pandora_lib_promethion/slurm-2557978.out

WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40': 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/part40 --region chr9:55624206-150617247 --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/part40/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chr9
[INFO] Number of chunks for each contig: 31

[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/part40
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/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/part40/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chr9:55624206-150617247
[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/part40/tmp/clair3_output/clair3_normal_output --ctg_name=chr9 --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/part40/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/part40/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr9
[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/part40/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr9 --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/part40/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr9
[INFO] Chunk number for each contig: 31
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr9 (chunk 12/31) : 1257
Total time elapsed: 17.96 s
Calling variants ...
Total processed positions in chr9 (chunk 13/31) : 2641
Total time elapsed: 20.38 s
Calling variants ...
Total processed positions in chr9 (chunk 15/31) : 17476
Total time elapsed: 48.85 s
Calling variants ...
Total processed positions in chr9 (chunk 14/31) : 21538
Total time elapsed: 53.60 s
Calling variants ...
Total processed positions in chr9 (chunk 10/31) : 33522
Total time elapsed: 78.54 s
Calling variants ...
Total processed positions in chr9 (chunk 11/31) : 37053
Total time elapsed: 86.05 s
Calling variants ...
Total processed positions in chr9 (chunk 16/31) : 56455
Total time elapsed: 119.76 s
Calling variants ...
Total processed positions in chr9 (chunk 17/31) : 62283
Total time elapsed: 127.62 s
Calling variants ...
Total processed positions in chr9 (chunk 9/31) : 63514
Total time elapsed: 131.78 s
Calling variants ...
Total processed positions in chr9 (chunk 3/31) : 71362
Total time elapsed: 135.99 s
Calling variants ...
Total processed positions in chr9 (chunk 5/31) : 74395
Total time elapsed: 139.66 s
Calling variants ...
Total processed positions in chr9 (chunk 24/31) : 79394
Total time elapsed: 141.54 s
Calling variants ...
Total processed positions in chr9 (chunk 29/31) : 78305
Total time elapsed: 142.68 s
Calling variants ...
Total processed positions in chr9 (chunk 7/31) : 76859
Total time elapsed: 143.38 s
Calling variants ...
Total processed positions in chr9 (chunk 8/31) : 79476
Total time elapsed: 144.97 s
Calling variants ...
Total processed positions in chr9 (chunk 25/31) : 76301
Total time elapsed: 145.07 s
Calling variants ...
Total processed positions in chr9 (chunk 6/31) : 72961
Total time elapsed: 146.47 s
Calling variants ...
Total processed positions in chr9 (chunk 26/31) : 82443
Total time elapsed: 148.27 s
Calling variants ...
Total processed positions in chr9 (chunk 20/31) : 75744
Total time elapsed: 148.83 s
Calling variants ...
Total processed positions in chr9 (chunk 23/31) : 81576
Total time elapsed: 150.46 s
Calling variants ...
Total processed positions in chr9 (chunk 2/31) : 77468
Total time elapsed: 151.04 s
Calling variants ...
Total processed positions in chr9 (chunk 4/31) : 76648
Total time elapsed: 151.73 s
Calling variants ...
Total processed positions in chr9 (chunk 22/31) : 81615
Total time elapsed: 154.06 s
Calling variants ...
Total processed positions in chr9 (chunk 19/31) : 78752
Total time elapsed: 154.05 s
Calling variants ...
Total processed positions in chr9 (chunk 28/31) : 79687
Total time elapsed: 155.51 s
Calling variants ...
Total processed positions in chr9 (chunk 18/31) : 77860
Total time elapsed: 155.64 s
Calling variants ...
Total processed positions in chr9 (chunk 27/31) : 81764
Total time elapsed: 157.11 s
Calling variants ...
Total processed positions in chr9 (chunk 1/31) : 85324
Total time elapsed: 159.15 s
Calling variants ...
Total processed positions in chr9 (chunk 30/31) : 88072
Total time elapsed: 162.12 s
Calling variants ...
Total processed positions in chr9 (chunk 21/31) : 89341
Total time elapsed: 152.60 s
Calling variants ...
Total processed positions in chr9 (chunk 31/31) : 95505
Total time elapsed: 155.05 s

real	3m4.784s
user	62m4.077s
sys	3m33.310s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
[INFO] Total heterozygous SNP positions selected: chr9: 77784

