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: 40.19 s Calling variants ... Total processed positions in chr21 (chunk 2/10) : 55447 Total time elapsed: 86.41 s Calling variants ... Total processed positions in chr21 (chunk 5/10) : 65383 Total time elapsed: 99.76 s Calling variants ... Total processed positions in chr21 (chunk 6/10) : 71156 Total time elapsed: 100.33 s Calling variants ... Total processed positions in chr21 (chunk 4/10) : 73057 Total time elapsed: 104.96 s Calling variants ... Total processed positions in chr21 (chunk 3/10) : 71284 Total time elapsed: 107.34 s Calling variants ... Total processed positions in chr21 (chunk 7/10) : 75897 Total time elapsed: 113.52 s Calling variants ... Total processed positions in chr21 (chunk 9/10) : 81308 Total time elapsed: 118.65 s Calling variants ... Total processed positions in chr21 (chunk 8/10) : 78139 Total time elapsed: 121.89 s Calling variants ... Total processed positions in chr21 (chunk 10/10) : 86992 Total time elapsed: 128.36 s real 2m15.199s user 16m24.968s sys 1m1.295s [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 0m1.926s user 0m1.806s sys 0m0.107s [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 (chr21,5s) parsing total: 5s merge results ... 0s writeResult SNP ... 0s total process: 5s real 0m5.642s user 0m11.272s sys 0m0.759s [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 0m1.996s user 0m1.789s sys 0m0.182s [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: 72.41 s Calling variants ... Total processed positions in chr21 (chunk 9/13) : 10000 Total time elapsed: 75.76 s Calling variants ... Total processed positions in chr21 (chunk 3/13) : 10000 Total time elapsed: 76.04 s Calling variants ... Total processed positions in chr21 (chunk 2/13) : 10000 Total time elapsed: 76.76 s Calling variants ... Total processed positions in chr21 (chunk 11/13) : 10000 Total time elapsed: 77.08 s Calling variants ... Total processed positions in chr21 (chunk 8/13) : 10000 Total time elapsed: 78.05 s Calling variants ... Total processed positions in chr21 (chunk 10/13) : 10000 Total time elapsed: 78.25 s Calling variants ... Total processed positions in chr21 (chunk 5/13) : 10000 Total time elapsed: 80.58 s Calling variants ... Total processed positions in chr21 (chunk 1/13) : 10000 Total time elapsed: 82.69 s Calling variants ... Total processed positions in chr21 (chunk 7/13) : 10000 Total time elapsed: 84.85 s Calling variants ... Total processed positions in chr21 (chunk 4/13) : 10000 Total time elapsed: 84.74 s Calling variants ... Total processed positions in chr21 (chunk 12/13) : 10000 Total time elapsed: 86.04 s Calling variants ... Total processed positions in chr21 (chunk 6/13) : 10000 Total time elapsed: 86.95 s real 1m30.619s user 16m49.687s sys 1m7.751s [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 0m2.641s user 0m2.759s sys 0m0.179s [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 4m8.696s user 33m41.706s sys 2m11.367s [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 5/10) : 11068 Total time elapsed: 44.07 s Calling variants ... Total processed positions in chr21 (chunk 7/10) : 9368 Total time elapsed: 44.86 s Calling variants ... Total processed positions in chr21 (chunk 4/10) : 10732 Total time elapsed: 45.33 s Calling variants ... Total processed positions in chr21 (chunk 6/10) : 10461 Total time elapsed: 45.62 s Calling variants ... Total processed positions in chr21 (chunk 9/10) : 11777 Total time elapsed: 48.59 s Calling variants ... Total processed positions in chr21 (chunk 8/10) : 11175 Total time elapsed: 50.18 s Calling variants ... Total processed positions in chr21 (chunk 10/10) : 15430 Total time elapsed: 53.54 s Calling variants ... Total processed positions in chr21 (chunk 1/10) : 36882 Total time elapsed: 81.42 s Calling variants ... Total processed positions in chr21 (chunk 3/10) : 32029 Total time elapsed: 89.59 s Calling variants ... Total processed positions in chr21 (chunk 2/10) : 75635 Total time elapsed: 132.33 s real 2m15.749s user 8m50.712s sys 0m36.304s [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 0m1.077s user 0m0.967s 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_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 ... 1s parsing SV VCF ... 0s parsing Meth VCF ... 0s reading reference ... 0s (chr21,18s) parsing total: 18s merge results ... 0s writeResult SNP ... 0s total process: 19s real 0m18.951s user 0m46.210s sys 0m3.036s [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 0m1.032s user 0m0.893s sys 0m0.124s [INFO] 6/7 Call low-quality variants using full-alignment model Calling variants ... Total processed positions in chr21 (chunk 1/9) : 10000 Total time elapsed: 85.71 s Calling variants ... Total processed positions in chr21 (chunk 3/9) : 10000 Total time elapsed: 89.12 s Calling variants ... Total processed positions in chr21 (chunk 4/9) : 10000 Total time elapsed: 98.05 s Calling variants ... Total processed positions in chr21 (chunk 2/9) : 10000 Total time elapsed: 101.27 s Calling variants ... Total processed positions in chr21 (chunk 6/9) : 10000 Total time elapsed: 103.79 s Calling variants ... Total processed positions in chr21 (chunk 7/9) : 10000 Total time elapsed: 105.16 s Calling variants ... Total processed positions in chr21 (chunk 9/9) : 8537 Total time elapsed: 105.70 s Calling variants ... Total processed positions in chr21 (chunk 5/9) : 10000 Total time elapsed: 110.43 s Calling variants ... Total processed positions in chr21 (chunk 8/9) : 10000 Total time elapsed: 110.81 s real 1m54.184s user 14m27.321s sys 0m46.063s [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 0m1.619s user 0m1.597s sys 0m0.153s [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 4m38.770s user 24m12.848s sys 1m26.479s [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 (chr21,34s) parsing total: 34s merge results ... 0s writeResult SNP ... 1s total process: 35s [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 phased SNP file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_chr21.vcf.gz phased SV file: phased MOD file: input bam file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam input ref file: /home/t_steimle/ref/hs1/chm13v2.0.fa output bam file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_chr21.bam number of threads: 1 write log file: false log file: ------------------------------------------- tag region: chr21 filter mapping quality below: 1 percentage threshold: 0.6 tag supplementary: false ------------------------------------------- parsing SNP VCF ... 1s tag read start ... chr: chr21 ... 615s tag read 616s ------------------------------------------- total process time: 617s total alignment: 890148 total supplementary: 22088 total secondary: 0 total unmapped: 0 total tag alignment: 306829 total untagged: 583319 [INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2} --chunk_num {3} --ctg_name {1} --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates --output_depth True --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES [INFO] chr21 chunk 0/10: Total snv candidates found: 5072, total indel candidates found: 757 [INFO] chr21 chunk 1/10: Total snv candidates found: 20319, total indel candidates found: 4282 [INFO] chr21 chunk 2/10: Total snv candidates found: 6136, total indel candidates found: 1125 [INFO] chr21 chunk 8/10: Total snv candidates found: 912, total indel candidates found: 1199 [INFO] chr21 chunk 9/10: Total snv candidates found: 3112, total indel candidates found: 2027 [faidx] Truncated sequence: chr21:40580649-45091721 [INFO] chr21 chunk 6/10: Total snv candidates found: 736, total indel candidates found: 1237 [INFO] chr21 chunk 7/10: Total snv candidates found: 1248, total indel candidates found: 1555 [INFO] chr21 chunk 3/10: Total snv candidates found: 616, total indel candidates found: 964 [INFO] chr21 chunk 4/10: Total snv