WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23': destination is already in the mount point list [COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23 --region chr20:27012964-66210255 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/split_beds [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/pileup_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/fa_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/tmp_vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/vcf [INFO] --include_all_ctgs enabled [INFO] Call variants in contigs: chr20 [INFO] Number of chunks for each contig: 14 [INFO] CALLER VERSION: 0.4.4 [INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam [INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa [INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs [INFO] THREADS: 40 [INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23 [INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/output.vcf.gz [INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl [INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl [INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/region.bed [INFO] GENOTYPING MODE VCF FILE PATH: None [INFO] HYBRID MODE VCF FILE PATH: None [INFO] REGION FOR CALLING: chr20:27012964-66210255 [INFO] CONTIGS FOR CALLING: None [INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs [INFO] SAMTOOLS BINARY PATH: samtools [INFO] PYTHON BINARY PATH: python3 [INFO] PYPY BINARY PATH: pypy3 [INFO] PARALLEL BINARY PATH: parallel [INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase [INFO] CHUNK SIZE: 5000000 [INFO] SNV MINIMUM AF: 0.05 [INFO] SNV MINIMUM QUAL: 8 [INFO] INDEL MINIMUM AF: 0.1 [INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl [INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl [INFO] INDEL MINIMUM QUAL: 8 [INFO] NORMAL VCF FILE PATH: None [INFO] DISABLE PHASING: False [INFO] ENABLE DRY RUN: False [INFO] ENABLE INDEL CALLING: True [INFO] ENABLE PRINTING REFERENCE CALLS: False [INFO] ENABLE PRINTING GERMLINE CALLS: True [INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True [INFO] ENABLE REMOVING INTERMEDIATE FILES: False [INFO] Call Germline Variants in Normal BAM using Clair3 [INFO] RUN THE FOLLOWING COMMAND: ( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output --ctg_name=chr20 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/1_CLAIR3_NORMAL.log [INFO] CLAIR3 VERSION: v1.0.8 [INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa [INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 [INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output [INFO] PLATFORM: ont [INFO] THREADS: 40 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: chr20 [INFO] CONDA PREFIX: [INFO] SAMTOOLS PATH: samtools [INFO] PYTHON PATH: python3 [INFO] PYPY PATH: pypy3 [INFO] PARALLEL PATH: parallel [INFO] WHATSHAP PATH: whatshap [INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase [INFO] CHUNK SIZE: 5000000 [INFO] FULL ALIGN PROPORTION: 0.7 [INFO] FULL ALIGN REFERENCE PROPORTION: 0.1 [INFO] PHASING PROPORTION: 0.7 [INFO] MINIMUM MQ: 5 [INFO] MINIMUM COVERAGE: 4 [INFO] SNP AF THRESHOLD: 0.08 [INFO] INDEL AF THRESHOLD: 0.15 [INFO] BASE ERROR IN GVCF: 0.001 [INFO] GQ BIN SIZE IN GVCF: 5 [INFO] ENABLE FILEUP ONLY CALLING: False [INFO] ENABLE FAST MODE CALLING: False [INFO] ENABLE CALLING SNP CANDIDATES ONLY: False [INFO] ENABLE PRINTING REFERENCE CALLS: False [INFO] ENABLE OUTPUT GVCF: False [INFO] ENABLE HAPLOID PRECISE MODE: False [INFO] ENABLE HAPLOID SENSITIVE MODE: False [INFO] ENABLE INCLUDE ALL CTGS CALLING: False [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False [INFO] ENABLE REMOVING INTERMEDIATE FILES: False [INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True [INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False [INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False [INFO] ENABLE HAPLOTAGGING FINAL BAM: False [INFO] ENABLE LONG INDEL CALLING: False [INFO] ENABLE C_IMPLEMENT: True + /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr20 