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+[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_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/DUMCO/diag/ClairS/part4 --region chr10:63341881-134758134 --sample_name DUMCO_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True
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+
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/split_beds
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/candidates
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/pileup_tensor_can
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/fa_tensor_can
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/vcf_output
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/tmp_vcf_output
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/vcf
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+[INFO] --include_all_ctgs enabled
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+[INFO] Call variants in contigs: chr10
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+[INFO] Number of chunks for each contig: 27
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+
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+[INFO] CALLER VERSION: 0.4.4
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+[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
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+[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam
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+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
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+[INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
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+[INFO] THREADS: 40
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+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4
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+[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/output.vcf.gz
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+[INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
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+[INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
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+[INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/region.bed
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+[INFO] GENOTYPING MODE VCF FILE PATH: None
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+[INFO] HYBRID MODE VCF FILE PATH: None
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+[INFO] REGION FOR CALLING: chr10:63341881-134758134
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+[INFO] CONTIGS FOR CALLING: None
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+[INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
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+[INFO] SAMTOOLS BINARY PATH: samtools
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+[INFO] PYTHON BINARY PATH: python3
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+[INFO] PYPY BINARY PATH: pypy3
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+[INFO] PARALLEL BINARY PATH: parallel
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+[INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
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+[INFO] CHUNK SIZE: 5000000
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+[INFO] SNV MINIMUM AF: 0.05
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+[INFO] SNV MINIMUM QUAL: 8
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+[INFO] INDEL MINIMUM AF: 0.1
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+[INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
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+[INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
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+[INFO] INDEL MINIMUM QUAL: 8
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+[INFO] NORMAL VCF FILE PATH: None
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+[INFO] DISABLE PHASING: False
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+[INFO] ENABLE DRY RUN: False
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+[INFO] ENABLE INDEL CALLING: True
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+[INFO] ENABLE PRINTING REFERENCE CALLS: False
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+[INFO] ENABLE PRINTING GERMLINE CALLS: True
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+[INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
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+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
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+
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+[INFO] Call Germline Variants in Normal BAM using Clair3
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+[INFO] RUN THE FOLLOWING COMMAND:
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+( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_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/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output --ctg_name=chr10 --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/DUMCO/diag/ClairS/part4/logs/clair3_log/1_CLAIR3_NORMAL.log
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+
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+[INFO] CLAIR3 VERSION: v1.0.8
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+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
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+[INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
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+[INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
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+[INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output
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+[INFO] PLATFORM: ont
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+[INFO] THREADS: 40
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+[INFO] BED FILE PATH: EMPTY
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+[INFO] VCF FILE PATH: EMPTY
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+[INFO] CONTIGS: chr10
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+[INFO] CONDA PREFIX:
