pandora_lib_promethion/slurm-2556292.out

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