pandora_lib_promethion/slurm-2556285.out

WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7': 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/part7 --region chr12:1-105185185 --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/part7/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chr12
[INFO] Number of chunks for each contig: 27

[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/part7
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chr12:1-105185185
[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/part7/tmp/clair3_output/clair3_normal_output --ctg_name=chr12 --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/part7/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/part7/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr12
[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/part7/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr12 --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/part7/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr12
[INFO] Chunk number for each contig: 27
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr12 (chunk 8/27) : 46499
Total time elapsed: 102.32 s
Calling variants ...
Total processed positions in chr12 (chunk 18/27) : 68095
Total time elapsed: 127.61 s
Calling variants ...
Total processed positions in chr12 (chunk 17/27) : 76214
Total time elapsed: 134.51 s
Calling variants ...
Total processed positions in chr12 (chunk 23/27) : 77100
Total time elapsed: 148.21 s
Calling variants ...
Total processed positions in chr12 (chunk 14/27) : 80772
Total time elapsed: 150.77 s
Calling variants ...
Total processed positions in chr12 (chunk 5/27) : 78381
Total time elapsed: 150.98 s
Calling variants ...
Total processed positions in chr12 (chunk 4/27) : 80255
Total time elapsed: 152.98 s
Calling variants ...
Total processed positions in chr12 (chunk 16/27) : 77789
Total time elapsed: 154.39 s
Calling variants ...
Total processed positions in chr12 (chunk 15/27) : 75894
Total time elapsed: 155.07 s
Calling variants ...
Total processed positions in chr12 (chunk 13/27) : 82126
Total time elapsed: 155.02 s
Calling variants ...
Total processed positions in chr12 (chunk 19/27) : 79762
Total time elapsed: 155.26 s
Calling variants ...
Total processed positions in chr12 (chunk 7/27) : 78143
Total time elapsed: 155.50 s
Calling variants ...
Total processed positions in chr12 (chunk 10/27) : 80443
Total time elapsed: 157.43 s
Calling variants ...
Total processed positions in chr12 (chunk 25/27) : 84367
Total time elapsed: 159.08 s
Calling variants ...
Total processed positions in chr12 (chunk 22/27) : 88103
Total time elapsed: 159.42 s
Calling variants ...
Total processed positions in chr12 (chunk 2/27) : 83654
Total time elapsed: 159.98 s
Calling variants ...
Total processed positions in chr12 (chunk 9/27) : 82193
Total time elapsed: 162.06 s
Calling variants ...
Total processed positions in chr12 (chunk 21/27) : 77458
Total time elapsed: 139.98 s
Calling variants ...
Total processed positions in chr12 (chunk 1/27) : 91053
Total time elapsed: 164.99 s
Calling variants ...
Total processed positions in chr12 (chunk 24/27) : 86005
Total time elapsed: 143.36 s
Calling variants ...
Total processed positions in chr12 (chunk 20/27) : 79950
Total time elapsed: 145.10 s
Calling variants ...
Total processed positions in chr12 (chunk 11/27) : 91029
Total time elapsed: 169.43 s
Calling variants ...
Total processed positions in chr12 (chunk 12/27) : 85366
Total time elapsed: 147.01 s
Calling variants ...
Total processed positions in chr12 (chunk 3/27) : 81325
Total time elapsed: 147.64 s
Calling variants ...
Total processed positions in chr12 (chunk 26/27) : 88022
Total time elapsed: 151.21 s
Calling variants ...
Total processed positions in chr12 (chunk 6/27) : 84846
Total time elapsed: 154.47 s
Calling variants ...
Total processed positions in chr12 (chunk 27/27) : 95023
Total time elapsed: 162.69 s

real	3m12.806s
user	65m23.912s
sys	3m50.478s

[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: chr12: 89219

real	0m5.088s
user	0m4.817s
sys	0m0.191s

[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/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr12.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/part7/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr12
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
(chr12,9s)
parsing total:  9s
merge results ... 0s
writeResult SNP ... 0s

total process: 11s

real	0m11.585s
user	0m23.044s
sys	0m1.534s

[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 chr12: 193804
[INFO] Low quality variants to be processed in chr12: 167735

