: &rust_htslib::bam::Header) -> anyhow::Result<HashMap<String, u64>> {
     let mut genome = HashMap::new();
     for (key, records) in header.to_hashmap() {
@@ -265,10 +261,7 @@ pub fn get_genome_sizes(header: &rust_htslib::bam::Header) -> anyhow::Result<Has
 
 /// Split the genome into N balanced region lists (`ctg:start-end` strings).
 /// Each element of the outer Vec is the list of `-r` regions for one batch.
-pub fn split_genome_into_n_regions(
-    genome: &HashMap<String, u64>,
-    n: usize,
-) -> Vec<Vec<String>> {
+pub fn split_genome_into_n_regions(genome: &HashMap<String, u64>, n: usize) -> Vec<Vec<String>> {
     if n == 0 || genome.is_empty() {
         return Vec::new();
     }
@@ -312,3 +305,447 @@ pub fn split_genome_into_n_regions(
 
     batches
 }
+
+/// Indicates which alignment segment appears first on the read.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
+pub enum SegmentOrder {
+    /// Primary alignment appears before supplementary on the read
+    PrimaryFirst,
+    /// Supplementary alignment appears before primary on the read
+    SuppFirst,
+}
+
+/// Fold-back inversion event detected from a primary/supplementary alignment pair.
+/// Thanks to: https://github.com/cortes-ciriano-lab/ont_fb-inv_artifacts/blob/main/fb-inv_artefact_rates.py
+///
+/// A fold-back inversion occurs when a read has two alignments on the same chromosome
+/// with opposite strands that overlap on the reference. This pattern suggests the
+/// presence of an inverted duplication or fold-back structure.
+///
+/// # Coordinate System
+/// - All coordinates are 0-based, half-open `[start, end)`
+/// - Alignments A and B are ordered by their position on the read (A first)
+/// - Breakpoint distances (`b_c`, `a_d`) use strand-aware coordinates
+///
+/// # Breakpoints
+/// Breakpoints (a, b, c, d) are strand-aware positions representing alignment termini:
+/// - For `+` strand: `a = start` (5'), `b = end` (3')
+/// - For `-` strand: `c = start` (3'), `d = end` (5')
+///
+/// ```text
+/// Case: A on '+' strand, B on '-' strand
+///
+///              a                      c
+///              |                      |
+///              v                      v
+/// Reference:---[=====A=================>]---------
+///           --------[<=============B======]-------
+///                   ^                     ^
+///                   |                     |
+///                   b                     d
+///
+/// Alignment A (+ strand):  a=aln_a_start, b=aln_a_end
+/// Alignment B (- strand):  c=aln_b_start, d=aln_b_end
+///
+/// Distances:
+///   aln_a_len = |a - b| = alignment A length
+///   aln_b_len = |c - d| = alignment B length
+///   b_c       = |b - c| = inner breakpoint distance (3' ends)
+///   a_d       = |a - d| = outer breakpoint distance (5' ends)
+/// ```
+#[derive(Debug)]
+pub struct FbInv {
+    /// Read name (QNAME from BAM)
+    pub read_name: String,
+    /// Chromosome/contig name
+    pub ref_name: String,
+    /// Alignment A reference start (0-based)
+    pub aln_a_start: i64,
+    /// Alignment A reference end (exclusive)
+    pub aln_a_end: i64,
+    /// Alignment A strand ('+' or '-')
+    pub aln_a_strand: char,
+    /// Alignment B reference start (0-based)
+    pub aln_b_start: i64,
+    /// Alignment B reference end (exclusive)
+    pub aln_b_end: i64,
+    /// Alignment B strand ('+' or '-')
+    pub aln_b_strand: char,
+    /// Alignment A length on reference (bp)
+    pub aln_a_len: i64,
+    /// Alignment B length on reference (bp)
+    pub aln_b_len: i64,
+    /// Distance between breakpoints B and C (strand-aware)
+    pub b_c: i64,
+    /// Distance between breakpoints A and D (strand-aware)
+    pub a_d: i64,