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False [INFO] Check environment variables [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/pileup_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/merge_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed [INFO] Call variant in contigs: chr20 [INFO] Chunk number for each contig: 14 [INFO] 1/7 Call variants using pileup model Calling variants ... Total processed positions in chr20 (chunk 6/14) : 49610 Total time elapsed: 84.48 s Calling variants ... Total processed positions in chr20 (chunk 3/14) : 78073 Total time elapsed: 125.01 s Calling variants ... Total processed positions in chr20 (chunk 8/14) : 79273 Total time elapsed: 125.47 s Calling variants ... Total processed positions in chr20 (chunk 2/14) : 76976 Total time elapsed: 127.90 s Calling variants ... Total processed positions in chr20 (chunk 1/14) : 83255 Total time elapsed: 128.77 s Calling variants ... Total processed positions in chr20 (chunk 7/14) : 75361 Total time elapsed: 133.50 s Calling variants ... Total processed positions in chr20 (chunk 5/14) : 77255 Total time elapsed: 138.58 s Calling variants ... Total processed positions in chr20 (chunk 14/14) : 92564 Total time elapsed: 142.19 s Calling variants ... Total processed positions in chr20 (chunk 9/14) : 81579 Total time elapsed: 141.82 s Calling variants ... Total processed positions in chr20 (chunk 12/14) : 85050 Total time elapsed: 142.79 s Calling variants ... Total processed positions in chr20 (chunk 4/14) : 79660 Total time elapsed: 145.64 s Calling variants ... Total processed positions in chr20 (chunk 10/14) : 84512 Total time elapsed: 145.78 s Calling variants ... Total processed positions in chr20 (chunk 13/14) : 85068 Total time elapsed: 146.93 s Calling variants ... Total processed positions in chr20 (chunk 11/14) : 84971 Total time elapsed: 151.69 s real 2m38.151s user 30m21.785s sys 1m14.744s [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15 [INFO] Total heterozygous SNP positions selected: chr20: 45551 real 0m1.811s user 0m1.647s sys 0m0.129s [INFO] 3/7 Phase VCF file using LongPhase LongPhase Ver 1.7 --- File Parameter --- SNP File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr20.vcf SV File : MOD File : REF File : /home/t_steimle/ref/hs1/chm13v2.0.fa Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr20 Generate Dot : False BAM File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --- Phasing Parameter --- Seq Platform : ONT Phase Indel : False Distance Threshold : 300000 Connect Adjacent : 20 Edge Threshold : 0.7 Mapping Quality : 1 Variant Confidence : 0.75 ReadTag Confidence : 0.65 parsing VCF ... 0s parsing SV VCF ... 0s parsing Meth VCF ... 0s reading reference ... 1s (chr20,4s) parsing total: 4s merge results ... 0s writeResult SNP ... 1s total process: 6s real 0m5.455s user 0m10.697s sys 0m0.887s [INFO] 5/7 Select candidates for full-alignment calling [INFO] Set variants quality cutoff 19.0 [INFO] Set reference calls quality cutoff 13.0 [INFO] Low quality reference calls to be processed in chr20: 99183 [INFO] Low quality variants to be processed in chr20: 84562 real 0m2.039s user 0m1.790s sys 0m0.194s [INFO] 6/7 Call low-quality variants using full-alignment model Calling variants ... Total processed positions in chr20 (chunk 19/19) : 3745 Total time elapsed: 45.38 s Calling variants ... Total processed positions in chr20 (chunk 12/19) : 10000 Total time elapsed: 97.11 s Calling variants ... Total processed positions in chr20 (chunk 8/19) : 10000 Total time elapsed: 98.44 s Calling variants ... Total processed positions in chr20 (chunk 4/19) : 10000 Total time elapsed: 99.77 s Calling variants ... Total processed positions in chr20 (chunk 5/19) : 10000 Total time elapsed: 100.40 s Calling variants ... Total processed positions in chr20 (chunk 3/19) : 10000 Total time elapsed: 99.75 s Calling variants ... Total processed positions in chr20 (chunk 10/19) : 10000 Total time elapsed: 100.00 s Calling variants ... Total processed positions in chr20 (chunk 6/19) : 10000 Total time elapsed: 100.45 s Calling