real	0m5.470s
user	0m5.099s
sys	0m0.282s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr12 (chunk 5/37) : 10000
Total time elapsed: 94.51 s
Calling variants ...
Total processed positions in chr12 (chunk 17/37) : 10000
Total time elapsed: 95.71 s
Calling variants ...
Total processed positions in chr12 (chunk 13/37) : 10000
Total time elapsed: 96.94 s
Calling variants ...
Total processed positions in chr12 (chunk 15/37) : 10000
Total time elapsed: 97.12 s
Calling variants ...
Total processed positions in chr12 (chunk 21/37) : 10000
Total time elapsed: 97.34 s
Calling variants ...
Total processed positions in chr12 (chunk 2/37) : 10000
Total time elapsed: 98.12 s
Calling variants ...
Total processed positions in chr12 (chunk 3/37) : 10000
Total time elapsed: 99.36 s
Calling variants ...
Total processed positions in chr12 (chunk 22/37) : 10000
Total time elapsed: 99.18 s
Calling variants ...
Total processed positions in chr12 (chunk 9/37) : 10000
Total time elapsed: 99.50 s
Calling variants ...
Total processed positions in chr12 (chunk 20/37) : 10000
Total time elapsed: 99.61 s
Calling variants ...
Total processed positions in chr12 (chunk 25/37) : 10000
Total time elapsed: 100.05 s
Calling variants ...
Total processed positions in chr12 (chunk 1/37) : 10000
Total time elapsed: 100.19 s
Calling variants ...
Total processed positions in chr12 (chunk 27/37) : 10000
Total time elapsed: 100.61 s
Calling variants ...
Total processed positions in chr12 (chunk 29/37) : 10000
Total time elapsed: 100.96 s
Calling variants ...
Total processed positions in chr12 (chunk 14/37) : 10000
Total time elapsed: 101.32 s
Calling variants ...
Total processed positions in chr12 (chunk 7/37) : 10000
Total time elapsed: 101.88 s
Calling variants ...
Total processed positions in chr12 (chunk 10/37) : 10000
Total time elapsed: 103.02 s
Calling variants ...
Total processed positions in chr12 (chunk 4/37) : 10000
Total time elapsed: 103.09 s
Calling variants ...
Total processed positions in chr12 (chunk 30/37) : 10000
Total time elapsed: 103.11 s
Calling variants ...
Total processed positions in chr12 (chunk 23/37) : 10000
Total time elapsed: 103.22 s
Calling variants ...
Total processed positions in chr12 (chunk 26/37) : 10000
Total time elapsed: 104.15 s
Calling variants ...
Total processed positions in chr12 (chunk 28/37) : 10000
Total time elapsed: 104.66 s
Calling variants ...
Total processed positions in chr12 (chunk 16/37) : 10000
Total time elapsed: 104.87 s
Calling variants ...
Total processed positions in chr12 (chunk 8/37) : 10000
Total time elapsed: 104.94 s
Calling variants ...
Total processed positions in chr12 (chunk 19/37) : 10000
Total time elapsed: 105.31 s
Calling variants ...
Total processed positions in chr12 (chunk 24/37) : 10000
Total time elapsed: 105.52 s
Calling variants ...
Total processed positions in chr12 (chunk 6/37) : 10000
Total time elapsed: 105.43 s
Calling variants ...
Total processed positions in chr12 (chunk 11/37) : 10000
Total time elapsed: 105.95 s
Calling variants ...
Total processed positions in chr12 (chunk 18/37) : 10000
Total time elapsed: 105.83 s
Calling variants ...
Total processed positions in chr12 (chunk 12/37) : 10000
Total time elapsed: 106.54 s
Calling variants ...
Total processed positions in chr12 (chunk 37/37) : 1539
Total time elapsed: 14.12 s
Calling variants ...
Total processed positions in chr12 (chunk 32/37) : 10000
Total time elapsed: 71.42 s
Calling variants ...
Total processed positions in chr12 (chunk 31/37) : 10000
Total time elapsed: 73.05 s
Calling variants ...
Total processed positions in chr12 (chunk 33/37) : 10000
Total time elapsed: 73.38 s
Calling variants ...
Total processed positions in chr12 (chunk 35/37) : 10000
Total time elapsed: 75.49 s
Calling variants ...
Total processed positions in chr12 (chunk 34/37) : 10000
Total time elapsed: 75.46 s
Calling variants ...
Total processed positions in chr12 (chunk 36/37) : 10000
Total time elapsed: 79.45 s

real	3m5.066s
user	56m29.138s
sys	3m33.101s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr12: 71993
[INFO] Full-alignment variants processed in chr12: 173431

real	0m6.791s
user	0m7.403s
sys	0m0.313s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz

real	7m14.030s
user	122m58.840s
sys	7m27.983s

[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/part7/tmp/clair3_output/clair3_tumor_output --ctg_name=chr12 --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/part7/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/part7/tmp/clair3_output/clair3_tumor_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr12
[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/part7/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr12 --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/part7/tmp/clair3_output/clair3_tumor_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr12
[INFO] Chunk number for each contig: 27
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr12 (chunk 21/27) : 9223
Total time elapsed: 82.61 s
Calling variants ...
Total processed positions in chr12 (chunk 16/27) : 9706
Total time elapsed: 86.50 s
Calling variants ...
Total processed positions in chr12 (chunk 14/27) : 9976
Total time elapsed: 86.89 s
Calling variants ...
Total processed positions in chr12 (chunk 10/27) : 11358
Total time elapsed: 87.25 s
Calling variants ...
Total processed positions in chr12 (chunk 5/27) : 11025
Total time elapsed: 88.34 s
Calling variants ...
Total processed positions in chr12 (chunk 20/27) : 11648
Total time elapsed: 88.30 s
Calling variants ...
Total processed positions in chr12 (chunk 9/27) : 12539
Total time elapsed: 88.93 s
Calling variants ...
Total processed positions in chr12 (chunk 12/27) : 11619
Total time elapsed: 88.95 s
Calling variants ...
Total processed positions in chr12 (chunk 6/27) : 11547
Total time elapsed: 88.97 s
Calling variants ...
Total processed positions in chr12 (chunk 13/27) : 12133
Total time elapsed: 89.37 s
Calling variants ...
Total processed positions in chr12 (chunk 3/27) : 14660
Total time elapsed: 92.08 s
Calling variants ...
Total processed positions in chr12 (chunk 26/27) : 13770
Total time elapsed: 92.12 s
Calling variants ...
Total processed positions in chr12 (chunk 27/27) : 19156
Total time elapsed: 100.86 s
Calling variants ...
Total processed positions in chr12 (chunk 2/27) : 12962
Total time elapsed: 61.41 s
Calling variants ...
Total processed positions in chr12 (chunk 15/27) : 9489
Total time elapsed: 56.67 s
Calling variants ...
Total processed positions in chr12 (chunk 17/27) : 9234
Total time elapsed: 57.27 s
Calling variants ...
Total processed positions in chr12 (chunk 19/27) : 9327
Total time elapsed: 56.49 s
Calling variants ...
Total processed positions in chr12 (chunk 23/27) : 9032
Total time elapsed: 57.46 s
Calling variants ...
Total processed positions in chr12 (chunk 4/27) : 9289
Total time elapsed: 57.43 s
Calling variants ...
Total processed positions in chr12 (chunk 22/27) : 11056
Total time elapsed: 59.00 s
Calling variants ...
Total processed positions in chr12 (chunk 25/27) : 12654
Total time elapsed: 60.01 s
Calling variants ...
Total processed positions in chr12 (chunk 24/27) : 11738
Total time elapsed: 60.45 s
Calling variants ...
Total processed positions in chr12 (chunk 11/27) : 11555
Total time elapsed: 60.07 s
Calling variants ...
Total processed positions in chr12 (chunk 7/27) : 14221
Total time elapsed: 62.79 s
Calling variants ...
Total processed positions in chr12 (chunk 18/27) : 8254
Total time elapsed: 42.19 s
Calling variants ...
Total processed positions in chr12 (chunk 1/27) : 14099
Total time elapsed: 47.15 s
Calling variants ...
Total processed positions in chr12 (chunk 8/27) : 36309
Total time elapsed: 86.95 s

real	3m2.591s
user	24m49.079s
sys	4m0.775s

[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: chr12: 93063

real	0m1.611s
user	0m1.378s
sys	0m0.164s

[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/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr12.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/part7/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr12
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 ... 1s
(chr12,42s)
parsing total:  42s
merge results ... 0s
writeResult SNP ... 1s

total process: 45s

real	0m44.569s
user	1m37.014s
sys	0m6.738s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 22.0
[INFO] Set reference calls quality cutoff 7.0
[INFO] Low quality reference calls to be processed in chr12: 9896
[INFO] Low quality variants to be processed in chr12: 166782

real	0m1.510s
user	0m1.321s
sys	0m0.156s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr12 (chunk 18/18) : 6678
Total time elapsed: 90.63 s
Calling variants ...
Total processed positions in chr12 (chunk 6/18) : 10000
Total time elapsed: 110.67 s
Calling variants ...
Total processed positions in chr12 (chunk 16/18) : 10000
Total time elapsed: 113.88 s
Calling variants ...
Total processed positions in chr12 (chunk 7/18) : 10000
Total time elapsed: 114.75 s
Calling variants ...
Total processed positions in chr12 (chunk 11/18) : 10000
Total time elapsed: 115.95 s
Calling variants ...
Total processed positions in chr12 (chunk 8/18) : 10000
Total time elapsed: 117.38 s
Calling variants ...
Total processed positions in chr12 (chunk 5/18) : 10000
Total time elapsed: 117.56 s
Calling variants ...
Total processed positions in chr12 (chunk 1/18) : 10000
Total time elapsed: 117.86 s
Calling variants ...
Total processed positions in chr12 (chunk 3/18) : 10000
Total time elapsed: 118.30 s
Calling variants ...
Total processed positions in chr12 (chunk 10/18) : 10000
Total time elapsed: 118.13 s
Calling variants ...
Total processed positions in chr12 (chunk 13/18) : 10000
Total time elapsed: 119.82 s
Calling variants ...
Total processed positions in chr12 (chunk 4/18) : 10000
Total time elapsed: 120.41 s
Calling variants ...
Total processed positions in chr12 (chunk 15/18) : 10000
Total time elapsed: 121.87 s
Calling variants ...
Total processed positions in chr12 (chunk 14/18) : 10000
Total time elapsed: 121.99 s
Calling variants ...
Total processed positions in chr12 (chunk 9/18) : 10000
Total time elapsed: 122.71 s
Calling variants ...
Total processed positions in chr12 (chunk 2/18) : 10000
Total time elapsed: 123.31 s
Calling variants ...
Total processed positions in chr12 (chunk 17/18) : 10000
Total time elapsed: 123.09 s
Calling variants ...
Total processed positions in chr12 (chunk 12/18) : 10000
Total time elapsed: 126.61 s