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+[INFO] SAMTOOLS PATH: samtools
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+[INFO] PYTHON PATH: python3
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+[INFO] PYPY PATH: pypy3
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+[INFO] PARALLEL PATH: parallel
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+[INFO] WHATSHAP PATH: whatshap
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+[INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
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+[INFO] CHUNK SIZE: 5000000
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+[INFO] FULL ALIGN PROPORTION: 0.7
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+[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
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+[INFO] PHASING PROPORTION: 0.7
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+[INFO] MINIMUM MQ: 5
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+[INFO] MINIMUM COVERAGE: 4
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+[INFO] SNP AF THRESHOLD: 0.08
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+[INFO] INDEL AF THRESHOLD: 0.15
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+[INFO] BASE ERROR IN GVCF: 0.001
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+[INFO] GQ BIN SIZE IN GVCF: 5
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+[INFO] ENABLE FILEUP ONLY CALLING: False
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+[INFO] ENABLE FAST MODE CALLING: False
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+[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
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+[INFO] ENABLE PRINTING REFERENCE CALLS: False
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+[INFO] ENABLE OUTPUT GVCF: False
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+[INFO] ENABLE HAPLOID PRECISE MODE: False
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+[INFO] ENABLE HAPLOID SENSITIVE MODE: False
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+[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
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+[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
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+[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
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+[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
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+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
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+[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
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+[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
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+[INFO] ENABLE LONG INDEL CALLING: False
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+[INFO] ENABLE C_IMPLEMENT: True
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+
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++ /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_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/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr10 --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
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+
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+[INFO] Check environment variables
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/log
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/merge_output
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
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+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
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+[INFO] Call variant in contigs: chr10
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+[INFO] Chunk number for each contig: 27
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+[INFO] 1/7 Call variants using pileup model
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 8/27) : 45826
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+Total time elapsed: 104.02 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 13/27) : 46506
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+Total time elapsed: 114.35 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 14/27) : 48034
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+Total time elapsed: 115.67 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 12/27) : 48340
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+Total time elapsed: 116.09 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 17/27) : 50227
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+Total time elapsed: 116.94 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 22/27) : 49884
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+Total time elapsed: 117.63 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 10/27) : 54843
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+Total time elapsed: 119.86 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 24/27) : 53181
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+Total time elapsed: 121.26 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 23/27) : 51547
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+Total time elapsed: 122.53 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 4/27) : 53706
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+Total time elapsed: 122.44 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 19/27) : 52944
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+Total time elapsed: 124.83 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 5/27) : 56433
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+Total time elapsed: 127.15 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 16/27) : 56555
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+Total time elapsed: 127.94 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 18/27) : 50434
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+Total time elapsed: 103.09 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 6/27) : 56922
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+Total time elapsed: 131.36 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 15/27) : 60420