+    /// Which alignment appears first on the read
+    pub first: SegmentOrder,
+    /// Primary alignment query start on read
+    pub primary_qbeg: u32,
+    /// Primary alignment query end on read
+    pub primary_qend: u32,
+    /// Supplementary alignment query start on read
+    pub sa_qbeg: u32,
+    /// Supplementary alignment query end on read
+    pub sa_qend: u32,
+}
+
+/// Parse a SAM CIGAR string into a vector of CIGAR operations.
+///
+/// Supports all standard CIGAR operations: M, I, D, N, S, H, P, =, X
+///
+/// # Arguments
+/// * `s` - CIGAR string (e.g., "10S100M5I50M20S")
+///
+/// # Returns
+/// `Some(Vec<Cigar>)` if valid, `None` if malformed or empty
+///
+/// # Examples
+/// ```
+/// let ops = parse_cigar_str("10S100M").unwrap();
+/// assert_eq!(ops.len(), 2);
+/// ```
+pub fn parse_cigar_str(s: &str) -> Option<Vec<Cigar>> {
+    if s.is_empty() {
+        return None;
+    }
+
+    // Pre-allocate: rough estimate ~1 op per 2-3 chars
+    let mut ops = Vec::with_capacity(s.len() / 2);
+    let mut num = String::new();
+
+    for c in s.chars() {
+        if c.is_ascii_digit() {
+            num.push(c);
+            continue;
+        }
+
+        // We hit an operator letter: parse the accumulated number
+        if num.is_empty() {
+            return None; // operator without length
+        }
+        let len: u32 = num.parse().ok()?;
+        num.clear();
+
+        let op = match c {
+            'M' => Cigar::Match(len),
+            'I' => Cigar::Ins(len),
+            'D' => Cigar::Del(len),
+            'N' => Cigar::RefSkip(len),
+            'S' => Cigar::SoftClip(len),
+            'H' => Cigar::HardClip(len),
+            'P' => Cigar::Pad(len),
+            '=' => Cigar::Equal(len),
+            'X' => Cigar::Diff(len),
+            _ => return None, // unknown operator
+        };
+
+        ops.push(op);
+    }
+
+    // CIGAR ending with digits only is invalid
+    if !num.is_empty() {
+        return None;
+    }
+
+    // Validation: CIGAR must have at least one operation
+    if ops.is_empty() {
+        return None;
+    }
+
+    Some(ops)
+}
+
+/// Compute query coordinates (start, end) on the read from a CIGAR.
+///
+/// For plus strand, the first CIGAR operation corresponds to the read start.
+/// For minus strand, the last CIGAR operation corresponds to the read start.
+///
+/// # Arguments
+/// * `ops` - CIGAR operations slice
+/// * `strand` - '+' or '-'
+///
+/// # Returns
+/// Tuple of (query_begin, query_end) in read coordinates (excluding hard clips)
+fn alignment_query_coords(ops: &[Cigar], strand: char) -> (u32, u32) {
+    if ops.is_empty() {
+        return (0, 0);
+    }
+
+    // For minus strand, the "first" op on the read is the last in the CIGAR
+    let first_op = if strand == '+' {
+        &ops[0]
+    } else {
+        ops.last().unwrap()
+    };
+
+    let query_beg = match first_op {
+        Cigar::SoftClip(len) => *len,
+        _ => 0,
+    };
+
+    // Alignment length on the read (consumes query bases)
+    let aln_len: u32 = ops
+        .iter()
+        .filter_map(|op| match op {
+            Cigar::Match(l) | Cigar::Ins(l) | Cigar::Equal(l) | Cigar::Diff(l) => Some(*l),
+            _ => None,
+        })
+        .sum();
+
+    (query_beg, query_beg + aln_len)
+}
+
+/// Compute alignment length on the reference from CIGAR operations.
+///
+/// Counts bases consumed by M, D, N, =, X operations.
+///
+/// # Arguments
+/// * `ops` - CIGAR operations slice
+///
+/// # Returns
+/// Reference-consuming length in base pairs
+fn alignment_ref_length(ops: &[Cigar]) -> u32 {
+    ops.iter()
+        .filter_map(|op| match op {
+            Cigar::Match(l)
+            | Cigar::Del(l)
+            | Cigar::RefSkip(l)