real	2m10.378s
user	33m30.002s
sys	1m43.285s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr12: 71593
[INFO] Full-alignment variants processed in chr12: 152759

real	0m2.637s
user	0m2.662s
sys	0m0.193s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz

real	6m12.925s
user	60m9.139s
sys	5m52.551s

[INFO] Select Heterozygous SNP for Phasing
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/1_select_hetero_snp_for_phasing.log

[INFO] Total HET SNP calls selected: chr12: 119818, not found:473, not match:28, low_qual_count:0. Total normal:120205 Total tumor:120319, pro: 0.9958

[INFO] Phase the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/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/part7/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS

LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/vcf/chr12.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/part7/tmp/clair3_output/phased_output/tumor_phased_chr12
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 ... 2s
(chr12,56s)
parsing total:  56s
merge results ... 0s
writeResult SNP ... 1s

total process: 59s

[INFO] Haplotag the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/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/part7/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/part7/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CONTIGS

phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_phased_chr12.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/part7/tmp/clair3_output/phased_output/tumor_chr12.bam
number of threads: 1
write log file:    false
log file:          
-------------------------------------------
tag region:                    chr12
filter mapping quality below:  1
percentage threshold:          0.6
tag supplementary:             false
-------------------------------------------
parsing SNP VCF ... 1s
tag read start ...
chr: chr12 ... 1123s
tag read 1125s
-------------------------------------------
total process time:  1126s
total alignment:     1449857
total supplementary: 63961
total secondary:     0
total unmapped:      0
total tag alignment: 918891
total untagged:      530966

[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/part7/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/part7/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 

[INFO] chr12 chunk 9/27: Total snv candidates found: 2526, total indel candidates found: 440
[INFO] chr12 chunk 8/27: Total snv candidates found: 2811, total indel candidates found: 1113
[INFO] chr12 chunk 0/27: Total snv candidates found: 1495, total indel candidates found: 1426
[INFO] chr12 chunk 3/27: Total snv candidates found: 664, total indel candidates found: 1140
[INFO] chr12 chunk 1/27: Total snv candidates found: 785, total indel candidates found: 1211
[INFO] chr12 chunk 13/27: Total snv candidates found: 833, total indel candidates found: 1517
[INFO] chr12 chunk 2/27: Total snv candidates found: 2279, total indel candidates found: 1237
[INFO] chr12 chunk 16/27: Total snv candidates found: 491, total indel candidates found: 1006
[INFO] chr12 chunk 12/27: Total snv candidates found: 804, total indel candidates found: 1380
[INFO] chr12 chunk 14/27: Total snv candidates found: 633, total indel candidates found: 1357
[INFO] chr12 chunk 17/27: Total snv candidates found: 600, total indel candidates found: 936
[INFO] chr12 chunk 4/27: Total snv candidates found: 415, total indel candidates found: 859
[INFO] chr12 chunk 6/27: Total snv candidates found: 599, total indel candidates found: 981
[INFO] chr12 chunk 5/27: Total snv candidates found: 667, total indel candidates found: 900
[INFO] chr12 chunk 11/27: Total snv candidates found: 480, total indel candidates found: 831
[INFO] chr12 chunk 15/27: Total snv candidates found: 777, total indel candidates found: 729
[INFO] chr12 chunk 7/27: Total snv candidates found: 1141, total indel candidates found: 964
[INFO] chr12 chunk 10/27: Total snv candidates found: 712, total indel candidates found: 916
[INFO] chr12 chunk 19/27: Total snv candidates found: 548, total indel candidates found: 788
[INFO] chr12 chunk 22/27: Total snv candidates found: 418, total indel candidates found: 752
[INFO] chr12 chunk 23/27: Total snv candidates found: 428, total indel candidates found: 890
[INFO] chr12 chunk 20/27: Total snv candidates found: 395, total indel candidates found: 782
[INFO] chr12 chunk 18/27: Total snv candidates found: 909, total indel candidates found: 816
[INFO] chr12 chunk 26/27: Total snv candidates found: 536, total indel candidates found: 979
[INFO] chr12 chunk 25/27: Total snv candidates found: 691, total indel candidates found: 913
[INFO] chr12 chunk 21/27: Total snv candidates found: 425, total indel candidates found: 750
[INFO] chr12 chunk 24/27: Total snv candidates found: 713, total indel candidates found: 1124