variants ... Total processed positions in chr20 (chunk 15/19) : 10000 Total time elapsed: 101.01 s Calling variants ... Total processed positions in chr20 (chunk 2/19) : 10000 Total time elapsed: 100.29 s Calling variants ... Total processed positions in chr20 (chunk 17/19) : 10000 Total time elapsed: 102.47 s Calling variants ... Total processed positions in chr20 (chunk 9/19) : 10000 Total time elapsed: 105.90 s Calling variants ... Total processed positions in chr20 (chunk 16/19) : 10000 Total time elapsed: 106.37 s Calling variants ... Total processed positions in chr20 (chunk 13/19) : 10000 Total time elapsed: 107.43 s Calling variants ... Total processed positions in chr20 (chunk 1/19) : 10000 Total time elapsed: 107.31 s Calling variants ... Total processed positions in chr20 (chunk 7/19) : 10000 Total time elapsed: 108.56 s Calling variants ... Total processed positions in chr20 (chunk 11/19) : 10000 Total time elapsed: 108.02 s Calling variants ... Total processed positions in chr20 (chunk 14/19) : 10000 Total time elapsed: 113.98 s Calling variants ... Total processed positions in chr20 (chunk 18/19) : 10000 Total time elapsed: 121.71 s real 2m5.361s user 31m13.765s sys 1m38.568s [INFO] 7/7 Merge pileup VCF and full-alignment VCF [INFO] Pileup variants processed in chr20: 36358 [INFO] Full-alignment variants processed in chr20: 87253 real 0m2.470s user 0m2.770s sys 0m0.178s [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz real 5m6.452s user 62m2.314s sys 2m55.903s [INFO] Call Germline Variant in Tumor BAM using Clair3 [INFO] RUN THE FOLLOWING COMMAND: ( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output --ctg_name=chr20 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/2_CLAIR3_TUMOR.log [INFO] CLAIR3 VERSION: v1.0.8 [INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa [INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 [INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output [INFO] PLATFORM: ont [INFO] THREADS: 40 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: chr20 [INFO] CONDA PREFIX: [INFO] SAMTOOLS PATH: samtools [INFO] PYTHON PATH: python3 [INFO] PYPY PATH: pypy3 [INFO] PARALLEL PATH: parallel [INFO] WHATSHAP PATH: whatshap [INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase [INFO] CHUNK SIZE: 5000000 [INFO] FULL ALIGN PROPORTION: 0.7 [INFO] FULL ALIGN REFERENCE PROPORTION: 0.1 [INFO] PHASING PROPORTION: 0.7 [INFO] MINIMUM MQ: 5 [INFO] MINIMUM COVERAGE: 4 [INFO] SNP AF THRESHOLD: 0.08 [INFO] INDEL AF THRESHOLD: 0.15 [INFO] BASE ERROR IN GVCF: 0.001 [INFO] GQ BIN SIZE IN GVCF: 5 [INFO] ENABLE FILEUP ONLY CALLING: False [INFO] ENABLE FAST MODE CALLING: False [INFO] ENABLE CALLING SNP CANDIDATES ONLY: False [INFO] ENABLE PRINTING REFERENCE CALLS: False [INFO] ENABLE OUTPUT GVCF: False [INFO] ENABLE HAPLOID PRECISE MODE: False [INFO] ENABLE HAPLOID SENSITIVE MODE: False [INFO] ENABLE INCLUDE ALL CTGS CALLING: False [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False [INFO] ENABLE REMOVING INTERMEDIATE FILES: False [INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True [INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False [INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False [INFO] ENABLE HAPLOTAGGING FINAL BAM: False [INFO] ENABLE LONG INDEL CALLING: False [INFO] ENABLE C_IMPLEMENT: True + /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr20 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False [INFO] Check environment variables [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/merge_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed [INFO] Call variant in contigs: chr20 [INFO] Chunk number for each contig: 14 [INFO] 1/7 Call variants using pileup model Calling variants ... Total processed positions in chr20 (chunk 5/14) : 8465 Total time elapsed: 49.20 s Calling variants ... Total processed positions in chr20 (chunk 8/14) : 9125 Total time elapsed: 50.86 s Calling variants ... Total processed positions in chr20 (chunk 9/14) : 8456 Total time elapsed: 51.46 s Calling variants ... Total processed