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