[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/part7/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/part7/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/2-1_CPT.log

[INFO] chr12 chunk 1-1/1 Tensors generated: 785
[INFO] chr12 chunk 1-1/22 Tensors generated: 417
[INFO] chr12 chunk 1-1/4 Tensors generated: 415
[INFO] chr12 chunk 1-1/21 Tensors generated: 417
[INFO] chr12 chunk 1-1/20 Tensors generated: 395
[INFO] chr12 chunk 1-1/23 Tensors generated: 428
[INFO] chr12 chunk 1-1/11 Tensors generated: 478
[INFO] chr12 chunk 1-1/16 Tensors generated: 491
[INFO] chr12 chunk 1-1/19 Tensors generated: 548
[INFO] chr12 chunk 1-1/0 Tensors generated: 1488
[INFO] chr12 chunk 1-1/26 Tensors generated: 535
[INFO] chr12 chunk 1-1/2 Tensors generated: 2241
[INFO] chr12 chunk 1-1/6 Tensors generated: 599
[INFO] chr12 chunk 1-1/3 Tensors generated: 657
[INFO] chr12 chunk 1-1/17 Tensors generated: 595
[INFO] chr12 chunk 1-1/5 Tensors generated: 667
[INFO] chr12 chunk 1-1/14 Tensors generated: 633
[INFO] chr12 chunk 1-1/10 Tensors generated: 712
[INFO] chr12 chunk 1-1/25 Tensors generated: 689
[INFO] chr12 chunk 1-1/15 Tensors generated: 777
[INFO] chr12 chunk 1-1/24 Tensors generated: 707
[INFO] chr12 chunk 1-1/18 Tensors generated: 909
[INFO] chr12 chunk 1-1/12 Tensors generated: 801
[INFO] chr12 chunk 1-1/13 Tensors generated: 833
[INFO] chr12 chunk 1-1/7 Tensors generated: 1134
[INFO] chr12 chunk 1-1/8 Tensors generated: 2811
[INFO] chr12 chunk 1-1/9 Tensors generated: 2526

[INFO] Pileup Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/2-2_PREDICT.log

[INFO] chr12 total processed positions: 417, time elapsed: 1.3s
[INFO] chr12 total processed positions: 415, time elapsed: 1.5s
[INFO] chr12 total processed positions: 395, time elapsed: 1.5s
[INFO] chr12 total processed positions: 428, time elapsed: 1.3s
[INFO] chr12 total processed positions: 417, time elapsed: 1.2s
[INFO] chr12 total processed positions: 478, time elapsed: 1.5s
[INFO] chr12 total processed positions: 491, time elapsed: 1.7s
[INFO] chr12 total processed positions: 548, time elapsed: 1.7s
[INFO] chr12 total processed positions: 712, time elapsed: 1.9s
[INFO] chr12 total processed positions: 595, time elapsed: 1.9s
[INFO] chr12 total processed positions: 667, time elapsed: 1.8s
[INFO] chr12 total processed positions: 535, time elapsed: 1.8s
[INFO] chr12 total processed positions: 657, time elapsed: 1.8s
[INFO] chr12 total processed positions: 689, time elapsed: 1.9s
[INFO] chr12 total processed positions: 633, time elapsed: 1.6s
[INFO] chr12 total processed positions: 599, time elapsed: 1.9s
[INFO] chr12 total processed positions: 785, time elapsed: 2.1s
[INFO] chr12 total processed positions: 707, time elapsed: 2.1s
[INFO] chr12 total processed positions: 777, time elapsed: 2.1s
[INFO] chr12 total processed positions: 801, time elapsed: 2.2s
[INFO] chr12 total processed positions: 833, time elapsed: 2.2s
[INFO] chr12 total processed positions: 909, time elapsed: 2.4s
[INFO] chr12 total processed positions: 1134, time elapsed: 2.6s
[INFO] chr12 total processed positions: 1488, time elapsed: 3.5s
[INFO] chr12 total processed positions: 2241, time elapsed: 4.9s
[INFO] chr12 total processed positions: 2526, time elapsed: 5.6s
[INFO] chr12 total processed positions: 2811, time elapsed: 6.3s

[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/part7/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/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/part7/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/part7/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/3-1_CPT.log

