WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44': 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/part44 --region chrY:1-62460029 --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/part44/logs [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/split_beds [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/pileup_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/fa_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/tmp_vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/vcf [INFO] --include_all_ctgs enabled [INFO] Call variants in contigs: chrY [INFO] Number of chunks for each contig: 13 [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/part44 [INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/region.bed [INFO] GENOTYPING MODE VCF FILE PATH: None [INFO] HYBRID MODE VCF FILE PATH: None [INFO] REGION FOR CALLING: chrY:1-62460029 [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/part44/tmp/clair3_output/clair3_normal_output --ctg_name=chrY --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/part44/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/part44/tmp/clair3_output/clair3_normal_output [INFO] PLATFORM: ont [INFO] THREADS: 40 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: chrY [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/part44/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chrY --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/part44/tmp/clair3_output/clair3_normal_output/log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/pileup_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/merge_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed [INFO] Call variant in contigs: chrY [INFO] Chunk number for each contig: 13 [INFO] 1/7 Call variants using pileup model Calling variants ... Total processed positions in chrY (chunk 10/13) : 2510 Total time elapsed: 14.69 s Calling variants ... Total processed positions in chrY (chunk 8/13) : 3198 Total time elapsed: 15.01 s Calling variants ... Total processed positions in chrY (chunk 9/13) : 5363 Total time elapsed: 19.82 s Calling variants ... Total processed positions in chrY (chunk 7/13) : 13555 Total time elapsed: 31.66 s Calling variants ... Total processed positions in chrY (chunk 13/13) : 20440 Total time elapsed: 40.73 s Calling variants ... Total processed positions in chrY (chunk 12/13) : 19252 Total time elapsed: 41.61 s Calling variants ... Total processed positions in chrY (chunk 6/13) : 20091 Total time elapsed: 46.89 s Calling variants ... Total processed positions in chrY (chunk 11/13) : 23275 Total time elapsed: 48.80 s Calling variants ... Total processed positions in chrY (chunk 4/13) : 37911 Total time elapsed: 64.24 s Calling variants ... Total processed positions in chrY (chunk 5/13) : 36533 Total time elapsed: 65.91 s Calling variants ... Total processed positions in chrY (chunk 3/13) : 38723 Total time elapsed: 66.37 s Calling variants ... Total processed positions in chrY (chunk 2/13) : 43770 Total time elapsed: 72.50 s Calling variants ... Total processed positions in chrY (chunk 1/13) : 47658 Total time elapsed: 80.74 s real 1m26.989s user 9m48.882s sys 0m30.243s [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 11 [INFO] Total heterozygous SNP positions selected: chrY: 21687 real 0m0.762s user 0m0.656s sys 0m0.088s [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/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chrY.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/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chrY 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 ... 0s (chrY,3s) parsing total: 3s merge results ... 0s writeResult SNP ... 0s total process: 3s real 0m3.472s user 0m8.235s sys 0m0.764s [INFO] 5/7 Select candidates for full-alignment calling [INFO] Set variants quality cutoff 17.0 [INFO] Set reference calls quality cutoff 11.0 [INFO] Low quality reference calls to be processed in chrY: 26213 [INFO] Low quality variants to be processed in chrY: 34866 real 0m0.792s user 0m0.667s sys 0m0.106s [INFO] 6/7 Call low-quality variants using full-alignment model Calling variants ... Total processed positions in chrY (chunk 7/7) : 1079 Total time elapsed: 11.23 s Calling variants ... Total processed positions in chrY (chunk 2/7) : 10000 Total time elapsed: 91.05 s Calling variants ... Total processed positions in chrY (chunk 1/7) : 10000 Total time elapsed: 91.43 s Calling variants ... Total processed positions in chrY (chunk 3/7) : 10000 Total time elapsed: 92.16 s Calling variants ... Total processed positions in chrY (chunk 5/7) : 10000 Total time elapsed: 92.18 s Calling variants ... Total processed positions in chrY (chunk 4/7) : 10000 Total time elapsed: 93.21 s Calling variants ... Total processed positions in chrY (chunk 6/7) : 10000 Total time elapsed: 93.30 s real 1m35.777s user 9m8.817s sys 0m28.111s [INFO] 7/7 Merge pileup VCF and full-alignment VCF [INFO] Pileup variants processed in chrY: 14986 [INFO] Full-alignment variants processed in chrY: 38380 real 0m1.052s user 0m1.067s sys 0m0.117s [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz real 3m13.768s user 19m12.062s sys 1m0.250s [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/part44/tmp/clair3_output/clair3_tumor_output --ctg_name=chrY --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/part44/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/part44/tmp/clair3_output/clair3_tumor_output [INFO] PLATFORM: ont [INFO] THREADS: 40 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: chrY [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/part44/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chrY --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/part44/tmp/clair3_output/clair3_tumor_output/log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/merge_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed [INFO] Call variant in contigs: chrY [INFO] Chunk number for each contig: 13 [INFO] 1/7 Call variants using pileup model Calling variants ... Total processed positions in chrY (chunk 8/13) : 7329 Total time elapsed: 39.08 s Calling variants ... Total processed positions in chrY (chunk 4/13) : 9532 Total time elapsed: 43.30 s Calling variants ... Total processed positions in chrY (chunk 2/13) : 7989 Total time elapsed: 44.10 s Calling variants ... Total processed positions in chrY (chunk 10/13) : 9348 Total time elapsed: 46.20 s Calling variants ... Total processed positions in chrY (chunk 9/13) : 13536 Total time elapsed: 51.94 s Calling variants ... Total processed positions in chrY (chunk 5/13) : 15812 Total time elapsed: 52.23 s Calling variants ... Total processed positions in chrY (chunk 3/13) : 16514 Total time elapsed: 54.48 s Calling variants ... Total processed positions in chrY (chunk 7/13) : 20564 Total time elapsed: 59.94 s Calling variants ... Total processed positions in chrY (chunk 13/13) : 23851 Total time elapsed: 66.40 s Calling variants ... Total processed positions in chrY (chunk 1/13) : 25344 Total time elapsed: 67.41 s Calling variants ... Total processed positions in chrY (chunk 6/13) : 27005 Total time elapsed: 70.73 s Calling variants ... Total processed positions in chrY (chunk 12/13) : 27326 Total time elapsed: 75.58 s Calling variants ... Total processed positions in chrY (chunk 11/13) : 32618 Total time elapsed: 80.59 s real 1m23.256s user 9m43.700s sys 0m39.007s [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 12 [INFO] Total heterozygous SNP positions selected: chrY: 31855 real 0m0.720s user 0m0.592s sys 0m0.097s [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/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chrY.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/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chrY 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 (chrY,13s) parsing total: 13s merge results ... 0s writeResult SNP ... 0s total process: 14s real 0m13.758s user 0m41.538s sys 0m2.887s [INFO] 5/7 Select candidates for full-alignment calling [INFO] Set variants quality cutoff 20.0 [INFO] Set reference calls quality cutoff 10.0 [INFO] Low quality reference calls to be processed in chrY: 15293 [INFO] Low quality variants to be processed in chrY: 58497 real 0m0.761s user 0m0.602s sys 0m0.098s [INFO] 6/7 Call low-quality variants using full-alignment model Calling variants ... Total processed positions in chrY (chunk 8/8) : 3790 Total time elapsed: 41.07 s Calling variants ... Total processed positions in chrY (chunk 3/8) : 10000 Total time elapsed: 100.57 s Calling variants ... Total processed positions in chrY (chunk 5/8) : 10000 Total time elapsed: 102.89 s Calling variants ... Total processed positions in chrY (chunk 6/8) : 10000 Total time elapsed: 103.29 s Calling variants ... Total processed positions in chrY (chunk 7/8) : 10000 Total time elapsed: 103.39 s Calling variants ... Total processed positions in chrY (chunk 1/8) : 10000 Total time elapsed: 110.52 s Calling variants ... Total processed positions in chrY (chunk 4/8) : 10000 Total time elapsed: 111.71 s Calling variants ... Total processed positions in chrY (chunk 2/8) : 10000 Total time elapsed: 113.96 s real 1m56.455s user 12m24.097s sys 0m37.720s [INFO] 7/7 Merge pileup VCF and full-alignment VCF [INFO] Pileup variants processed in chrY: 25148 [INFO] Full-alignment variants processed in chrY: 60787 real 0m1.113s user 0m1.054s sys 0m0.123s [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz real 3m40.589s user 22m55.153s sys 1m20.559s [INFO] Select Heterozygous SNP for Phasing [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/1_select_hetero_snp_for_phasing.log [INFO] Total HET SNP calls selected: chrY: 51398, not found:568, not match:45, low_qual_count:0. Total normal:36068 Total tumor:52011, pro: 0.9882 [INFO] Phase the Tumor BAM [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/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/part44/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS LongPhase Ver 1.7 --- File Parameter --- SNP File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/vcf/chrY.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/part44/tmp/clair3_output/phased_output/tumor_phased_chrY 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 (chrY,23s) parsing total: 23s merge results ... 0s writeResult SNP ... 0s total process: 23s [INFO] Haplotag the Tumor BAM [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/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/part44/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/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS phased SNP file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_chrY.