+            | Cigar::Equal(l)
+            | Cigar::Diff(l) => Some(*l),
+            _ => None,
+        })
+        .sum()
+}
+
+/// Compute gap between two intervals. Negative value means overlap.
+///
+/// # Arguments
+/// * `a_start`, `a_end` - First interval `[a_start, a_end)`
+/// * `b_start`, `b_end` - Second interval `[b_start, b_end)`
+///
+/// # Returns
+/// Gap in bp (negative if overlapping, 0 if adjacent, positive if separated)
+#[inline]
+fn interval_gap(a_start: i64, a_end: i64, b_start: i64, b_end: i64) -> i64 {
+    a_start.max(b_start) - a_end.min(b_end)
+}
+
+/// Compute strand-aware breakpoint coordinates.
+///
+/// For fold-back inversions, breakpoints depend on strand orientation:
+/// - Plus strand: breakpoints are (start, end) - 5' to 3' direction
+/// - Minus strand: breakpoints are (end, start) - reversed direction
+///
+/// # Arguments
+/// * `start` - Alignment start (0-based)
+/// * `end` - Alignment end (exclusive)
+/// * `strand` - '+' or '-'
+///
+/// # Returns
+/// Tuple of (breakpoint_a, breakpoint_b) in strand-aware order
+#[inline]
+fn breakpoints(start: i64, end: i64, strand: char) -> (i64, i64) {
+    if strand == '+' {
+        (start, end)
+    } else {
+        (end, start)
+    }
+}
+
+/// Extract a fold-back inversion event from a BAM record.
+///
+/// Analyzes a primary alignment and its supplementary alignment (from SA tag)
+/// to detect fold-back inversion patterns characterized by:
+/// - Same chromosome
+/// - Opposite strands
+/// - Reference coordinates within proximity threshold
+/// - Exactly one supplementary alignment
+///
+/// # Arguments
+/// * `record` - BAM record (must be primary alignment)
+/// * `header` - BAM header for reference name lookup
+/// * `min_mapq` - Minimum mapping quality threshold for both alignments
+/// * `max_overlap` - Maximum allowed overlap in bp (None = no limit)
+/// * `max_gap` - Maximum allowed gap in bp (None = no limit, 0 = require overlap or adjacent)
+///   default should be [-150, 200) Some(150), Some(200)
+///
+/// # Returns
+/// `Some(FbInv)` if a valid fold-back pattern is detected, `None` otherwise
+///
+/// # Filtering
+/// Returns `None` if any of these conditions are met:
+/// - Record is unmapped, secondary, or supplementary
+/// - MAPQ below threshold (primary or supplementary)
+/// - No SA tag or multiple supplementary alignments
+/// - Supplementary on different chromosome
+/// - Same strand orientation
+/// - Overlap exceeds `max_overlap` (if set)
+/// - Gap exceeds `max_gap` (if set)
+pub fn fb_inv_from_record(
+    record: &bam::Record,
+    header: &bam::HeaderView,
+    min_mapq: u8,
+    max_overlap: Option<i64>,
+    max_gap: Option<i64>,
+) -> Option<FbInv> {
+    // Basic filters (primary only, mapped, MAPQ)
+    if record.is_unmapped()
+        || record.is_secondary()
+        || record.is_supplementary()
+        || record.mapq() < min_mapq
+    {
+        return None;
+    }
+
+    // SA tag required
+    let sa_str = match record.aux(b"SA") {
+        Ok(Aux::String(s)) => s,
+        _ => return None,
+    };
+
+    let sa_entries: Vec<&str> = sa_str.split(';').filter(|s| !s.is_empty()).collect();
+
+    // Require exactly one SA (like the Python code)
+    if sa_entries.len() != 1 {
+        return None;
+    }
+    let sa = sa_entries[0];
+
+    // SA format: chr,pos,strand,cigar,mapq,nm
+    let fields: Vec<&str> = sa.split(',').collect();
+    if fields.len() < 6 {
+        return None;
+    }
+    let sa_rname = fields[0];
+    let sa_pos_1based: i64 = fields[1].parse().ok()?; // SAM is 1-based
+    let sa_strand_char: char = fields[2].chars().next()?;
+    let sa_cigar_str = fields[3];
+    let sa_mapq: u8 = fields[4].parse().ok()?;
+
+    if sa_mapq < min_mapq {
