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