pandora_lib_promethion/slurm-2556289.out

WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22': 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/part22 --region chr20:1-27012963 --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/part22/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chr20
[INFO] Number of chunks for each contig: 14

[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/part22
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chr20:1-27012963
[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/part22/tmp/clair3_output/clair3_normal_output --ctg_name=chr20 --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/part22/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/part22/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr20
[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/part22/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr20 --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/part22/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr20
[INFO] Chunk number for each contig: 14
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr20 (chunk 6/14) : 49610
Total time elapsed: 90.94 s
Calling variants ...
Total processed positions in chr20 (chunk 3/14) : 78073
Total time elapsed: 125.83 s
Calling variants ...
Total processed positions in chr20 (chunk 2/14) : 76976
Total time elapsed: 126.84 s
Calling variants ...
Total processed positions in chr20 (chunk 8/14) : 79273
Total time elapsed: 129.36 s
Calling variants ...
Total processed positions in chr20 (chunk 4/14) : 79660
Total time elapsed: 129.80 s
Calling variants ...
Total processed positions in chr20 (chunk 5/14) : 77255
Total time elapsed: 131.21 s
Calling variants ...
Total processed positions in chr20 (chunk 7/14) : 75361
Total time elapsed: 131.45 s
Calling variants ...
Total processed positions in chr20 (chunk 9/14) : 81579
Total time elapsed: 133.29 s
Calling variants ...
Total processed positions in chr20 (chunk 11/14) : 84971
Total time elapsed: 137.57 s
Calling variants ...
Total processed positions in chr20 (chunk 1/14) : 83255
Total time elapsed: 138.84 s
Calling variants ...
Total processed positions in chr20 (chunk 13/14) : 85068
Total time elapsed: 139.19 s
Calling variants ...
Total processed positions in chr20 (chunk 12/14) : 85050
Total time elapsed: 141.22 s
Calling variants ...
Total processed positions in chr20 (chunk 10/14) : 84512
Total time elapsed: 141.50 s
Calling variants ...
Total processed positions in chr20 (chunk 14/14) : 92564
Total time elapsed: 144.24 s

real	2m30.596s
user	29m39.254s
sys	1m19.921s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15
[INFO] Total heterozygous SNP positions selected: chr20: 45551

real	0m1.782s
user	0m1.627s
sys	0m0.118s

[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/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr20.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/part22/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr20
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 ... 1s
(chr20,4s)
parsing total:  4s
merge results ... 0s
writeResult SNP ... 1s

total process: 6s

real	0m5.682s
user	0m10.592s
sys	0m0.850s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 19.0
[INFO] Set reference calls quality cutoff 13.0
[INFO] Low quality reference calls to be processed in chr20: 99183
[INFO] Low quality variants to be processed in chr20: 84562