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+Total time elapsed: 133.49 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 25/27) : 56153
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+Total time elapsed: 133.36 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 1/27) : 60078
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+Total time elapsed: 134.57 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 20/27) : 50606
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+Total time elapsed: 108.22 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 7/27) : 52716
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+Total time elapsed: 109.48 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 11/27) : 50928
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+Total time elapsed: 110.13 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 27/27) : 64119
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+Total time elapsed: 138.75 s
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 9/27) : 62446
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+Total time elapsed: 139.40 s
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|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 2/27) : 56222
|
|
|
+Total time elapsed: 113.42 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 3/27) : 58962
|
|
|
+Total time elapsed: 118.98 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 21/27) : 59650
|
|
|
+Total time elapsed: 119.24 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 26/27) : 61242
|
|
|
+Total time elapsed: 120.26 s
|
|
|
+
|
|
|
+real 2m35.699s
|
|
|
+user 49m49.438s
|
|
|
+sys 5m19.265s
|
|
|
+
|
|
|
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
|
|
|
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 18
|
|
|
+[INFO] Total heterozygous SNP positions selected: chr10: 110588
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+
|
|
|
+real 0m4.020s
|
|
|
+user 0m3.715s
|
|
|
+sys 0m0.222s
|
|
|
+
|
|
|
+[INFO] 3/7 Phase VCF file using LongPhase
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+LongPhase Ver 1.7
|
|
|
+
|
|
|
+--- File Parameter ---
|
|
|
+SNP File : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr10.vcf
|
|
|
+SV File :
|
|
|
+MOD File :
|
|
|
+REF File : /home/t_steimle/ref/hs1/chm13v2.0.fa
|
|
|
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr10
|
|
|
+Generate Dot : False
|
|
|
+BAM File : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_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
|
|
|
+(chr10,12s)
|
|
|
+parsing total: 12s
|
|
|
+merge results ... 0s
|
|
|
+writeResult SNP ... 1s
|
|
|
+
|
|
|
+total process: 15s
|
|
|
+
|
|
|
+real 0m15.388s
|
|
|
+user 0m29.173s
|
|
|
+sys 0m1.943s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+
|
|
|
+[INFO] 5/7 Select candidates for full-alignment calling
|
|
|
+[INFO] Set variants quality cutoff 21.0
|
|
|
+[INFO] Set reference calls quality cutoff 14.0
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+[INFO] Low quality reference calls to be processed in chr10: 118735
|
|
|
+[INFO] Low quality variants to be processed in chr10: 196574
|
|
|
+
|
|
|
+real 0m4.194s
|
|
|
+user 0m3.841s
|
|
|
+sys 0m0.267s
|
|
|
+
|
|
|
+[INFO] 6/7 Call low-quality variants using full-alignment model
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 14/32) : 10000
|
|
|
+Total time elapsed: 103.73 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 22/32) : 10000
|
|
|
+Total time elapsed: 105.81 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 21/32) : 10000
|
|
|
+Total time elapsed: 109.43 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 25/32) : 10000
|
|
|
+Total time elapsed: 109.97 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 9/32) : 10000
|
|
|
+Total time elapsed: 110.82 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 6/32) : 10000
|
|
|
+Total time elapsed: 111.30 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 12/32) : 10000
|
|
|
+Total time elapsed: 111.57 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 20/32) : 10000
|
|
|
+Total time elapsed: 112.54 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 19/32) : 10000
|
|
|
+Total time elapsed: 112.27 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 11/32) : 10000
|
|
|
+Total time elapsed: 112.56 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 16/32) : 10000
|
|
|
+Total time elapsed: 113.47 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 18/32) : 10000
|
|
|
+Total time elapsed: 113.41 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 24/32) : 10000
|
|
|
+Total time elapsed: 114.29 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 13/32) : 10000
|
|
|
+Total time elapsed: 114.42 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 23/32) : 10000
|
|
|
+Total time elapsed: 114.13 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 8/32) : 10000
|
|
|
+Total time elapsed: 114.16 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 4/32) : 10000
|
|
|
+Total time elapsed: 114.52 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 29/32) : 10000
|
|
|
+Total time elapsed: 114.46 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 28/32) : 10000
|
|
|
+Total time elapsed: 116.02 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 26/32) : 10000
|
|
|
+Total time elapsed: 116.08 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 30/32) : 10000
|
|
|
+Total time elapsed: 115.50 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 15/32) : 10000
|
|
|
+Total time elapsed: 116.81 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 27/32) : 10000
|
|
|
+Total time elapsed: 116.33 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 7/32) : 10000
|
|
|
+Total time elapsed: 117.18 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 3/32) : 10000
|
|
|
+Total time elapsed: 117.48 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 2/32) : 10000
|
|
|
+Total time elapsed: 118.46 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 17/32) : 10000
|
|
|
+Total time elapsed: 117.81 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 5/32) : 10000
|
|
|
+Total time elapsed: 119.33 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 1/32) : 10000
|
|
|