+        return None;
+    }
+
+    // Same chromosome: compare SA rname with primary reference name
+    let tid = record.tid();
+    if tid < 0 {
+        return None;
+    }
+    let primary_rname = std::str::from_utf8(header.tid2name(tid as u32)).ok()?;
+    if sa_rname != primary_rname {
+        return None;
+    }
+
+    // Strand check: need opposite strands for fold-back inversion
+    let primary_strand_char = if record.is_reverse() { '-' } else { '+' };
+    if primary_strand_char == sa_strand_char {
+        return None;
+    }
+
+    // Primary ref coords (0-based, half-open)
+    let primary_start = record.pos();
+    let primary_end = record.cigar().end_pos();
+
+    // Parse SA CIGAR
+    let sa_cigar_ops = parse_cigar_str(sa_cigar_str)?;
+    let sa_ref_len = alignment_ref_length(&sa_cigar_ops);
+
+    // Validation: SA must have non-zero reference length
+    if sa_ref_len == 0 {
+        return None;
+    }
+
+    // SA ref coords: convert POS from 1-based to 0-based
+    let sa_start = sa_pos_1based - 1;
+    let sa_end = sa_start + sa_ref_len as i64;
+
+    // Check proximity between alignments
+    // gap < 0: overlap of |gap| bp
+    // gap = 0: adjacent (touching)
+    // gap > 0: separated by gap bp
+    let gap = interval_gap(primary_start, primary_end, sa_start, sa_end);
+
+    // Check max_overlap: reject if overlap exceeds limit
+    if let Some(max_ovl) = max_overlap {
+        if gap < 0 && gap.abs() > max_ovl {
+            return None;
+        }
+    }
+
+    // Check max_gap: reject if gap exceeds limit
+    if let Some(max_g) = max_gap {
+        if gap > max_g {
+            return None;
+        }
+    }
+
+    // Query coords for primary and SA
+    let primary_cigar: Vec<Cigar> = record.cigar().iter().cloned().collect();
+    let (primary_qbeg, primary_qend) = alignment_query_coords(&primary_cigar, primary_strand_char);
+    let (sa_qbeg, sa_qend) = alignment_query_coords(&sa_cigar_ops, sa_strand_char);
+
+    // Decide which segment is first on the read
+    let first = if primary_qbeg <= sa_qbeg {
+        SegmentOrder::PrimaryFirst
+    } else {
+        SegmentOrder::SuppFirst
+    };
+
+    // Build FbInv with A/B ordered by read position
+    let (aln_a_start, aln_a_end, aln_a_strand, aln_b_start, aln_b_end, aln_b_strand) =
+        if first == SegmentOrder::PrimaryFirst {
+            (
+                primary_start,
+                primary_end,
+                primary_strand_char,
+                sa_start,
+                sa_end,
+                sa_strand_char,
+            )
+        } else {
+            (
+                sa_start,
+                sa_end,
+                sa_strand_char,
+                primary_start,
+                primary_end,
+                primary_strand_char,
+            )
+        };
+
+    // Distances a_b, c_d, b_c, a_d (like the Python class)
+    let (a, b) = breakpoints(aln_a_start, aln_a_end, aln_a_strand);
+    let (c, d) = breakpoints(aln_b_start, aln_b_end, aln_b_strand);
+
+    let aln_a_len = (a - b).abs();
+    let aln_b_len = (c - d).abs();
+    let b_c = (b - c).abs();
+    let a_d = (a - d).abs();
+
+    let read_name = std::str::from_utf8(record.qname())
+        .map(|s| s.to_string())
+        .unwrap_or_else(|_| String::from_utf8_lossy(record.qname()).into_owned());
+    let ref_name = primary_rname.to_string();
+
+    Some(FbInv {
+        read_name,
+        ref_name,
+        aln_a_start,
+        aln_a_end,
+        aln_a_strand,
+        aln_b_start,
+        aln_b_end,
+        aln_b_strand,
+        aln_a_len,
+        aln_b_len,
+        b_c,
+        a_d,
+        first,
+        primary_qbeg,
+        primary_qend,
+        sa_qbeg,
+        sa_qend,
+    })
+}

