WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24': 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/part24 --region chr21:1-45090682 --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/part24/logs [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/split_beds [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/pileup_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/fa_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/tmp_vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf [INFO] --include_all_ctgs enabled [INFO] Call variants in contigs: chr21 [INFO] Number of chunks for each contig: 10 [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/part24 [INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/region.bed [INFO] GENOTYPING MODE VCF FILE PATH: None [INFO] HYBRID MODE VCF FILE PATH: None [INFO] REGION FOR CALLING: chr21:1-45090682 [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/part24/tmp/clair3_output/clair3_normal_output --ctg_name=chr21 --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/part24/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/part24/tmp/clair3_output/clair3_normal_output [INFO] PLATFORM: ont [INFO] THREADS: 40 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: chr21 [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/part24/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr21 --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/part24/tmp/clair3_output/clair3_normal_output/log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/pileup_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/merge_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed [INFO] Call variant in contigs: chr21 [INFO] Chunk number for each contig: 10 [INFO] 1/7 Call variants using pileup model Calling variants ... Total processed positions in chr21 (chunk 1/10) : 21247 Total time elapsed: 41.35 s Calling variants ... Total processed positions in chr21 (chunk 2/10) : 55447 Total time elapsed: 92.05 s Calling variants ... Total processed positions in chr21 (chunk 5/10) : 65383 Total time elapsed: 103.81 s Calling variants ... Total processed positions in chr21 (chunk 6/10) : 71156 Total time elapsed: 106.40 s Calling variants ... Total processed positions in chr21 (chunk 3/10) : 71284 Total time elapsed: 108.33 s Calling variants ... Total processed positions in chr21 (chunk 4/10) : 73057 Total time elapsed: 115.65 s Calling variants ... Total processed positions in chr21 (chunk 7/10) : 75897 Total time elapsed: 120.81 s Calling variants ... Total processed positions in chr21 (chunk 9/10) : 81308 Total time elapsed: 120.97 s Calling variants ... Total processed positions in chr21 (chunk 8/10) : 78139 Total time elapsed: 124.79 s Calling variants ... Total processed positions in chr21 (chunk 10/10) : 86992 Total time elapsed: 134.60 s real 2m21.035s user 17m6.093s sys 0m58.159s [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14 [INFO] Total heterozygous SNP positions selected: chr21: 38730 real 0m1.266s user 0m1.125s 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/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr21.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/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr21 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 (chr21,4s) parsing total: 4s merge results ... 0s writeResult SNP ... 1s total process: 5s real 0m4.675s user 0m10.375s sys 0m0.761s [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 chr21: 57899 [INFO] Low quality variants to be processed in chr21: 69711 real 0m1.477s user 0m1.179s sys 0m0.155s [INFO] 6/7 Call low-quality variants using full-alignment model Calling variants ... Total processed positions in chr21 (chunk 13/13) : 7610 Total time elapsed: 77.34 s Calling variants ... Total processed positions in chr21 (chunk 10/13) : 10000 Total time elapsed: 93.29 s Calling variants ... Total processed positions in chr21 (chunk 9/13) : 10000 Total time elapsed: 93.47 s Calling variants ... Total processed positions in chr21 (chunk 8/13) : 10000 Total time elapsed: 93.64 s Calling variants ... Total processed positions in chr21 (chunk 6/13) : 10000 Total time elapsed: 94.19 s Calling variants ... Total processed positions in chr21 (chunk 3/13) : 10000 Total time elapsed: 93.99 s Calling variants ... Total processed positions in chr21 (chunk 4/13) : 10000 Total time elapsed: 94.03 s Calling variants ... Total processed positions in chr21 (chunk 12/13) : 10000 Total time elapsed: 94.45 s Calling variants ... Total processed positions in chr21 (chunk 7/13) : 10000 Total time elapsed: 95.22 s Calling variants ... Total processed positions in chr21 (chunk 11/13) : 10000 Total time elapsed: 95.42 s Calling variants ... Total processed positions in chr21 (chunk 5/13) : 10000 Total time elapsed: 95.72 s Calling variants ... Total processed positions in chr21 (chunk 2/13) : 10000 Total time elapsed: 95.91 s Calling variants ... Total processed positions in chr21 (chunk 1/13) : 10000 Total time elapsed: 96.01 s real 1m38.621s user 19m32.131s sys 1m4.775s [INFO] 7/7 Merge pileup VCF and full-alignment VCF [INFO] Pileup variants processed in chr21: 29908 [INFO] Full-alignment variants processed in chr21: 74068 real 0m1.761s user 0m1.912s sys 0m0.145s [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz real 4m16.843s user 36m59.599s sys 2m5.097s [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/part24/tmp/clair3_output/clair3_tumor_output --ctg_name=chr21 --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/part24/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/part24/tmp/clair3_output/clair3_tumor_output [INFO] PLATFORM: ont [INFO] THREADS: 40 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: chr21 [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/part24/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr21 --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/part24/tmp/clair3_output/clair3_tumor_output/log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/merge_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed [INFO] Call variant in contigs: chr21 [INFO] Chunk number for each contig: 10 [INFO] 1/7 Call variants using pileup model Calling variants ... Total processed positions in chr21 (chunk 7/10) : 9368 Total time elapsed: 44.16 s Calling variants ... Total processed positions in chr21 (chunk 6/10) : 10461 Total time elapsed: 44.92 s Calling variants ... Total processed positions in chr21 (chunk 4/10) : 10732 Total time elapsed: 46.14 s Calling variants ... Total processed positions in chr21 (chunk 5/10) : 11068 Total time elapsed: 46.09 s Calling variants ... Total processed positions in chr21 (chunk 8/10) : 11175 Total time elapsed: 47.12 s Calling variants ... Total processed positions in chr21 (chunk 9/10) : 11777 Total time elapsed: 47.74 s Calling variants ... Total processed positions in chr21 (chunk 10/10) : 15430 Total time elapsed: 53.78 s Calling variants ... Total processed positions in chr21 (chunk 1/10) : 36882 Total time elapsed: 83.76 s Calling variants ... Total processed positions in chr21 (chunk 3/10) : 32029 Total time elapsed: 93.36 s Calling variants ... Total processed positions in chr21 (chunk 2/10) : 75635 Total time elapsed: 140.71 s real 2m23.464s user 8m51.533s sys 0m36.386s [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 17 [INFO] Total heterozygous SNP positions selected: chr21: 39429 real 0m0.724s user 0m0.608s 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/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr21.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/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr21 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 (chr21,17s) parsing total: 17s merge results ... 0s writeResult SNP ... 0s total process: 17s real 0m17.072s user 0m51.072s sys 0m3.322s [INFO] 5/7 Select candidates for full-alignment calling [INFO] Set variants quality cutoff 21.0 [INFO] Set reference calls quality cutoff 9.0 [INFO] Low quality reference calls to be processed in chr21: 11425 [INFO] Low quality variants to be processed in chr21: 77112 real 0m0.771s user 0m0.589s sys 0m0.114s [INFO] 6/7 Call low-quality variants using full-alignment model Calling variants ... Total processed positions in chr21 (chunk 9/9) : 8537 Total time elapsed: 100.99 s Calling variants ... Total processed positions in chr21 (chunk 1/9) : 10000 Total time elapsed: 101.80 s Calling variants ... Total processed positions in chr21 (chunk 3/9) : 10000 Total time elapsed: 105.89 s Calling variants ... Total processed positions in chr21 (chunk 4/9) : 10000 Total time elapsed: 108.09 s Calling variants ... Total processed positions in chr21 (chunk 2/9) : 10000 Total time elapsed: 111.57 s Calling variants ... Total processed positions in chr21 (chunk 6/9) : 10000 Total time elapsed: 113.03 s Calling variants ... Total processed positions in chr21 (chunk 7/9) : 10000 Total time elapsed: 117.18 s Calling variants ... Total processed positions in chr21 (chunk 5/9) : 10000 Total time elapsed: 120.80 s Calling variants ... Total processed positions in chr21 (chunk 8/9) : 10000 Total time elapsed: 120.76 s real 2m3.456s user 15m42.135s sys 0m48.676s [INFO] 7/7 Merge pileup VCF and full-alignment VCF [INFO] Pileup variants processed in chr21: 33077 [INFO] Full-alignment variants processed in chr21: 73272 real 0m1.099s user 0m1.102s sys 0m0.113s [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz real 4m51.155s user 25m30.754s sys 1m29.337s [INFO] Select Heterozygous SNP for Phasing [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/1_select_hetero_snp_for_phasing.log [INFO] Total HET SNP calls selected: chr21: 54974, not found:1251, not match:50, low_qual_count:0. Total normal:57735 Total tumor:56275, pro: 0.9769 [INFO] Phase the Tumor BAM [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/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/part24/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS LongPhase Ver 1.7 --- File Parameter --- SNP File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf/chr21.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/part24/tmp/clair3_output/phased_output/tumor_phased_chr21 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 (chr21,31s) parsing total: 31s merge results ... 0s writeResult SNP ... 1s total process: 32s [INFO] Haplotag the Tumor BAM [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/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/part24/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/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS