pandora_lib_promethion/slurm-2556287.out

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