[INFO] chr12 chunk 1-1/22 Tensors generated: 417
[INFO] chr12 chunk 1-1/20 Tensors generated: 395
[INFO] chr12 chunk 1-1/4 Tensors generated: 415
[INFO] chr12 chunk 1-1/23 Tensors generated: 428
[INFO] chr12 chunk 1-1/21 Tensors generated: 417
[INFO] chr12 chunk 1-1/16 Tensors generated: 491
[INFO] chr12 chunk 1-1/11 Tensors generated: 478
[INFO] chr12 chunk 1-1/26 Tensors generated: 535
[INFO] chr12 chunk 1-1/19 Tensors generated: 548
[INFO] chr12 chunk 1-1/1 Tensors generated: 785
[INFO] chr12 chunk 1-1/6 Tensors generated: 599
[INFO] chr12 chunk 1-1/14 Tensors generated: 633
[INFO] chr12 chunk 1-1/17 Tensors generated: 595
[INFO] chr12 chunk 1-1/3 Tensors generated: 657
[INFO] chr12 chunk 1-1/10 Tensors generated: 712
[INFO] chr12 chunk 1-1/5 Tensors generated: 667
[INFO] chr12 chunk 1-1/25 Tensors generated: 689
[INFO] chr12 chunk 1-1/24 Tensors generated: 707
[INFO] chr12 chunk 1-1/15 Tensors generated: 777
[INFO] chr12 chunk 1-1/12 Tensors generated: 801
[INFO] chr12 chunk 1-1/13 Tensors generated: 833
[INFO] chr12 chunk 1-1/18 Tensors generated: 909
[INFO] chr12 chunk 1-1/7 Tensors generated: 1134
[INFO] chr12 chunk 1-1/0 Tensors generated: 1488
[INFO] chr12 chunk 1-1/2 Tensors generated: 2241
[INFO] chr12 chunk 1-1/9 Tensors generated: 2280
[INFO] chr12 chunk 1-1/8 Tensors generated: 2778

[INFO] Full-alignment Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/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/part7/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/3-2_PREDICT.log

[INFO] chr12 total processed positions: 415, time elapsed: 48.3s
[INFO] chr12 total processed positions: 417, time elapsed: 48.5s
[INFO] chr12 total processed positions: 395, time elapsed: 49.5s
[INFO] chr12 total processed positions: 428, time elapsed: 50.3s
[INFO] chr12 total processed positions: 417, time elapsed: 54.0s
[INFO] chr12 total processed positions: 491, time elapsed: 57.1s
[INFO] chr12 total processed positions: 478, time elapsed: 58.8s
[INFO] chr12 total processed positions: 548, time elapsed: 66.7s
[INFO] chr12 total processed positions: 535, time elapsed: 69.2s
[INFO] chr12 total processed positions: 599, time elapsed: 69.5s
[INFO] chr12 total processed positions: 595, time elapsed: 72.0s
[INFO] chr12 total processed positions: 633, time elapsed: 78.3s
[INFO] chr12 total processed positions: 667, time elapsed: 79.4s
[INFO] chr12 total processed positions: 689, time elapsed: 79.8s
[INFO] chr12 total processed positions: 657, time elapsed: 80.2s
[INFO] chr12 total processed positions: 707, time elapsed: 87.6s
[INFO] chr12 total processed positions: 712, time elapsed: 88.7s
[INFO] chr12 total processed positions: 801, time elapsed: 93.8s
[INFO] chr12 total processed positions: 777, time elapsed: 94.4s
[INFO] chr12 total processed positions: 833, time elapsed: 96.2s
[INFO] chr12 total processed positions: 785, time elapsed: 97.4s
[INFO] chr12 total processed positions: 909, time elapsed: 108.8s
[INFO] chr12 total processed positions: 1134, time elapsed: 132.7s
[INFO] chr12 total processed positions: 1488, time elapsed: 183.2s
[INFO] chr12 total processed positions: 2241, time elapsed: 257.5s
[INFO] chr12 total processed positions: 2280, time elapsed: 270.4s
[INFO] chr12 total processed positions: 2778, time elapsed: 323.0s

[INFO] Merge Full-alignment 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/part7/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --vcf_fn_prefix fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/full_alignment.vcf

[INFO] Sorting VCFs...
[INFO] Finished VCF sorting!

[INFO] STEP 4: Haplotype filtering
[INFO] RUN THE FOLLOWING COMMAND:
( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/4_HAP_FILTER.log

[INFO] Processing in chr12, total processed positions: 1000
[INFO] Processing in chr12, total processed positions: 2000
Total input calls: 7861, filtered by haplotype match 34

[INFO] STEP 5: Merge and sort VCF
[INFO] RUN THE FOLLOWING COMMAND:
( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/output.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/5_MV.log

[INFO] Full-alignment variants filtered by pileup:  818

[INFO] STEP 6: Indel Pileup Model Calling
[INFO] Create Paired Tensors
[INFO] RUN THE FOLLOWING COMMAND:
pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates --input_prefix INDEL_CANDIDATES_FILE_ --output_fn INDEL_CANDIDATES_FILES  && ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_6-1_create_pair_tensor_indel.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/part7/tmp/pileup_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/6-1_CPTI.log