+Total time elapsed: 119.57 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 10/32) : 10000
|
|
|
+Total time elapsed: 120.78 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 32/32) : 5309
|
|
|
+Total time elapsed: 49.62 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 31/32) : 10000
|
|
|
+Total time elapsed: 86.49 s
|
|
|
+
|
|
|
+real 3m19.572s
|
|
|
+user 57m4.441s
|
|
|
+sys 3m27.409s
|
|
|
+
|
|
|
+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+[INFO] Pileup variants processed in chr10: 84279
|
|
|
+[INFO] Full-alignment variants processed in chr10: 203368
|
|
|
+
|
|
|
+real 0m5.865s
|
|
|
+user 0m6.249s
|
|
|
+sys 0m0.277s
|
|
|
+
|
|
|
+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
|
|
|
+
|
|
|
+real 6m46.315s
|
|
|
+user 107m56.463s
|
|
|
+sys 8m51.260s
|
|
|
+
|
|
|
+[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/DUMCO/diag/DUMCO_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/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output --ctg_name=chr10 --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/DUMCO/diag/ClairS/part4/logs/clair3_log/2_CLAIR3_TUMOR.log
|
|
|
+
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+[INFO] CLAIR3 VERSION: v1.0.8
|
|
|
+[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_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/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output
|
|
|
+[INFO] PLATFORM: ont
|
|
|
+[INFO] THREADS: 40
|
|
|
+[INFO] BED FILE PATH: EMPTY
|
|
|
+[INFO] VCF FILE PATH: EMPTY
|
|
|
+[INFO] CONTIGS: chr10
|
|
|
+[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/DUMCO/diag/DUMCO_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/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr10 --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
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+
|
|
|
+[INFO] Check environment variables
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/log
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
|
|
|
+[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
|
|
|
+[INFO] Call variant in contigs: chr10
|
|
|
+[INFO] Chunk number for each contig: 27
|
|
|
+[INFO] 1/7 Call variants using pileup model
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 18/27) : 11051
|
|
|
+Total time elapsed: 105.59 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 23/27) : 11192
|
|
|
+Total time elapsed: 106.77 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 21/27) : 11362
|
|
|
+Total time elapsed: 106.82 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 17/27) : 11922
|
|
|
+Total time elapsed: 107.36 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 14/27) : 13677
|
|
|
+Total time elapsed: 110.36 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 2/27) : 15217
|
|
|
+Total time elapsed: 112.66 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 24/27) : 8754
|
|
|
+Total time elapsed: 72.39 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 15/27) : 11427
|
|
|
+Total time elapsed: 73.80 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 20/27) : 10846
|
|
|
+Total time elapsed: 74.03 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 12/27) : 12345
|
|
|
+Total time elapsed: 76.32 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 13/27) : 10935
|
|
|
+Total time elapsed: 77.12 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 22/27) : 10696
|
|
|
+Total time elapsed: 75.58 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 7/27) : 12351
|
|
|
+Total time elapsed: 75.81 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 11/27) : 13324
|
|
|
+Total time elapsed: 79.17 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 26/27) : 14623
|
|
|
+Total time elapsed: 80.54 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 25/27) : 14602
|
|
|
+Total time elapsed: 82.14 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 6/27) : 17479
|
|
|
+Total time elapsed: 84.72 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 27/27) : 17701
|
|
|
+Total time elapsed: 86.03 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 16/27) : 8751
|
|
|
+Total time elapsed: 58.17 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 4/27) : 12459
|
|
|
+Total time elapsed: 61.01 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 19/27) : 11053
|
|
|
+Total time elapsed: 65.79 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 1/27) : 16613
|
|
|
+Total time elapsed: 66.04 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 5/27) : 11341
|
|
|
+Total time elapsed: 51.41 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 10/27) : 15398
|
|
|
+Total time elapsed: 72.51 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 3/27) : 14619
|
|
|
+Total time elapsed: 50.54 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 8/27) : 21116
|
|
|
+Total time elapsed: 57.86 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 9/27) : 71597
|
|
|
+Total time elapsed: 154.81 s
|
|
|
+
|
|
|
+real 4m30.245s
|
|
|
+user 30m10.643s
|
|
|
+sys 4m30.118s
|
|
|
+
|
|
|
+[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
|
|
|
+[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 20
|
|
|
+[INFO] Total heterozygous SNP positions selected: chr10: 114549
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+
|
|
|
+real 0m1.928s
|
|
|
+user 0m1.668s
|
|
|
+sys 0m0.180s
|
|
|
+
|
|
|
+[INFO] 3/7 Phase VCF file using LongPhase
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+LongPhase Ver 1.7
|
|
|
+
|
|
|
+--- File Parameter ---
|
|
|
+SNP File : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr10.vcf
|
|
|
+SV File :
|
|
|
+MOD File :
|
|
|
+REF File : /home/t_steimle/ref/hs1/chm13v2.0.fa
|
|
|
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr10
|
|
|
+Generate Dot : False
|
|
|
+BAM File : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_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 ... 2s
|
|
|
+(chr10,54s)
|
|
|
+parsing total: 54s
|
|
|
+merge results ... 0s
|
|
|
+writeResult SNP ... 1s
|
|
|
+
|
|
|
+total process: 57s
|
|
|
+
|
|
|
+real 0m57.409s
|
|
|
+user 2m3.634s
|
|
|
+sys 0m8.114s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+
|
|
|
+[INFO] 5/7 Select candidates for full-alignment calling
|
|
|
+[INFO] Set variants quality cutoff 21.0
|
|
|
+[INFO] Set reference calls quality cutoff 7.0