candidates found: 805, total indel candidates found: 947 [INFO] chr21 chunk 5/10: Total snv candidates found: 741, total indel candidates found: 1069 [INFO] STEP 2: Pileup Model Calling [INFO] Create Paired Tensors [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/pileup_tensor_can/{1/} --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/2-1_CPT.log [INFO] chr21 chunk 3-3/1 Tensors generated: 318 [INFO] chr21 chunk 1-1/3 Tensors generated: 616 [INFO] chr21 chunk 1-1/5 Tensors generated: 741 [INFO] chr21 chunk 1-1/4 Tensors generated: 805 [INFO] chr21 chunk 1-1/6 Tensors generated: 729 [INFO] chr21 chunk 1-1/8 Tensors generated: 912 [INFO] chr21 chunk 1-1/0 Tensors generated: 5057 [INFO] chr21 chunk 1-1/7 Tensors generated: 1248 [INFO] chr21 chunk 2-3/1 Tensors generated: 9316 [INFO] chr21 chunk 1-1/9 Tensors generated: 3109 [faidx] Truncated sequence: chr21:40603737-45091575 [INFO] chr21 chunk 1-3/1 Tensors generated: 9761 [INFO] chr21 chunk 1-1/2 Tensors generated: 6135 [INFO] Pileup Model Prediction [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/pileup_tensor_can/{1/} --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup --show_germline :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/2-2_PREDICT.log [INFO] chr21 total processed positions: 318, time elapsed: 1.2s [INFO] chr21 total processed positions: 616, time elapsed: 1.7s [INFO] chr21 total processed positions: 729, time elapsed: 2.0s [INFO] chr21 total processed positions: 741, time elapsed: 2.0s [INFO] chr21 total processed positions: 805, time elapsed: 2.2s [INFO] chr21 total processed positions: 912, time elapsed: 2.4s [INFO] chr21 total processed positions: 1248, time elapsed: 3.0s [INFO] chr21 total processed positions: 3109, time elapsed: 6.7s [INFO] chr21 total processed positions: 5057, time elapsed: 10.3s [INFO] chr21 total processed positions: 6135, time elapsed: 12.9s [INFO] chr21 total processed positions: 9316, time elapsed: 18.5s [INFO] chr21 total processed positions: 9761, time elapsed: 20.0s [INFO] Merge Pileup VCFs [INFO] RUN THE FOLLOWING COMMAND: pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output/pileup.vcf [INFO] Sorting VCFs... [INFO] Finished VCF sorting! [INFO] STEP 3: Full-alignment Model Calling [INFO] Create Full-alignment Paired Tensors [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/fa_tensor_can/{1/} --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/3-1_CPT.log [INFO] chr21 chunk 3-3/1 Tensors generated: 316 [INFO] chr21 chunk 1-1/3 Tensors generated: 616 [INFO] chr21 chunk 1-1/6 Tensors generated: 729 [INFO] chr21 chunk 1-1/5 Tensors generated: 741 [INFO] chr21 chunk 1-1/4 Tensors generated: 805 [INFO] chr21 chunk 1-1/8 Tensors generated: 912 [INFO] chr21 chunk 1-1/7 Tensors generated: 1248 [INFO] chr21 chunk 1-1/0 Tensors generated: 4472 [INFO] chr21 chunk 2-3/1 Tensors generated: 8494 [INFO] chr21 chunk 1-1/9 Tensors generated: 3109 [faidx] Truncated sequence: chr21:40603737-45091575 [INFO] chr21 chunk 1-1/2 Tensors generated: 6067 [INFO] chr21 chunk 1-3/1 Tensors generated: 9502 [INFO] Full-alignment Model Prediction [INFO] RUN THE FOLLOWING COMMAND: ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/fa_tensor_can/{1/} --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/3-2_PREDICT.log [INFO] chr21 total processed positions: 316, time elapsed: 37.3s [INFO] chr21 total processed positions: 616, time elapsed: 71.5s slurmstepd: error: *** JOB 2556291 ON n01 CANCELLED AT 2025-12-08T16:49:54 *** ---------------------------------------------- | SLURM EPILOG | ---------------------------------------------- Job ID: 2556291 Cluster: flamingo User/Group: t_steimle/gs_hpc_biopath Nodelist: n01 Nodes: 1 Cores per node: 40 Job started at: 2025-12-08 16:24:11 Job ended at: 2025-12-08 16:49:54 Job Wall-clock time: 00:25:43 CPU Utilized: 02:07:35 CPU Efficiency: 12.40% of 17:08:40 core-walltime Memory Utilized: 16.69 GB Memory Efficiency: 41.71% of 40.00 GB