[INFO] chr12  Tensors generated: 1211
[INFO] chr12  Tensors generated: 1424
[INFO] chr12  Tensors generated: 1236
[INFO] chr12  Tensors generated: 440
[INFO] chr12  Tensors generated: 729
[INFO] chr12  Tensors generated: 750
[INFO] chr12  Tensors generated: 788
[INFO] chr12  Tensors generated: 748
[INFO] chr12  Tensors generated: 782
[INFO] chr12  Tensors generated: 858
[INFO] chr12  Tensors generated: 890
[INFO] chr12  Tensors generated: 831
[INFO] chr12  Tensors generated: 816
[INFO] chr12  Tensors generated: 900
[INFO] chr12  Tensors generated: 916
[INFO] chr12  Tensors generated: 931
[INFO] chr12  Tensors generated: 962
[INFO] chr12  Tensors generated: 913
[INFO] chr12  Tensors generated: 978
[INFO] chr12  Tensors generated: 981
[INFO] chr12  Tensors generated: 1006
[INFO] chr12  Tensors generated: 1113
[INFO] chr12  Tensors generated: 1123
[INFO] chr12  Tensors generated: 1138
[INFO] chr12  Tensors generated: 1357
[INFO] chr12  Tensors generated: 1371
[INFO] chr12  Tensors generated: 1517

[INFO] Indel Pileup Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_6-2_predict_indel.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/pileup_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/6-2_PREDICT_INDEL.log

[INFO] chr12 total processed positions: 440, time elapsed: 1.1s
[INFO] chr12 total processed positions: 748, time elapsed: 1.7s
[INFO] chr12 total processed positions: 782, time elapsed: 2.0s
[INFO] chr12 total processed positions: 750, time elapsed: 2.0s
[INFO] chr12 total processed positions: 729, time elapsed: 2.0s
[INFO] chr12 total processed positions: 816, time elapsed: 2.1s
[INFO] chr12 total processed positions: 858, time elapsed: 2.1s
[INFO] chr12 total processed positions: 788, time elapsed: 2.0s
[INFO] chr12 total processed positions: 890, time elapsed: 2.3s
[INFO] chr12 total processed positions: 962, time elapsed: 2.2s
[INFO] chr12 total processed positions: 916, time elapsed: 2.1s
[INFO] chr12 total processed positions: 831, time elapsed: 2.0s
[INFO] chr12 total processed positions: 931, time elapsed: 2.2s
[INFO] chr12 total processed positions: 900, time elapsed: 2.4s
[INFO] chr12 total processed positions: 978, time elapsed: 2.4s
[INFO] chr12 total processed positions: 981, time elapsed: 2.4s
[INFO] chr12 total processed positions: 1113, time elapsed: 2.4s
[INFO] chr12 total processed positions: 1006, time elapsed: 2.7s
[INFO] chr12 total processed positions: 913, time elapsed: 2.4s
[INFO] chr12 total processed positions: 1138, time elapsed: 2.6s
[INFO] chr12 total processed positions: 1123, time elapsed: 2.7s
[INFO] chr12 total processed positions: 1357, time elapsed: 3.1s
[INFO] chr12 total processed positions: 1236, time elapsed: 2.7s
[INFO] chr12 total processed positions: 1211, time elapsed: 2.8s
[INFO] chr12 total processed positions: 1517, time elapsed: 3.2s
[INFO] chr12 total processed positions: 1371, time elapsed: 3.0s
[INFO] chr12 total processed positions: 1424, time elapsed: 3.1s

[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/part7/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --vcf_fn_prefix indel_p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_pileup.vcf

[INFO] Sorting VCFs...
[INFO] Finished VCF sorting!

[INFO] STEP 7: Indel 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/part7/logs/parallel_7-1_create_pair_tensor_fa_indel.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/part7/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/part7/tmp/fa_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/7-1_CPTI.log

[INFO] chr12  Tensors generated: 425
[INFO] chr12  Tensors generated: 729
[INFO] chr12  Tensors generated: 750
[INFO] chr12  Tensors generated: 1236
[INFO] chr12  Tensors generated: 748
[INFO] chr12  Tensors generated: 1211
[INFO] chr12  Tensors generated: 788
[INFO] chr12  Tensors generated: 782
[INFO] chr12  Tensors generated: 831
[INFO] chr12  Tensors generated: 816
[INFO] chr12  Tensors generated: 858
[INFO] chr12  Tensors generated: 890
[INFO] chr12  Tensors generated: 1424
[INFO] chr12  Tensors generated: 900
[INFO] chr12  Tensors generated: 916
[INFO] chr12  Tensors generated: 931
[INFO] chr12  Tensors generated: 913
[INFO] chr12  Tensors generated: 1006
[INFO] chr12  Tensors generated: 962
[INFO] chr12  Tensors generated: 978
[INFO] chr12  Tensors generated: 981
[INFO] chr12  Tensors generated: 1112
[INFO] chr12  Tensors generated: 1123
[INFO] chr12  Tensors generated: 1138
[INFO] chr12  Tensors generated: 1357
[INFO] chr12  Tensors generated: 1371
[INFO] chr12  Tensors generated: 1517