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+[INFO] Low quality reference calls to be processed in chr10: 12658
|
|
|
+[INFO] Low quality variants to be processed in chr10: 199885
|
|
|
+
|
|
|
+real 0m1.785s
|
|
|
+user 0m1.545s
|
|
|
+sys 0m0.190s
|
|
|
+
|
|
|
+[INFO] 6/7 Call low-quality variants using full-alignment model
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 22/22) : 2543
|
|
|
+Total time elapsed: 31.87 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 7/22) : 10000
|
|
|
+Total time elapsed: 101.21 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 8/22) : 10000
|
|
|
+Total time elapsed: 109.22 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 5/22) : 10000
|
|
|
+Total time elapsed: 114.37 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 9/22) : 10000
|
|
|
+Total time elapsed: 115.27 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 2/22) : 10000
|
|
|
+Total time elapsed: 117.07 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 13/22) : 10000
|
|
|
+Total time elapsed: 117.79 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 3/22) : 10000
|
|
|
+Total time elapsed: 118.03 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 1/22) : 10000
|
|
|
+Total time elapsed: 118.85 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 11/22) : 10000
|
|
|
+Total time elapsed: 120.41 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 18/22) : 10000
|
|
|
+Total time elapsed: 122.32 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 20/22) : 10000
|
|
|
+Total time elapsed: 122.68 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 10/22) : 10000
|
|
|
+Total time elapsed: 123.28 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 19/22) : 10000
|
|
|
+Total time elapsed: 123.74 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 16/22) : 10000
|
|
|
+Total time elapsed: 124.21 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 15/22) : 10000
|
|
|
+Total time elapsed: 125.40 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 4/22) : 10000
|
|
|
+Total time elapsed: 127.23 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 12/22) : 10000
|
|
|
+Total time elapsed: 127.26 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
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+Calling variants ...
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+Total processed positions in chr10 (chunk 21/22) : 10000
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+Total time elapsed: 128.78 s
|
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
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+Calling variants ...
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+Total processed positions in chr10 (chunk 6/22) : 10000
|
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+Total time elapsed: 129.25 s
|
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+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
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|
+Total processed positions in chr10 (chunk 17/22) : 10000
|
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|
+Total time elapsed: 129.52 s
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
|
|
+Calling variants ...
|
|
|
+Total processed positions in chr10 (chunk 14/22) : 10000
|
|
|
+Total time elapsed: 133.03 s
|
|
|
+
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|
+real 2m16.589s
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+user 40m23.948s
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+sys 2m13.182s
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+
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+[INFO] 7/7 Merge pileup VCF and full-alignment VCF
|
|
|
+/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
|
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+[INFO] Pileup variants processed in chr10: 85952
|
|
|
+[INFO] Full-alignment variants processed in chr10: 189193
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|
+
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|
+real 0m3.285s
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|
+user 0m3.344s
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+sys 0m0.202s
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+
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+[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
|
|
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+
|
|
|
+real 8m2.537s
|
|
|
+user 72m53.947s
|
|
|
+sys 6m53.306s
|
|
|
+
|
|
|
+[INFO] Select Heterozygous SNP for Phasing
|
|
|
+[INFO] RUN THE FOLLOWING COMMAND:
|
|
|
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/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/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/1_select_hetero_snp_for_phasing.log
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+
|
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|
+[INFO] Total HET SNP calls selected: chr10: 154989, not found:991, not match:82, low_qual_count:0. Total normal:154772 Total tumor:156062, pro: 0.9931
|
|
|
+
|
|
|
+[INFO] Phase the Tumor BAM
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|
|
+[INFO] RUN THE FOLLOWING COMMAND:
|
|
|
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/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/DUMCO/diag/ClairS/part4/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS
|
|
|
+
|
|
|
+LongPhase Ver 1.7
|
|
|
+
|
|
|
+--- File Parameter ---
|
|
|
+SNP File : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/vcf/chr10.vcf
|
|
|
+SV File :
|
|
|
+MOD File :
|
|
|
+REF File : /home/t_steimle/ref/hs1/chm13v2.0.fa
|
|
|
+Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_chr10
|
|
|
+Generate Dot : False
|
|
|
+BAM File : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_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 ... 2s
|
|
|
+(chr10,78s)
|
|
|
+parsing total: 78s
|
|
|
+merge results ... 0s
|
|
|
+writeResult SNP ... 1s
|
|
|
+
|
|
|
+total process: 81s
|
|
|
+
|
|
|
+[INFO] Haplotag the Tumor BAM
|
|
|
+[INFO] RUN THE FOLLOWING COMMAND:
|
|
|
+( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/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/DUMCO/diag/ClairS/part4/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/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part4/tmp/CONTIGS
|
|
|
+
|
