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