real	0m4.754s
user	0m4.489s
sys	0m0.192s

[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/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr9.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/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr9
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
(chr9,10s)
parsing total:  10s
merge results ... 0s
writeResult SNP ... 0s

total process: 12s

real	0m12.323s
user	0m23.247s
sys	0m1.686s

[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 chr9: 181543
[INFO] Low quality variants to be processed in chr9: 165238

real	0m5.203s
user	0m4.807s
sys	0m0.313s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr9 (chunk 19/35) : 10000
Total time elapsed: 92.62 s
Calling variants ...
Total processed positions in chr9 (chunk 17/35) : 10000
Total time elapsed: 96.32 s
Calling variants ...
Total processed positions in chr9 (chunk 29/35) : 10000
Total time elapsed: 96.61 s
Calling variants ...
Total processed positions in chr9 (chunk 2/35) : 10000
Total time elapsed: 96.49 s
Calling variants ...
Total processed positions in chr9 (chunk 26/35) : 10000
Total time elapsed: 98.14 s
Calling variants ...
Total processed positions in chr9 (chunk 10/35) : 10000
Total time elapsed: 98.23 s
Calling variants ...
Total processed positions in chr9 (chunk 7/35) : 10000
Total time elapsed: 98.31 s
Calling variants ...
Total processed positions in chr9 (chunk 1/35) : 10000
Total time elapsed: 102.22 s
Calling variants ...
Total processed positions in chr9 (chunk 30/35) : 10000
Total time elapsed: 102.47 s
Calling variants ...
Total processed positions in chr9 (chunk 25/35) : 10000
Total time elapsed: 102.89 s
Calling variants ...
Total processed positions in chr9 (chunk 4/35) : 10000
Total time elapsed: 103.42 s
Calling variants ...
Total processed positions in chr9 (chunk 23/35) : 10000
Total time elapsed: 103.94 s
Calling variants ...
Total processed positions in chr9 (chunk 28/35) : 10000
Total time elapsed: 104.38 s
Calling variants ...
Total processed positions in chr9 (chunk 6/35) : 10000
Total time elapsed: 104.32 s
Calling variants ...
Total processed positions in chr9 (chunk 3/35) : 10000
Total time elapsed: 104.69 s
Calling variants ...
Total processed positions in chr9 (chunk 20/35) : 10000
Total time elapsed: 104.80 s
Calling variants ...
Total processed positions in chr9 (chunk 15/35) : 10000
Total time elapsed: 105.81 s
Calling variants ...
Total processed positions in chr9 (chunk 24/35) : 10000
Total time elapsed: 106.00 s
Calling variants ...
Total processed positions in chr9 (chunk 12/35) : 10000
Total time elapsed: 106.02 s
Calling variants ...
Total processed positions in chr9 (chunk 18/35) : 10000
Total time elapsed: 106.35 s
Calling variants ...
Total processed positions in chr9 (chunk 16/35) : 10000
Total time elapsed: 106.68 s
Calling variants ...
Total processed positions in chr9 (chunk 8/35) : 10000
Total time elapsed: 106.87 s
Calling variants ...
Total processed positions in chr9 (chunk 9/35) : 10000
Total time elapsed: 106.89 s
Calling variants ...
Total processed positions in chr9 (chunk 27/35) : 10000
Total time elapsed: 107.09 s
Calling variants ...
Total processed positions in chr9 (chunk 21/35) : 10000
Total time elapsed: 107.27 s
Calling variants ...
Total processed positions in chr9 (chunk 14/35) : 10000
Total time elapsed: 107.48 s
Calling variants ...
Total processed positions in chr9 (chunk 13/35) : 10000
Total time elapsed: 107.50 s
Calling variants ...
Total processed positions in chr9 (chunk 11/35) : 10000
Total time elapsed: 107.78 s
Calling variants ...
Total processed positions in chr9 (chunk 5/35) : 10000
Total time elapsed: 107.99 s
Calling variants ...
Total processed positions in chr9 (chunk 22/35) : 10000
Total time elapsed: 108.92 s
Calling variants ...
Total processed positions in chr9 (chunk 35/35) : 6781
Total time elapsed: 55.49 s
Calling variants ...
Total processed positions in chr9 (chunk 32/35) : 10000
Total time elapsed: 69.14 s
Calling variants ...
Total processed positions in chr9 (chunk 31/35) : 10000
Total time elapsed: 74.70 s
Calling variants ...
Total processed positions in chr9 (chunk 34/35) : 10000
Total time elapsed: 78.02 s
Calling variants ...
Total processed positions in chr9 (chunk 33/35) : 10000
Total time elapsed: 81.45 s