positions in chr20 (chunk 12/14) : 9736 Total time elapsed: 52.16 s Calling variants ... Total processed positions in chr20 (chunk 2/14) : 9407 Total time elapsed: 52.80 s Calling variants ... Total processed positions in chr20 (chunk 10/14) : 9956 Total time elapsed: 54.30 s Calling variants ... Total processed positions in chr20 (chunk 3/14) : 9839 Total time elapsed: 54.72 s Calling variants ... Total processed positions in chr20 (chunk 4/14) : 10680 Total time elapsed: 55.26 s Calling variants ... Total processed positions in chr20 (chunk 13/14) : 11784 Total time elapsed: 55.93 s Calling variants ... Total processed positions in chr20 (chunk 11/14) : 12944 Total time elapsed: 58.61 s Calling variants ... Total processed positions in chr20 (chunk 14/14) : 17216 Total time elapsed: 62.82 s Calling variants ... Total processed positions in chr20 (chunk 6/14) : 17711 Total time elapsed: 64.45 s Calling variants ... Total processed positions in chr20 (chunk 1/14) : 17838 Total time elapsed: 64.88 s Calling variants ... Total processed positions in chr20 (chunk 7/14) : 53609 Total time elapsed: 108.72 s real 1m51.540s user 10m29.002s sys 0m52.148s [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19 [INFO] Total heterozygous SNP positions selected: chr20: 45273 real 0m0.719s user 0m0.598s sys 0m0.087s [INFO] 3/7 Phase VCF file using LongPhase LongPhase Ver 1.7 --- File Parameter --- SNP File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr20.vcf SV File : MOD File : REF File : /home/t_steimle/ref/hs1/chm13v2.0.fa Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr20 Generate Dot : False BAM File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --- Phasing Parameter --- Seq Platform : ONT Phase Indel : False Distance Threshold : 300000 Connect Adjacent : 20 Edge Threshold : 0.7 Mapping Quality : 1 Variant Confidence : 0.75 ReadTag Confidence : 0.65 parsing VCF ... 0s parsing SV VCF ... 0s parsing Meth VCF ... 0s reading reference ... 1s (chr20,15s) parsing total: 15s merge results ... 0s writeResult SNP ... 1s total process: 17s real 0m16.687s user 0m51.253s sys 0m3.133s [INFO] 5/7 Select candidates for full-alignment calling [INFO] Set variants quality cutoff 21.0 [INFO] Set reference calls quality cutoff 8.0 [INFO] Low quality reference calls to be processed in chr20: 8756 [INFO] Low quality variants to be processed in chr20: 83160 real 0m0.739s user 0m0.596s sys 0m0.103s [INFO] 6/7 Call low-quality variants using full-alignment model Calling variants ... Total processed positions in chr20 (chunk 10/10) : 1916 Total time elapsed: 25.33 s Calling variants ... Total processed positions in chr20 (chunk 5/10) : 10000 Total time elapsed: 97.80 s Calling variants ... Total processed positions in chr20 (chunk 4/10) : 10000 Total time elapsed: 107.36 s Calling variants ... Total processed positions in chr20 (chunk 1/10) : 10000 Total time elapsed: 112.12 s Calling variants ... Total processed positions in chr20 (chunk 9/10) : 10000 Total time elapsed: 114.33 s Calling variants ... Total processed positions in chr20 (chunk 7/10) : 10000 Total time elapsed: 116.06 s Calling variants ... Total processed positions in chr20 (chunk 6/10) : 10000 Total time elapsed: 116.78 s Calling variants ... Total processed positions in chr20 (chunk 8/10) : 10000 Total time elapsed: 118.37 s Calling variants ... Total processed positions in chr20 (chunk 3/10) : 10000 Total time elapsed: 122.36 s Calling variants ... Total processed positions in chr20 (chunk 2/10) : 10000 Total time elapsed: 123.53 s real 2m6.049s user 16m32.611s sys 0m52.581s [INFO] 7/7 Merge pileup VCF and full-alignment VCF [INFO] Pileup variants processed in chr20: 35964 [INFO] Full-alignment variants processed in chr20: 74344 real 0m1.116s user 0m1.113s sys 0m0.115s [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz real 4m21.554s user 27m58.893s sys 1m48.758s [INFO] Select Heterozygous SNP for Phasing [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/1_select_hetero_snp_for_phasing.log [INFO] Total HET SNP calls selected: chr20: 57143, not