real	0m2.034s
user	0m1.780s
sys	0m0.192s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr20 (chunk 19/19) : 3745
Total time elapsed: 41.35 s
Calling variants ...
Total processed positions in chr20 (chunk 14/19) : 10000
Total time elapsed: 95.62 s
Calling variants ...
Total processed positions in chr20 (chunk 11/19) : 10000
Total time elapsed: 99.19 s
Calling variants ...
Total processed positions in chr20 (chunk 9/19) : 10000
Total time elapsed: 99.86 s
Calling variants ...
Total processed positions in chr20 (chunk 13/19) : 10000
Total time elapsed: 101.51 s
Calling variants ...
Total processed positions in chr20 (chunk 4/19) : 10000
Total time elapsed: 102.27 s
Calling variants ...
Total processed positions in chr20 (chunk 2/19) : 10000
Total time elapsed: 102.14 s
Calling variants ...
Total processed positions in chr20 (chunk 17/19) : 10000
Total time elapsed: 102.57 s
Calling variants ...
Total processed positions in chr20 (chunk 15/19) : 10000
Total time elapsed: 102.86 s
Calling variants ...
Total processed positions in chr20 (chunk 10/19) : 10000
Total time elapsed: 102.14 s
Calling variants ...
Total processed positions in chr20 (chunk 8/19) : 10000
Total time elapsed: 102.25 s
Calling variants ...
Total processed positions in chr20 (chunk 1/19) : 10000
Total time elapsed: 103.03 s
Calling variants ...
Total processed positions in chr20 (chunk 5/19) : 10000
Total time elapsed: 104.46 s
Calling variants ...
Total processed positions in chr20 (chunk 6/19) : 10000
Total time elapsed: 104.69 s
Calling variants ...
Total processed positions in chr20 (chunk 7/19) : 10000
Total time elapsed: 104.23 s
Calling variants ...
Total processed positions in chr20 (chunk 18/19) : 10000
Total time elapsed: 104.54 s
Calling variants ...
Total processed positions in chr20 (chunk 16/19) : 10000
Total time elapsed: 105.26 s
Calling variants ...
Total processed positions in chr20 (chunk 12/19) : 10000
Total time elapsed: 107.25 s
Calling variants ...
Total processed positions in chr20 (chunk 3/19) : 10000
Total time elapsed: 108.64 s

real	1m52.186s
user	30m40.864s
sys	1m38.953s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr20: 36358
[INFO] Full-alignment variants processed in chr20: 87253

real	0m2.457s
user	0m2.727s
sys	0m0.200s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz

real	4m45.880s
user	60m46.687s
sys	3m1.485s

[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/part22/tmp/clair3_output/clair3_tumor_output --ctg_name=chr20 --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/part22/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/part22/tmp/clair3_output/clair3_tumor_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr20
[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/part22/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr20 --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/part22/tmp/clair3_output/clair3_tumor_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr20
[INFO] Chunk number for each contig: 14
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr20 (chunk 12/14) : 9736
Total time elapsed: 53.63 s
Calling variants ...
Total processed positions in chr20 (chunk 5/14) : 8465
Total time elapsed: 53.96 s
Calling variants ...
Total processed positions in chr20 (chunk 9/14) : 8456
Total time elapsed: 54.09 s
Calling variants ...
Total processed positions in chr20 (chunk 3/14) : 9839
Total time elapsed: 55.44 s
Calling variants ...
Total processed positions in chr20 (chunk 2/14) : 9407
Total time elapsed: 55.96 s
Calling variants ...
Total processed positions in chr20 (chunk 8/14) : 9125
Total time elapsed: 56.09 s
Calling variants ...
Total processed positions in chr20 (chunk 10/14) : 9956
Total time elapsed: 56.82 s
Calling variants ...
Total processed positions in chr20 (chunk 13/14) : 11784
Total time elapsed: 57.14 s
Calling variants ...
Total processed positions in chr20 (chunk 4/14) : 10680
Total time elapsed: 57.59 s
Calling variants ...
Total processed positions in chr20 (chunk 11/14) : 12944
Total time elapsed: 60.10 s
Calling variants ...
Total processed positions in chr20 (chunk 14/14) : 17216
Total time elapsed: 66.58 s
Calling variants ...
Total processed positions in chr20 (chunk 1/14) : 17838
Total time elapsed: 66.97 s
Calling variants ...
Total processed positions in chr20 (chunk 6/14) : 17711
Total time elapsed: 69.12 s
Calling variants ...
Total processed positions in chr20 (chunk 7/14) : 53609
Total time elapsed: 112.80 s

real	1m55.654s
user	11m9.215s
sys	0m54.337s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19
[INFO] Total heterozygous SNP positions selected: chr20: 45273

real	0m0.721s
user	0m0.593s
sys	0m0.103s

[INFO] 3/7 Phase VCF file using LongPhase
LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr20.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/part22/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr20
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 ... 1s
(chr20,20s)
parsing total:  20s
merge results ... 0s
writeResult SNP ... 1s