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/part44/tmp/clair3_output/phased_output/tumor_chrY.bam number of threads: 1 write log file: false log file: ------------------------------------------- tag region: chrY filter mapping quality below: 1 percentage threshold: 0.6 tag supplementary: false ------------------------------------------- parsing SNP VCF ... 0s tag read start ... chr: chrY ... 723s tag read 724s ------------------------------------------- total process time: 724s total alignment: 1029125 total supplementary: 12705 total secondary: 0 total unmapped: 0 total tag alignment: 118794 total untagged: 910331 [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/part44/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/part44/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES [INFO] chrY chunk 7/13: Total snv candidates found: 761, total indel candidates found: 37 [INFO] chrY chunk 9/13: Total snv candidates found: 309, total indel candidates found: 16 [INFO] chrY chunk 8/13: Total snv candidates found: 821, total indel candidates found: 52 [INFO] chrY chunk 6/13: Total snv candidates found: 3048, total indel candidates found: 258 [INFO] chrY chunk 5/13: Total snv candidates found: 2009, total indel candidates found: 445 [INFO] chrY chunk 11/13: Total snv candidates found: 4319, total indel candidates found: 270 [INFO] chrY chunk 12/13: Total snv candidates found: 5416, total indel candidates found: 610 [faidx] Truncated sequence: chrY:57654453-62461074 [INFO] chrY chunk 10/13: Total snv candidates found: 5980, total indel candidates found: 374 [INFO] chrY chunk 4/13: Total snv candidates found: 2127, total indel candidates found: 1355 [INFO] chrY chunk 0/13: Total snv candidates found: 4192, total indel candidates found: 3001 [INFO] chrY chunk 2/13: Total snv candidates found: 2871, total indel candidates found: 1731 [INFO] chrY chunk 3/13: Total snv candidates found: 357, total indel candidates found: 1566 [INFO] chrY chunk 1/13: Total snv candidates found: 421, total indel candidates found: 1763 [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/part44/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/part44/tmp/pileup_tensor_can/{1/} --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/2-1_CPT.log [INFO] chrY chunk 1-1/3 Tensors generated: 352 [INFO] chrY chunk 1-1/1 Tensors generated: 405 [INFO] chrY chunk 1-1/7 Tensors generated: 758 [INFO] chrY chunk 1-1/9 Tensors generated: 309 [INFO] chrY chunk 1-1/8 Tensors generated: 812 [INFO] chrY chunk 1-1/2 Tensors generated: 2762 [INFO] chrY chunk 1-1/5 Tensors generated: 1950 [INFO] chrY chunk 1-1/0 Tensors generated: 4115 [INFO] chrY chunk 1-1/4 Tensors generated: 2055 [INFO] chrY chunk 1-1/6 Tensors generated: 3015 [INFO] chrY chunk 1-1/11 Tensors generated: 4309 [INFO] chrY chunk 1-1/10 Tensors generated: 5972 [INFO] chrY chunk 1-1/12 Tensors generated: 5342 [INFO] Pileup Model Prediction [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/pileup_tensor_can/{1/} --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/2-2_PREDICT.log [INFO] chrY total processed positions: 309, time elapsed: 0.7s [INFO] No variant output for p_chrY.9_0_1.vcf, remove empty VCF [INFO] chrY total processed positions: 352, time elapsed: 1.0s [INFO] chrY total processed positions: 405, time elapsed: 1.0s [INFO] chrY total processed positions: 758, time elapsed: 1.4s [INFO] No variant output for p_chrY.7_0_1.vcf, remove empty VCF [INFO] chrY total processed positions: 812, time elapsed: 1.5s [INFO] chrY total processed positions: 1950, time elapsed: 3.2s [INFO] chrY total processed positions: 2055, time elapsed: 3.6s [INFO] chrY total processed positions: 2762, time elapsed: 4.7s [INFO] chrY total processed positions: 3015, time elapsed: 5.0s [INFO] chrY total processed positions: 4115, time elapsed: 6.7s [INFO] chrY total processed positions: 4309, time elapsed: 7.2s [INFO] chrY total processed positions: 5342, time elapsed: 8.5s [INFO] chrY total processed positions: 5972, time elapsed: 9.5s [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/part44/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/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/part44/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/part44/tmp/fa_tensor_can/{1/} --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/3-1_CPT.log [INFO] chrY chunk 1-1/3 Tensors generated: 347 [INFO] chrY chunk 1-1/9 Tensors generated: 173 [INFO] chrY chunk 1-1/1 Tensors generated: 399 [INFO] chrY chunk 1-1/8 Tensors generated: 396 [INFO] chrY chunk 1-1/7 Tensors generated: 588 [INFO] chrY chunk 1-1/5 Tensors generated: 1815 [INFO] chrY chunk 1-1/6 Tensors generated: 2359 [INFO] chrY chunk 1-1/2 Tensors generated: 2616 [INFO] chrY chunk 1-1/0 Tensors generated: 3907 [INFO] chrY chunk 1-1/4 Tensors generated: 2046 [INFO] chrY chunk 1-1/11 Tensors generated: 3394 [INFO] chrY chunk 1-1/12 Tensors generated: 4768 [INFO] chrY chunk 1-1/10 Tensors generated: 5087 [INFO] Full-alignment Model Prediction [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/fa_tensor_can/{1/} --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/3-2_PREDICT.log [INFO] chrY total processed positions: 173, time elapsed: 30.6s [INFO] chrY total processed positions: 347, time elapsed: 61.0s [INFO] chrY total processed positions: 396, time elapsed: 69.7s [INFO] chrY total processed positions: 399, time elapsed: 70.2s [INFO] chrY total processed positions: 588, time elapsed: 104.2s