WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6': 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/part6 --region chr11:84448351-135127769 --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/part6/logs [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/split_beds [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/candidates [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/pileup_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/fa_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/tmp_vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/logs/clair3_log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/phased_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/vcf [INFO] --include_all_ctgs enabled [INFO] Call variants in contigs: chr11 [INFO] Number of chunks for each contig: 28 [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/part6 [INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/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/part6/tmp/region.bed [INFO] GENOTYPING MODE VCF FILE PATH: None [INFO] HYBRID MODE VCF FILE PATH: None [INFO] REGION FOR CALLING: chr11:84448351-135127769 [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/part6/tmp/clair3_output/clair3_normal_output --ctg_name=chr11 --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/part6/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/part6/tmp/clair3_output/clair3_normal_output [INFO] PLATFORM: ont [INFO] THREADS: 40 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: chr11 [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/part6/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr11 --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/part6/tmp/clair3_output/clair3_normal_output/log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/pileup_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/merge_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed [INFO] Call variant in contigs: chr11 [INFO] Chunk number for each contig: 28 [INFO] 1/7 Call variants using pileup model Calling variants ... Total processed positions in chr11 (chunk 11/28) : 49165 Total time elapsed: 178.48 s Calling variants ... Total processed positions in chr11 (chunk 12/28) : 56920 Total time elapsed: 181.36 s Calling variants ... Total processed positions in chr11 (chunk 22/28) : 75977 Total time elapsed: 209.99 s Calling variants ... Total processed positions in chr11 (chunk 19/28) : 71613 Total time elapsed: 214.42 s Calling variants ... Total processed positions in chr11 (chunk 9/28) : 70940 Total time elapsed: 222.08 s Calling variants ... Total processed positions in chr11 (chunk 6/28) : 73742 Total time elapsed: 222.47 s Calling variants ... Total processed positions in chr11 (chunk 5/28) : 75204 Total time elapsed: 224.15 s Calling variants ... Total processed positions in chr11 (chunk 21/28) : 71045 Total time elapsed: 224.79 s Calling variants ... Total processed positions in chr11 (chunk 7/28) : 73918 Total time elapsed: 227.41 s Calling variants ... Total processed positions in chr11 (chunk 17/28) : 78578 Total time elapsed: 229.56 s Calling variants ... Total processed positions in chr11 (chunk 18/28) : 73703 Total time elapsed: 234.10 s Calling variants ... Total processed positions in chr11 (chunk 4/28) : 81512 Total time elapsed: 236.81 s Calling variants ... Total processed positions in chr11 (chunk 14/28) : 83931 Total time elapsed: 237.93 s Calling variants ... Total processed positions in chr11 (chunk 16/28) : 82083 Total time elapsed: 240.35 s Calling variants ... Total processed positions in chr11 (chunk 3/28) : 82458 Total time elapsed: 241.23 s Calling variants ... Total processed positions in chr11 (chunk 13/28) : 79284 Total time elapsed: 243.04 s Calling variants ... Total processed positions in chr11 (chunk 2/28) : 79749 Total time elapsed: 243.40 s Calling variants ... Total processed positions in chr11 (chunk 15/28) : 84644 Total time elapsed: 247.06 s Calling variants ... Total processed positions in chr11 (chunk 20/28) : 78075 Total time elapsed: 249.18 s Calling variants ... Total processed positions in chr11 (chunk 26/28) : 89044 Total time elapsed: 249.72 s Calling variants ... Total processed positions in chr11 (chunk 24/28) : 84661 Total time elapsed: 253.22 s Calling variants ... Total processed positions in chr11 (chunk 10/28) : 85066 Total time elapsed: 253.66 s Calling variants ... Total processed positions in chr11 (chunk 28/28) : 83894 Total time elapsed: 253.82 s Calling variants ... Total processed positions in chr11 (chunk 23/28) : 77217 Total time elapsed: 229.34 s Calling variants ... Total processed positions in chr11 (chunk 8/28) : 83397 Total time elapsed: 256.16 s Calling variants ... Total processed positions in chr11 (chunk 25/28) : 85368 Total time elapsed: 235.94 s Calling variants ... Total processed positions in chr11 (chunk 1/28) : 94486 Total time elapsed: 265.61 s Calling variants ... Total processed positions in chr11 (chunk 27/28) : 84745 Total time elapsed: 246.95 s real 4m41.889s user 104m58.241s sys 4m37.088s [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16 [INFO] Total heterozygous SNP positions selected: chr11: 85688 real 0m4.179s user 0m3.753s sys 0m0.321s [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/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr11.