total process: 22s

real	0m21.693s
user	0m53.644s
sys	0m3.527s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 21.0
[INFO] Set reference calls quality cutoff 8.0
[INFO] Low quality reference calls to be processed in chr20: 8756
[INFO] Low quality variants to be processed in chr20: 83160

real	0m0.744s
user	0m0.573s
sys	0m0.119s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr20 (chunk 10/10) : 1916
Total time elapsed: 25.36 s
Calling variants ...
Total processed positions in chr20 (chunk 5/10) : 10000
Total time elapsed: 96.98 s
Calling variants ...
Total processed positions in chr20 (chunk 4/10) : 10000
Total time elapsed: 109.94 s
Calling variants ...
Total processed positions in chr20 (chunk 1/10) : 10000
Total time elapsed: 113.66 s
Calling variants ...
Total processed positions in chr20 (chunk 7/10) : 10000
Total time elapsed: 115.35 s
Calling variants ...
Total processed positions in chr20 (chunk 9/10) : 10000
Total time elapsed: 117.39 s
Calling variants ...
Total processed positions in chr20 (chunk 8/10) : 10000
Total time elapsed: 117.62 s
Calling variants ...
Total processed positions in chr20 (chunk 6/10) : 10000
Total time elapsed: 120.35 s
Calling variants ...
Total processed positions in chr20 (chunk 3/10) : 10000
Total time elapsed: 122.99 s
Calling variants ...
Total processed positions in chr20 (chunk 2/10) : 10000
Total time elapsed: 123.58 s

real	2m6.084s
user	16m42.289s
sys	0m51.652s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr20: 35964
[INFO] Full-alignment variants processed in chr20: 74344

real	0m1.091s
user	0m1.090s
sys	0m0.122s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz

real	4m30.742s
user	28m51.125s
sys	1m50.480s

[INFO] Select Heterozygous SNP for Phasing
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/1_select_hetero_snp_for_phasing.log

[INFO] Total HET SNP calls selected: chr20: 57143, not found:460, not match:37, low_qual_count:0. Total normal:61825 Total tumor:57640, pro: 0.9914

[INFO] Phase the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/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/part22/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS

LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/vcf/chr20.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/part22/tmp/clair3_output/phased_output/tumor_phased_chr20
Generate Dot  : False
BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 

--- Phasing Parameter --- 
Seq Platform       : ONT
Phase Indel        : False
Distance Threshold : 300000
Connect Adjacent   : 20
Edge Threshold     : 0.7
Mapping Quality    : 1
Variant Confidence : 0.75
ReadTag Confidence : 0.65

parsing VCF ... 0s
parsing SV VCF ... 0s
parsing Meth VCF ... 0s
reading reference ... 0s
(chr20,30s)
parsing total:  30s
merge results ... 0s
writeResult SNP ... 0s

total process: 30s

[INFO] Haplotag the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/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/part22/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/part22/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/CONTIGS

phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/phased_output/tumor_phased_chr20.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/part22/tmp/clair3_output/phased_output/tumor_chr20.bam
number of threads: 1
write log file:    false
log file:          
-------------------------------------------
tag region:                    chr20
filter mapping quality below:  1
percentage threshold:          0.6
tag supplementary:             false
-------------------------------------------
parsing SNP VCF ... 0s
tag read start ...
chr: chr20 ... 666s
tag read 667s
-------------------------------------------
total process time:  667s
total alignment:     784888
total supplementary: 30142
total secondary:     0
total unmapped:      0
total tag alignment: 403864
total untagged:      381024

[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/part22/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/part22/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 