real	3m4.889s
user	55m57.941s
sys	3m16.335s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr9: 70909
[INFO] Full-alignment variants processed in chr9: 180962

real	0m6.255s
user	0m6.847s
sys	0m0.266s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz

real	7m3.909s
user	119m5.300s
sys	6m54.136s

[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/part40/tmp/clair3_output/clair3_tumor_output --ctg_name=chr9 --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/part40/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/part40/tmp/clair3_output/clair3_tumor_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr9
[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/part40/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr9 --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/part40/tmp/clair3_output/clair3_tumor_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr9
[INFO] Chunk number for each contig: 31
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr9 (chunk 12/31) : 3313
Total time elapsed: 63.75 s
Calling variants ...
Total processed positions in chr9 (chunk 13/31) : 9677
Total time elapsed: 75.54 s
Calling variants ...
Total processed positions in chr9 (chunk 8/31) : 8048
Total time elapsed: 76.99 s
Calling variants ...
Total processed positions in chr9 (chunk 5/31) : 8157
Total time elapsed: 78.17 s
Calling variants ...
Total processed positions in chr9 (chunk 18/31) : 8449
Total time elapsed: 78.96 s
Calling variants ...
Total processed positions in chr9 (chunk 23/31) : 9152
Total time elapsed: 80.13 s
Calling variants ...
Total processed positions in chr9 (chunk 27/31) : 10222
Total time elapsed: 80.37 s
Calling variants ...
Total processed positions in chr9 (chunk 9/31) : 7557
Total time elapsed: 81.04 s
Calling variants ...
Total processed positions in chr9 (chunk 19/31) : 11050
Total time elapsed: 81.73 s
Calling variants ...
Total processed positions in chr9 (chunk 4/31) : 11173
Total time elapsed: 81.98 s
Calling variants ...
Total processed positions in chr9 (chunk 6/31) : 10501
Total time elapsed: 82.23 s
Calling variants ...
Total processed positions in chr9 (chunk 20/31) : 11420
Total time elapsed: 83.61 s
Calling variants ...
Total processed positions in chr9 (chunk 24/31) : 11713
Total time elapsed: 84.00 s
Calling variants ...
Total processed positions in chr9 (chunk 26/31) : 12517
Total time elapsed: 84.11 s
Calling variants ...
Total processed positions in chr9 (chunk 2/31) : 13146
Total time elapsed: 86.25 s
Calling variants ...
Total processed positions in chr9 (chunk 17/31) : 11841
Total time elapsed: 87.22 s
Calling variants ...
Total processed positions in chr9 (chunk 1/31) : 15967
Total time elapsed: 89.50 s
Calling variants ...
Total processed positions in chr9 (chunk 15/31) : 22912
Total time elapsed: 93.68 s
Calling variants ...
Total processed positions in chr9 (chunk 28/31) : 6980
Total time elapsed: 47.43 s
Calling variants ...
Total processed positions in chr9 (chunk 7/31) : 10077
Total time elapsed: 48.37 s
Calling variants ...
Total processed positions in chr9 (chunk 29/31) : 8642
Total time elapsed: 49.57 s
Calling variants ...
Total processed positions in chr9 (chunk 3/31) : 9920
Total time elapsed: 49.92 s
Calling variants ...
Total processed positions in chr9 (chunk 25/31) : 9578
Total time elapsed: 50.63 s
Calling variants ...
Total processed positions in chr9 (chunk 22/31) : 12435
Total time elapsed: 51.57 s
Calling variants ...
Total processed positions in chr9 (chunk 11/31) : 40307
Total time elapsed: 115.89 s
Calling variants ...
Total processed positions in chr9 (chunk 30/31) : 12175
Total time elapsed: 53.41 s
Calling variants ...
Total processed positions in chr9 (chunk 21/31) : 11701
Total time elapsed: 54.40 s
Calling variants ...
Total processed positions in chr9 (chunk 10/31) : 17506
Total time elapsed: 58.44 s
Calling variants ...
Total processed positions in chr9 (chunk 31/31) : 16000
Total time elapsed: 55.65 s
Calling variants ...
Total processed positions in chr9 (chunk 14/31) : 27421
Total time elapsed: 65.13 s
Calling variants ...
Total processed positions in chr9 (chunk 16/31) : 56368
Total time elapsed: 141.70 s