found:460, not match:37, low_qual_count:0. Total normal:61825 Total tumor:57640, pro: 0.9914 [INFO] Phase the Tumor BAM [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS LongPhase Ver 1.7 --- File Parameter --- SNP File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/vcf/chr20.vcf SV File : MOD File : REF File : /home/t_steimle/ref/hs1/chm13v2.0.fa Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_chr20 Generate Dot : False BAM File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --- Phasing Parameter --- Seq Platform : ONT Phase Indel : False Distance Threshold : 300000 Connect Adjacent : 20 Edge Threshold : 0.7 Mapping Quality : 1 Variant Confidence : 0.75 ReadTag Confidence : 0.65 parsing VCF ... 0s parsing SV VCF ... 0s parsing Meth VCF ... 0s reading reference ... 0s (chr20,25s) parsing total: 25s merge results ... 0s writeResult SNP ... 0s total process: 25s [INFO] Haplotag the Tumor BAM [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1} -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS phased SNP file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_phased_chr20.vcf.gz phased SV file: phased MOD file: input bam file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam input ref file: /home/t_steimle/ref/hs1/chm13v2.0.fa output bam file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_chr20.bam number of threads: 1 write log file: false log file: ------------------------------------------- tag region: chr20 filter mapping quality below: 1 percentage threshold: 0.6 tag supplementary: false ------------------------------------------- parsing SNP VCF ... 0s tag read start ... chr: chr20 ... 667s tag read 668s ------------------------------------------- total process time: 668s total alignment: 784888 total supplementary: 30142 total secondary: 0 total unmapped: 0 total tag alignment: 403864 total untagged: 381024 [INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2} --chunk_num {3} --ctg_name {1} --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates --output_depth True --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES [INFO] chr20 chunk 0/14: Total snv candidates found: 1070, total indel candidates found: 104 [INFO] chr20 chunk 1/14: Total snv candidates found: 11957, total indel candidates found: 1867 [INFO] chr20 chunk 7/14: Total snv candidates found: 534, total indel candidates found: 936 [INFO] chr20 chunk 13/14: Total snv candidates found: 3413, total indel candidates found: 1701 [faidx] Truncated sequence: chr20:63409487-66211299 [INFO] chr20 chunk 5/14: Total snv candidates found: 287, total indel candidates found: 577 [INFO] chr20 chunk 11/14: Total snv candidates found: 821, total indel candidates found: 885 [INFO] chr20 chunk 8/14: Total snv candidates found: 1520, total indel candidates found: 926 [INFO] chr20 chunk 2/14: Total snv candidates found: 2770, total indel candidates found: 1316 [INFO] chr20 chunk 6/14: Total snv candidates found: 469, total indel candidates found: 780 [INFO] chr20 chunk 3/14: Total snv candidates found: 391, total indel candidates found: 1105 [INFO] chr20 chunk 4/14: Total snv candidates found: 464, total indel candidates found: 1081 [INFO] chr20 chunk 12/14: Total snv candidates found: 666, total indel candidates found: 725 [INFO] chr20 chunk 10/14: Total snv candidates found: 440, total indel candidates found: 728 [INFO] chr20 chunk 9/14: Total snv candidates found: 430, total indel candidates found: 953 [INFO] STEP 2: Pileup Model Calling [INFO] Create Paired Tensors [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/pileup_tensor_can/{1/} --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/2-1_CPT.log [INFO] chr20 chunk 1-1/0 Tensors generated: 998 [INFO] chr20 chunk 2-2/1 Tensors generated: 1950 [INFO] chr20 chunk 1-1/5 Tensors generated: 287 [INFO] chr20 chunk 1-1/3 Tensors generated: 391 [INFO] chr20 chunk 1-1/10 Tensors generated: 440 [INFO] chr20 chunk 1-1/9 Tensors generated: 430 [INFO] chr20 chunk 1-1/6 Tensors generated: 469 [INFO] chr20 chunk 1-1/4 Tensors generated: 464 [INFO] chr20 