[INFO] chr20 chunk 13/14: Total snv candidates found: 2265, total indel candidates found: 352
[INFO] chr20 chunk 3/14: Total snv candidates found: 201, total indel candidates found: 432
[INFO] chr20 chunk 0/14: Total snv candidates found: 2422, total indel candidates found: 1064
[INFO] chr20 chunk 12/14: Total snv candidates found: 317, total indel candidates found: 393
[INFO] chr20 chunk 10/14: Total snv candidates found: 302, total indel candidates found: 412
[INFO] chr20 chunk 2/14: Total snv candidates found: 544, total indel candidates found: 668
[INFO] chr20 chunk 8/14: Total snv candidates found: 429, total indel candidates found: 383
[INFO] chr20 chunk 9/14: Total snv candidates found: 328, total indel candidates found: 507
[INFO] chr20 chunk 6/14: Total snv candidates found: 225, total indel candidates found: 366
[INFO] chr20 chunk 11/14: Total snv candidates found: 221, total indel candidates found: 467
[INFO] chr20 chunk 5/14: Total snv candidates found: 271, total indel candidates found: 392
[INFO] chr20 chunk 4/14: Total snv candidates found: 166, total indel candidates found: 403
[INFO] chr20 chunk 1/14: Total snv candidates found: 484, total indel candidates found: 710
[INFO] chr20 chunk 7/14: Total snv candidates found: 126, total indel candidates found: 410

[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/part22/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/part22/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/2-1_CPT.log

[INFO] chr20 chunk 1-1/4 Tensors generated: 166
[INFO] chr20 chunk 1-1/7 Tensors generated: 126
[INFO] chr20 chunk 1-1/11 Tensors generated: 215
[INFO] chr20 chunk 1-1/6 Tensors generated: 225
[INFO] chr20 chunk 1-1/3 Tensors generated: 200
[INFO] chr20 chunk 1-1/1 Tensors generated: 484
[INFO] chr20 chunk 1-1/5 Tensors generated: 271
[INFO] chr20 chunk 1-1/10 Tensors generated: 302
[INFO] chr20 chunk 1-1/2 Tensors generated: 537
[INFO] chr20 chunk 1-1/12 Tensors generated: 317
[INFO] chr20 chunk 1-1/9 Tensors generated: 328
[INFO] chr20 chunk 1-1/8 Tensors generated: 428
[INFO] chr20 chunk 1-1/0 Tensors generated: 2421
[INFO] chr20 chunk 1-1/13 Tensors generated: 2234

[INFO] Pileup Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/2-2_PREDICT.log

[INFO] chr20 total processed positions: 126, time elapsed: 0.7s
[INFO] chr20 total processed positions: 166, time elapsed: 0.4s
[INFO] chr20 total processed positions: 200, time elapsed: 0.5s
[INFO] chr20 total processed positions: 215, time elapsed: 0.4s
[INFO] chr20 total processed positions: 225, time elapsed: 0.7s
[INFO] chr20 total processed positions: 317, time elapsed: 0.9s
[INFO] chr20 total processed positions: 328, time elapsed: 0.7s
[INFO] chr20 total processed positions: 271, time elapsed: 0.5s
[INFO] chr20 total processed positions: 428, time elapsed: 0.9s
[INFO] chr20 total processed positions: 302, time elapsed: 0.6s
[INFO] chr20 total processed positions: 484, time elapsed: 0.9s
[INFO] chr20 total processed positions: 537, time elapsed: 1.2s
[INFO] chr20 total processed positions: 2234, time elapsed: 3.6s
[INFO] chr20 total processed positions: 2421, time elapsed: 4.1s

[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/part22/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/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/part22/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/part22/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/3-1_CPT.log