[INFO] Indel Full-alignment Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/parallel_7-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/fa_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --enable_indel_calling True  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/7-2_PREDICT_INDEL.log

[INFO] chr12 total processed positions: 425, time elapsed: 53.4s
[INFO] chr12 total processed positions: 729, time elapsed: 83.3s
[INFO] chr12 total processed positions: 750, time elapsed: 85.7s
[INFO] chr12 total processed positions: 748, time elapsed: 87.5s
[INFO] chr12 total processed positions: 788, time elapsed: 89.9s
[INFO] chr12 total processed positions: 782, time elapsed: 95.2s
[INFO] chr12 total processed positions: 816, time elapsed: 97.1s
[INFO] chr12 total processed positions: 831, time elapsed: 101.4s
[INFO] chr12 total processed positions: 916, time elapsed: 105.7s
[INFO] chr12 total processed positions: 900, time elapsed: 106.1s
[INFO] chr12 total processed positions: 858, time elapsed: 106.5s
[INFO] chr12 total processed positions: 890, time elapsed: 106.7s
[INFO] chr12 total processed positions: 931, time elapsed: 108.3s
[INFO] chr12 total processed positions: 913, time elapsed: 110.0s
[INFO] chr12 total processed positions: 962, time elapsed: 112.2s
[INFO] chr12 total processed positions: 981, time elapsed: 115.5s
[INFO] chr12 total processed positions: 978, time elapsed: 115.8s
[INFO] chr12 total processed positions: 1006, time elapsed: 119.8s
[INFO] chr12 total processed positions: 1123, time elapsed: 129.9s
[INFO] chr12 total processed positions: 1112, time elapsed: 130.7s
[INFO] chr12 total processed positions: 1138, time elapsed: 131.7s
[INFO] chr12 total processed positions: 1211, time elapsed: 144.9s
[INFO] chr12 total processed positions: 1236, time elapsed: 155.4s
[INFO] chr12 total processed positions: 1357, time elapsed: 158.8s
[INFO] chr12 total processed positions: 1371, time elapsed: 160.5s
[INFO] chr12 total processed positions: 1517, time elapsed: 171.4s
[INFO] chr12 total processed positions: 1424, time elapsed: 172.8s

[INFO] Merge Full-alignment 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/part7/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --vcf_fn_prefix indel_fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_full_alignment.vcf

[INFO] Sorting VCFs...
[INFO] Finished VCF sorting!

[INFO] Indel Haplotype filtering
[INFO] RUN THE FOLLOWING COMMAND:
( pypy3 /opt/bin/clairs.py haplotype_filtering --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/phased_output/tumor_ --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --germline_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 --is_indel  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/8_INDEL_HAP_FILTER.log

Total input calls: 2224, filtered by haplotype match 22

[INFO] STEP 8: Merge and sort Indel VCF
[INFO] RUN THE FOLLOWING COMMAND:
( pypy3 /opt/bin/clairs.py merge_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/vcf_output/indel_full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/indel.vcf --platform ont --qual 8 --sample_name CHAHA_diag --enable_indel_calling True --indel_calling  --prefer_recall False --cmdline /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/logs/8_MVI.log

[INFO] Full-alignment variants filtered by pileup:  256

[INFO] Total time elapsed: 47m44.00s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/output.vcf.gz

[INFO] Finish calling, snv output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/snv.vcf.gz

[INFO] Finish calling, indel output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/indel.vcf.gz

[INFO] Finish calling, Clair3 tumor BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/clair3_tumor_germline_output.vcf.gz

[INFO] Finish calling, Clair3 normal BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/clair3_normal_germline_output.vcf.gz

cp /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part7/clair3_tumor_germline_output.vcf.gz
slurmstepd: error: Detected 24 oom_kill events in StepId=2556285.batch. Some of the step tasks have been OOM Killed.

----------------------------------------------
|                SLURM EPILOG                |
----------------------------------------------
Job ID: 2556285
Cluster: flamingo
User/Group: t_steimle/gs_hpc_biopath
Nodelist: n01
Nodes: 1
Cores per node: 40
Job started at: 2025-12-08 15:36:00
Job ended at:   2025-12-08 16:23:46
Job Wall-clock time: 00:47:46
CPU Utilized: 07:37:54
CPU Efficiency: 23.97% of 1-07:50:40 core-walltime
Memory Utilized: 38.49 GB
Memory Efficiency: 96.23% of 40.00 GB