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/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr11 Generate Dot : False BAM File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --- Phasing Parameter --- Seq Platform : ONT Phase Indel : False Distance Threshold : 300000 Connect Adjacent : 20 Edge Threshold : 0.7 Mapping Quality : 1 Variant Confidence : 0.75 ReadTag Confidence : 0.65 parsing VCF ... 0s parsing SV VCF ... 0s parsing Meth VCF ... 0s reading reference ... 2s (chr11,10s) parsing total: 10s merge results ... 0s writeResult SNP ... 1s total process: 13s real 0m13.103s user 0m44.278s sys 0m3.402s [INFO] 5/7 Select candidates for full-alignment calling [INFO] Set variants quality cutoff 20.0 [INFO] Set reference calls quality cutoff 14.0 [INFO] Low quality reference calls to be processed in chr11: 195328 [INFO] Low quality variants to be processed in chr11: 162732 real 0m4.471s user 0m4.035s sys 0m0.344s [INFO] 6/7 Call low-quality variants using full-alignment model Calling variants ... Total processed positions in chr11 (chunk 4/36) : 10000 Total time elapsed: 143.44 s Calling variants ... Total processed positions in chr11 (chunk 22/36) : 10000 Total time elapsed: 143.91 s Calling variants ... Total processed positions in chr11 (chunk 2/36) : 10000 Total time elapsed: 145.31 s Calling variants ... Total processed positions in chr11 (chunk 10/36) : 10000 Total time elapsed: 148.91 s Calling variants ... Total processed positions in chr11 (chunk 9/36) : 10000 Total time elapsed: 158.77 s Calling variants ... Total processed positions in chr11 (chunk 16/36) : 10000 Total time elapsed: 160.86 s Calling variants ... Total processed positions in chr11 (chunk 13/36) : 10000 Total time elapsed: 161.73 s Calling variants ... Total processed positions in chr11 (chunk 26/36) : 10000 Total time elapsed: 162.70 s Calling variants ... Total processed positions in chr11 (chunk 5/36) : 10000 Total time elapsed: 163.82 s Calling variants ... Total processed positions in chr11 (chunk 25/36) : 10000 Total time elapsed: 164.25 s Calling variants ... Total processed positions in chr11 (chunk 21/36) : 10000 Total time elapsed: 165.81 s Calling variants ... Total processed positions in chr11 (chunk 19/36) : 10000 Total time elapsed: 166.75 s Calling variants ... Total processed positions in chr11 (chunk 7/36) : 10000 Total time elapsed: 172.07 s Calling variants ... Total processed positions in chr11 (chunk 18/36) : 10000 Total time elapsed: 172.46 s Calling variants ... Total processed positions in chr11 (chunk 30/36) : 10000 Total time elapsed: 178.30 s Calling variants ... Total processed positions in chr11 (chunk 1/36) : 10000 Total time elapsed: 179.50 s Calling variants ... Total processed positions in chr11 (chunk 15/36) : 10000 Total time elapsed: 179.65 s Calling variants ... Total processed positions in chr11 (chunk 24/36) : 10000 Total time elapsed: 179.97 s Calling variants ... Total processed positions in chr11 (chunk 12/36) : 10000 Total time elapsed: 179.65 s Calling variants ... Total processed positions in chr11 (chunk 8/36) : 10000 Total time elapsed: 181.87 s Calling variants ... Total processed positions in chr11 (chunk 3/36) : 10000 Total time elapsed: 182.80 s Calling variants ... Total processed positions in chr11 (chunk 29/36) : 10000 Total time elapsed: 183.85 s Calling variants ... Total processed positions in chr11 (chunk 27/36) : 10000 Total time elapsed: 183.49 s Calling variants ... Total processed positions in chr11 (chunk 17/36) : 10000 Total time elapsed: 184.91 s Calling variants ... Total processed positions in chr11 (chunk 11/36) : 10000 Total time elapsed: 185.82 s Calling variants ... Total processed positions in chr11 (chunk 28/36) : 10000 Total time elapsed: 186.43 s Calling variants ... Total processed positions in chr11 (chunk 6/36) : 10000 Total time elapsed: 187.85 s Calling variants ... Total processed positions in chr11 (chunk 14/36) : 10000 Total time elapsed: 188.97 s Calling variants ... Total processed positions in chr11 (chunk 23/36) : 10000 Total time elapsed: 189.86 s Calling variants ... Total processed positions in chr11 (chunk 20/36) : 10000 Total time elapsed: 191.75 s