[INFO] chr20 chunk 1-1/7 Tensors generated: 126
[INFO] chr20 chunk 1-1/4 Tensors generated: 166
[INFO] chr20 chunk 1-1/3 Tensors generated: 200
[INFO] chr20 chunk 1-1/6 Tensors generated: 225
[INFO] chr20 chunk 1-1/11 Tensors generated: 215
[INFO] chr20 chunk 1-1/10 Tensors generated: 302
[INFO] chr20 chunk 1-1/5 Tensors generated: 271
[INFO] chr20 chunk 1-1/9 Tensors generated: 328
[INFO] chr20 chunk 1-1/12 Tensors generated: 317
[INFO] chr20 chunk 1-1/1 Tensors generated: 484
[INFO] chr20 chunk 1-1/2 Tensors generated: 537
[INFO] chr20 chunk 1-1/8 Tensors generated: 428
[INFO] chr20 chunk 1-1/13 Tensors generated: 2150
[INFO] chr20 chunk 1-1/0 Tensors generated: 2421

[INFO] Full-alignment Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/3-2_PREDICT.log

[INFO] chr20 total processed positions: 126, time elapsed: 23.1s
[INFO] chr20 total processed positions: 166, time elapsed: 29.9s
[INFO] chr20 total processed positions: 200, time elapsed: 35.6s
[INFO] chr20 total processed positions: 215, time elapsed: 38.1s
[INFO] chr20 total processed positions: 225, time elapsed: 39.7s
[INFO] chr20 total processed positions: 271, time elapsed: 48.8s
[INFO] chr20 total processed positions: 302, time elapsed: 54.7s
[INFO] chr20 total processed positions: 317, time elapsed: 56.1s
[INFO] chr20 total processed positions: 328, time elapsed: 58.7s
[INFO] chr20 total processed positions: 428, time elapsed: 75.6s
[INFO] chr20 total processed positions: 484, time elapsed: 85.6s
[INFO] chr20 total processed positions: 537, time elapsed: 95.0s
[INFO] chr20 total processed positions: 2150, time elapsed: 379.7s
[INFO] chr20 total processed positions: 2421, time elapsed: 427.3s

[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/part22/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --vcf_fn_prefix fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/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/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --samtools samtools --pypy3 pypy3 --parallel parallel --threads 40 ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/4_HAP_FILTER.log

Total input calls: 1929, filtered by haplotype match 5

[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/part22/tmp/vcf_output/pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/5_MV.log

[INFO] Full-alignment variants filtered by pileup:  176

[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/part22/tmp/candidates --input_prefix INDEL_CANDIDATES_FILE_ --output_fn INDEL_CANDIDATES_FILES  && ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/pileup_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/6-1_CPTI.log

[INFO] chr20  Tensors generated: 0
[INFO] chr20  Tensors generated: 349
[INFO] chr20  Tensors generated: 708
[INFO] chr20  Tensors generated: 393
[INFO] chr20  Tensors generated: 668
[INFO] chr20  Tensors generated: 411
[INFO] chr20  Tensors generated: 392
[INFO] chr20  Tensors generated: 383
[INFO] chr20  Tensors generated: 403
[INFO] chr20  Tensors generated: 366
[INFO] chr20  Tensors generated: 410
[INFO] chr20  Tensors generated: 459
[INFO] chr20  Tensors generated: 507
[INFO] chr20  Tensors generated: 431

[INFO] Indel Pileup Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/pileup_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/6-2_PREDICT_INDEL.log

[INFO] chr20 total processed positions: 0, time elapsed: 0.1s
[INFO] No variant output for indel_p_chr20.0_0_1_indel.vcf, remove empty VCF
[INFO] chr20 total processed positions: 383, time elapsed: 0.7s
[INFO] chr20 total processed positions: 403, time elapsed: 0.9s
[INFO] chr20 total processed positions: 410, time elapsed: 0.8s
[INFO] chr20 total processed positions: 349, time elapsed: 0.7s
[INFO] chr20 total processed positions: 431, time elapsed: 0.9s
[INFO] chr20 total processed positions: 393, time elapsed: 0.8s
[INFO] chr20 total processed positions: 366, time elapsed: 0.7s
[INFO] chr20 total processed positions: 507, time elapsed: 1.0s
[INFO] chr20 total processed positions: 392, time elapsed: 0.8s
[INFO] chr20 total processed positions: 411, time elapsed: 0.8s
[INFO] chr20 total processed positions: 668, time elapsed: 1.2s
[INFO] chr20 total processed positions: 459, time elapsed: 1.0s
[INFO] chr20 total processed positions: 708, time elapsed: 1.3s

