WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27': 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/part27 --region chr3:20251704-176116306 --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/part27/logs [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/split_beds [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/candidates [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/pileup_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/fa_tensor_can [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/tmp_vcf_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/logs/clair3_log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/phased_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/vcf [INFO] --include_all_ctgs enabled [INFO] Call variants in contigs: chr3 [INFO] Number of chunks for each contig: 41 [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/part27 [INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/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/part27/tmp/region.bed [INFO] GENOTYPING MODE VCF FILE PATH: None [INFO] HYBRID MODE VCF FILE PATH: None [INFO] REGION FOR CALLING: chr3:20251704-176116306 [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/part27/tmp/clair3_output/clair3_normal_output --ctg_name=chr3 --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/part27/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/part27/tmp/clair3_output/clair3_normal_output [INFO] PLATFORM: ont [INFO] THREADS: 40 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: chr3 [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/part27/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr3 --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/part27/tmp/clair3_output/clair3_normal_output/log [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/pileup_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/merge_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part27/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed [INFO] Call variant in contigs: chr3 [INFO] Chunk number for each contig: 41 [INFO] 1/7 Call variants using pileup model Calling variants ... Total processed positions in chr3 (chunk 20/41) : 46480 Total time elapsed: 170.63 s Calling variants ... Total processed positions in chr3 (chunk 19/41) : 56068 Total time elapsed: 196.00 s Calling variants ... Total processed positions in chr3 (chunk 17/41) : 69035 Total time elapsed: 236.76 s Calling variants ... Total processed positions in chr3 (chunk 21/41) : 70599 Total time elapsed: 237.59 s Calling variants ... Total processed positions in chr3 (chunk 5/41) : 74479 Total time elapsed: 243.32 s Calling variants ... Total processed positions in chr3 (chunk 14/41) : 74855 Total time elapsed: 246.58 s Calling variants ... Total processed positions in chr3 (chunk 1/41) : 79390 Total time elapsed: 247.69 s Calling variants ... Total processed positions in chr3 (chunk 6/41) : 75949 Total time elapsed: 249.08 s Calling variants ... Total processed positions in chr3 (chunk 18/41) : 74745 Total time elapsed: 250.59 s Calling variants ... Total processed positions in chr3 (chunk 22/41) : 78103 Total time elapsed: 253.62 s Calling variants ... Total processed positions in chr3 (chunk 9/41) : 81163 Total time elapsed: 260.02 s Calling variants ... Total processed positions in chr3 (chunk 16/41) : 76388 Total time elapsed: 261.10 s Calling variants ... Total processed positions in chr3 (chunk 23/41) : 79301 Total time elapsed: 262.87 s Calling variants ... Total processed positions in chr3 (chunk 25/41) : 78250 Total time elapsed: 263.37 s Calling variants ... Total processed positions in chr3 (chunk 24/41) : 81383 Total time elapsed: 265.82 s Calling variants ... Total processed positions in chr3 (chunk 7/41) : 82908 Total time elapsed: 266.83 s Calling variants ... Total processed positions in chr3 (chunk 4/41) : 79370 Total time elapsed: 267.67 s Calling variants ... Total processed positions in chr3 (chunk 12/41) : 80581 Total time elapsed: 271.61 s Calling variants ... Total processed positions in chr3 (chunk 26/41) : 79342 Total time elapsed: 243.81 s Calling variants ... Total processed positions in chr3 (chunk 8/41) : 83199 Total