src/io/straglr.rs

@@ -15,7 +15,7 @@ use super::readers::get_reader;
 ///
 /// Each row corresponds to one STR locus with its genotype information,
 /// read support, and confidence metrics.
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, PartialEq)]
 pub struct StraglrRow {
     /// Chromosome name (e.g., "chr4", "chrX")
     pub chrom: String,
@@ -75,6 +75,10 @@ impl FromStr for StraglrRow {
             .filter_map(|s| s.parse().ok())
             .collect();
 
+        if copy_numbers.is_empty() && fields[5] != "." {
+            warn!("Failed to parse any copy numbers from: {}", fields[5]);
+        }
+
         let support: u32 = fields[6]
             .parse()
             .context(format!("Failed to parse support: {}", fields[6]))?;
@@ -181,7 +185,12 @@ pub fn read_straglr_tsv(path: &str) -> anyhow::Result<Vec<StraglrRow>> {
 
                 match line.parse::<StraglrRow>() {
                     Ok(row) => results.push(row),
-                    Err(e) => warn!("Failed to parse line {}: {} (error: {})", line_num + 1, line, e),
+                    Err(e) => warn!(
+                        "Failed to parse line {}: {} (error: {})",
+                        line_num + 1,
+                        line,
+                        e
+                    ),
                 }
             }
             Err(e) => warn!("Failed to read line {}: {}", line_num + 1, e),
@@ -212,12 +221,14 @@ pub fn filter_expanded(rows: Vec<StraglrRow>, min_copy_number: u32) -> Vec<Strag
 ///
 /// # Returns
 /// HashMap mapping chromosome names to vectors of STR loci
-pub fn group_by_chromosome(rows: Vec<StraglrRow>) -> std::collections::HashMap<String, Vec<StraglrRow>> {
+pub fn group_by_chromosome(
+    rows: Vec<StraglrRow>,
+) -> std::collections::HashMap<String, Vec<StraglrRow>> {
     use std::collections::HashMap;
 
     let mut map: HashMap<String, Vec<StraglrRow>> = HashMap::new();
     for row in rows {
-        map.entry(row.chrom.clone()).or_insert_with(Vec::new).push(row);
+        map.entry(row.chrom.clone()).or_default().push(row);
     }
     map
 }

src/pipes/somatic_slurm.rs

@@ -460,11 +460,8 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
             // remove unsorted chunk
             fs::remove_file(&bam)?;
 
-            let mut index_cmd = SamtoolsIndex {
-                bin: config.align.samtools_bin.clone(),
-                threads: config.align.samtools_view_threads,
-                bam: sorted_bam.to_string_lossy().to_string(),
-            };
+            let mut index_cmd =
+                SamtoolsIndex::from_config(config, sorted_bam.to_string_lossy().to_string().as_ref());
             SlurmRunner::exec(&mut index_cmd)?;
 
             // replace path in case_bam_map with sorted version
@@ -556,18 +553,12 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
             );
 
             // Index both source (per-case) and destination BAMs
-            let mut index_cmd = SamtoolsIndex {
-                bin: config.align.samtools_bin.clone(),
-                threads: config.align.samtools_view_threads,
-                bam: case_merged_bam.to_string_lossy().to_string(),
-            };
+            let mut index_cmd =
+                SamtoolsIndex::from_config(config, case_merged_bam.to_string_lossy().as_ref());
             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(),
-            };
+            let mut index_cmd =
+                SamtoolsIndex::from_config(config, final_bam_path.to_string_lossy().as_ref());
             SlurmRunner::exec(&mut index_cmd)?;
 
             // Merge into existing final BAM.
@@ -604,11 +595,8 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
         fs::rename(&sorted_tmp, &final_bam_path)?;
 
         // Index the **sorted** final BAM
-        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(),
-        };
+        let mut index_cmd =
+            SamtoolsIndex::from_config(config, final_bam_path.to_string_lossy().as_ref());
         SlurmRunner::exec(&mut index_cmd)?;
 
         info!("  Output: {}", final_bam_path.display());