[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/part22/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --vcf_fn_prefix indel_p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/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/part22/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/part22/tmp/fa_tensor_can/indel_{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/7-1_CPTI.log

[INFO] chr20  Tensors generated: 0
[INFO] chr20  Tensors generated: 348
[INFO] chr20  Tensors generated: 366
[INFO] chr20  Tensors generated: 383
[INFO] chr20  Tensors generated: 411
[INFO] chr20  Tensors generated: 392
[INFO] chr20  Tensors generated: 410
[INFO] chr20  Tensors generated: 403
[INFO] chr20  Tensors generated: 393
[INFO] chr20  Tensors generated: 431
[INFO] chr20  Tensors generated: 459
[INFO] chr20  Tensors generated: 507
[INFO] chr20  Tensors generated: 708
[INFO] chr20  Tensors generated: 668

[INFO] Indel Full-alignment Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/fa_tensor_can/indel_{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/candidates/INDEL_CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/7-2_PREDICT_INDEL.log

[INFO] chr20 total processed positions: 0, time elapsed: 0.0s
[INFO] No variant output for indel_fa_chr20.0_0_1_indel.vcf, remove empty VCF
[INFO] chr20 total processed positions: 348, time elapsed: 59.2s
[INFO] chr20 total processed positions: 366, time elapsed: 62.4s
[INFO] chr20 total processed positions: 383, time elapsed: 65.0s
[INFO] chr20 total processed positions: 392, time elapsed: 66.6s
[INFO] chr20 total processed positions: 393, time elapsed: 66.6s
[INFO] chr20 total processed positions: 403, time elapsed: 68.2s
[INFO] chr20 total processed positions: 410, time elapsed: 69.7s
[INFO] chr20 total processed positions: 411, time elapsed: 70.1s
[INFO] chr20 total processed positions: 431, time elapsed: 74.2s
[INFO] chr20 total processed positions: 459, time elapsed: 78.8s
[INFO] chr20 total processed positions: 507, time elapsed: 85.5s
[INFO] chr20 total processed positions: 668, time elapsed: 112.5s
[INFO] chr20 total processed positions: 708, time elapsed: 118.7s

[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/part22/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output --vcf_fn_prefix indel_fa_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/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/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --pileup_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_pileup.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_full_alignment.vcf --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/logs/8_INDEL_HAP_FILTER.log

Total input calls: 486, filtered by haplotype match 3

[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/part22/tmp/vcf_output/indel_pileup_filter.vcf --full_alignment_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/vcf_output/indel_full_alignment_filter.vcf --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/tmp/CMD ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/logs/8_MVI.log

[INFO] Full-alignment variants filtered by pileup:  47

[INFO] Total time elapsed: 32m19.00s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/output.vcf.gz

[INFO] Finish calling, snv output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/snv.vcf.gz

[INFO] Finish calling, indel output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/indel.vcf.gz

[INFO] Finish calling, Clair3 tumor BAM germline output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/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/part22/clair3_normal_germline_output.vcf.gz

cp /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part22/clair3_tumor_germline_output.vcf.gz

----------------------------------------------
|                SLURM EPILOG                |
----------------------------------------------
Job ID: 2556289
Cluster: flamingo
User/Group: t_steimle/gs_hpc_biopath
Nodelist: n17
Nodes: 1
Cores per node: 40
Job started at: 2025-12-08 16:10:07
Job ended at:   2025-12-08 16:42:28
Job Wall-clock time: 00:32:21
CPU Utilized: 02:57:02
CPU Efficiency: 13.68% of 21:34:00 core-walltime
Memory Utilized: 22.24 GB
Memory Efficiency: 55.60% of 40.00 GB