chunk 1-1/12 Tensors generated: 665 [INFO] chr20 chunk 1-1/7 Tensors generated: 533 [INFO] chr20 chunk 1-1/11 Tensors generated: 821 [INFO] chr20 chunk 1-1/8 Tensors generated: 1520 [INFO] chr20 chunk 1-1/13 Tensors generated: 3368 [INFO] chr20 chunk 1-1/2 Tensors generated: 2767 [INFO] chr20 chunk 1-2/1 Tensors generated: 9999 [INFO] Pileup Model Prediction [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/pileup_tensor_can/{1/} --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup --show_germline :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/2-2_PREDICT.log [INFO] chr20 total processed positions: 391, time elapsed: 0.8s [INFO] chr20 total processed positions: 287, time elapsed: 0.9s [INFO] chr20 total processed positions: 430, time elapsed: 1.2s [INFO] chr20 total processed positions: 440, time elapsed: 1.0s [INFO] chr20 total processed positions: 469, time elapsed: 1.2s [INFO] chr20 total processed positions: 533, time elapsed: 1.3s [INFO] chr20 total processed positions: 665, time elapsed: 1.3s [INFO] chr20 total processed positions: 464, time elapsed: 1.3s [INFO] chr20 total processed positions: 821, time elapsed: 1.5s [INFO] chr20 total processed positions: 998, time elapsed: 1.9s [INFO] chr20 total processed positions: 1520, time elapsed: 3.1s [INFO] chr20 total processed positions: 1950, time elapsed: 3.5s [INFO] chr20 total processed positions: 2767, time elapsed: 5.1s [INFO] chr20 total processed positions: 3368, time elapsed: 6.0s [INFO] chr20 total processed positions: 9999, time elapsed: 16.2s [INFO] Merge Pileup VCFs [INFO] RUN THE FOLLOWING COMMAND: pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output/pileup.vcf [INFO] Sorting VCFs... [INFO] Finished VCF sorting! [INFO] STEP 3: Full-alignment Model Calling [INFO] Create Full-alignment Paired Tensors [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/fa_tensor_can/{1/} --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/3-1_CPT.log [INFO] chr20 chunk 1-1/0 Tensors generated: 908 [INFO] chr20 chunk 1-1/5 Tensors generated: 287 [INFO] chr20 chunk 1-1/3 Tensors generated: 391 [INFO] chr20 chunk 1-1/6 Tensors generated: 469 [INFO] chr20 chunk 1-1/9 Tensors generated: 430 [INFO] chr20 chunk 1-1/4 Tensors generated: 464 [INFO] chr20 chunk 1-1/10 Tensors generated: 440 [INFO] chr20 chunk 1-1/7 Tensors generated: 533 [INFO] chr20 chunk 2-2/1 Tensors generated: 1895 [INFO] chr20 chunk 1-1/12 Tensors generated: 665 [INFO] chr20 chunk 1-1/11 Tensors generated: 821 [INFO] chr20 chunk 1-1/8 Tensors generated: 1520 [INFO] chr20 chunk 1-1/2 Tensors generated: 2761 [INFO] chr20 chunk 1-1/13 Tensors generated: 3359 [INFO] chr20 chunk 1-2/1 Tensors generated: 9830 [INFO] Full-alignment Model Prediction [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/fa_tensor_can/{1/} --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part23/logs/3-2_PREDICT.log [INFO] chr20 total processed positions: 287, time elapsed: 51.0s [INFO] chr20 total processed positions: 391, time elapsed: 70.0s [INFO] chr20 total processed positions: 440, time elapsed: 78.2s [INFO] chr20 total processed positions: 430, time elapsed: 81.4s [INFO] chr20 total processed positions: 464, time elapsed: 82.3s [INFO] chr20 total processed positions: 469, time elapsed: 82.9s [INFO] chr20 total processed positions: 533, time elapsed: 99.1s [INFO] chr20 total processed positions: 665, time elapsed: 117.3s [INFO] chr20 total processed positions: 821, time elapsed: 145.1s [INFO] chr20 total processed positions: 908, time elapsed: 161.0s slurmstepd: error: *** JOB 2556290 ON n13 CANCELLED AT 2025-12-08T16:49:54 *** ---------------------------------------------- | SLURM EPILOG | ---------------------------------------------- Job ID: 2556290 Cluster: flamingo User/Group: t_steimle/gs_hpc_biopath Nodelist: n13 Nodes: 1 Cores per node: 40 Job started at: 2025-12-08 16:21:40 Job ended at: 2025-12-08 16:49:54 Job Wall-clock time: 00:28:14 CPU Utilized: 02:54:10 CPU Efficiency: 15.42% of 18:49:20 core-walltime Memory Utilized: 21.68 GB Memory Efficiency: 54.19% of 40.00 GB