time elapsed: 276.33 s Calling variants ... Total processed positions in chr3 (chunk 28/41) : 77518 Total time elapsed: 245.70 s Calling variants ... Total processed positions in chr3 (chunk 29/41) : 75850 Total time elapsed: 248.04 s Calling variants ... Total processed positions in chr3 (chunk 13/41) : 80100 Total time elapsed: 248.50 s Calling variants ... Total processed positions in chr3 (chunk 30/41) : 77260 Total time elapsed: 248.39 s Calling variants ... Total processed positions in chr3 (chunk 10/41) : 79740 Total time elapsed: 251.52 s Calling variants ... Total processed positions in chr3 (chunk 11/41) : 82947 Total time elapsed: 260.02 s Calling variants ... Total processed positions in chr3 (chunk 27/41) : 86290 Total time elapsed: 291.60 s Calling variants ... Total processed positions in chr3 (chunk 2/41) : 83369 Total time elapsed: 261.26 s Calling variants ... Total processed positions in chr3 (chunk 15/41) : 82728 Total time elapsed: 261.34 s Calling variants ... Total processed positions in chr3 (chunk 3/41) : 87168 Total time elapsed: 263.77 s Calling variants ... Total processed positions in chr3 (chunk 31/41) : 77286 Total time elapsed: 189.04 s Calling variants ... Total processed positions in chr3 (chunk 32/41) : 83710 Total time elapsed: 200.27 s Calling variants ... Total processed positions in chr3 (chunk 33/41) : 75437 Total time elapsed: 161.14 s Calling variants ... Total processed positions in chr3 (chunk 34/41) : 75899 Total time elapsed: 168.99 s Calling variants ... Total processed positions in chr3 (chunk 36/41) : 77630 Total time elapsed: 165.08 s Calling variants ... Total processed positions in chr3 (chunk 38/41) : 75120 Total time elapsed: 163.08 s Calling variants ... Total processed positions in chr3 (chunk 35/41) : 74299 Total time elapsed: 169.32 s Calling variants ... Total processed positions in chr3 (chunk 37/41) : 75513 Total time elapsed: 166.41 s Calling variants ... Total processed positions in chr3 (chunk 39/41) : 82603 Total time elapsed: 175.52 s Calling variants ... Total processed positions in chr3 (chunk 40/41) : 83507 Total time elapsed: 175.41 s Calling variants ... Total processed positions in chr3 (chunk 41/41) : 89682 Total time elapsed: 174.30 s real 7m29.196s user 153m14.000s sys 7m27.400s [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16 [INFO] Total heterozygous SNP positions selected: chr3: 123767 real 0m5.433s user 0m4.980s sys 0m0.357s [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/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr3.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/part27/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr3 Generate Dot : False BAM File : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --- Phasing Parameter --- Seq Platform : ONT Phase Indel : False Distance Threshold : 300000 Connect Adjacent : 20 Edge Threshold : 0.7 Mapping Quality : 1 Variant Confidence : 0.75 ReadTag Confidence : 0.65 parsing VCF ... 0s parsing SV VCF ... 0s parsing Meth VCF ... 0s reading reference ... 2s (chr3,15s) parsing total: 15s merge results ... 0s writeResult SNP ... 2s total process: 19s real 0m19.284s user 1m2.234s sys 0m3.715s [INFO] 5/7 Select candidates for full-alignment calling [INFO] Set variants quality cutoff 20.0 [INFO] Set reference calls quality cutoff 14.0 [INFO] Low quality reference calls to be processed in chr3: 283652 [INFO] Low quality variants to be processed in chr3: 238359 real 0m6.292s user 0m5.718s sys 0m0.454s [INFO] 6/7 Call low-quality variants using full-alignment model slurmstepd: error: *** JOB 2556292 ON n11 CANCELLED AT 2025-12-08T16:49:54 *** slurmstepd: error: Detected 10 oom_kill events in StepId=2556292.batch. Some of the step tasks have been OOM Killed. ---------------------------------------------- | SLURM EPILOG | ---------------------------------------------- Job ID: 2556292 Cluster: flamingo User/Group: t_steimle/gs_hpc_biopath Nodelist: n11 Nodes: 1 Cores per node: 40 Job started at: 2025-12-08 16:41:15 Job ended at: 2025-12-08 16:49:54 Job Wall-clock time: 00:08:39 CPU Utilized: 02:45:28 CPU Efficiency: 47.82% of 05:46:00 core-walltime Memory Utilized: 32.81 GB Memory Efficiency: 82.02% of 40.00 GB