real	2m25.563s
user	26m45.350s
sys	3m12.482s

[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: chr9: 77791

real	0m1.682s
user	0m1.459s
sys	0m0.151s

[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/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr9.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/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr9
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
(chr9,45s)
parsing total:  45s
merge results ... 0s
writeResult SNP ... 1s

total process: 48s

real	0m47.622s
user	1m39.107s
sys	0m6.712s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 22.0
[INFO] Set reference calls quality cutoff 8.0
[INFO] Low quality reference calls to be processed in chr9: 19049
[INFO] Low quality variants to be processed in chr9: 171149

real	0m1.655s
user	0m1.429s
sys	0m0.187s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr9 (chunk 20/20) : 198
Total time elapsed: 5.14 s
Calling variants ...
Total processed positions in chr9 (chunk 9/20) : 10000
Total time elapsed: 103.97 s
Calling variants ...
Total processed positions in chr9 (chunk 6/20) : 10000
Total time elapsed: 106.05 s
Calling variants ...
Total processed positions in chr9 (chunk 1/20) : 10000
Total time elapsed: 108.09 s
Calling variants ...
Total processed positions in chr9 (chunk 8/20) : 10000
Total time elapsed: 109.62 s
Calling variants ...
Total processed positions in chr9 (chunk 2/20) : 10000
Total time elapsed: 112.64 s
Calling variants ...
Total processed positions in chr9 (chunk 3/20) : 10000
Total time elapsed: 115.34 s
Calling variants ...
Total processed positions in chr9 (chunk 19/20) : 10000
Total time elapsed: 118.04 s
Calling variants ...
Total processed positions in chr9 (chunk 13/20) : 10000
Total time elapsed: 118.74 s
Calling variants ...
Total processed positions in chr9 (chunk 17/20) : 10000
Total time elapsed: 119.76 s
Calling variants ...
Total processed positions in chr9 (chunk 10/20) : 10000
Total time elapsed: 119.63 s
Calling variants ...
Total processed positions in chr9 (chunk 14/20) : 10000
Total time elapsed: 120.51 s
Calling variants ...
Total processed positions in chr9 (chunk 7/20) : 10000
Total time elapsed: 121.34 s
Calling variants ...
Total processed positions in chr9 (chunk 15/20) : 10000
Total time elapsed: 123.04 s
Calling variants ...
Total processed positions in chr9 (chunk 18/20) : 10000
Total time elapsed: 123.50 s
Calling variants ...
Total processed positions in chr9 (chunk 4/20) : 10000
Total time elapsed: 125.47 s
Calling variants ...
Total processed positions in chr9 (chunk 12/20) : 10000
Total time elapsed: 131.99 s
Calling variants ...
Total processed positions in chr9 (chunk 16/20) : 10000
Total time elapsed: 134.56 s
Calling variants ...
Total processed positions in chr9 (chunk 11/20) : 10000
Total time elapsed: 139.32 s
Calling variants ...
Total processed positions in chr9 (chunk 5/20) : 10000
Total time elapsed: 155.07 s

real	2m38.507s
user	35m49.457s
sys	1m53.587s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr9: 73865
[INFO] Full-alignment variants processed in chr9: 160201

real	0m2.867s
user	0m2.939s
sys	0m0.181s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz

real	6m8.256s
user	64m28.253s
sys	5m14.468s

[INFO] Select Heterozygous SNP for Phasing
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/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/part40/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/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/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/1_select_hetero_snp_for_phasing.log

[INFO] Total HET SNP calls selected: chr9: 107191, not found:2348, not match:108, low_qual_count:0. Total normal:119728 Total tumor:109647, pro: 0.9776

[INFO] Phase the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/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/part40/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/part40/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS

LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf/chr9.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/part40/tmp/clair3_output/phased_output/tumor_phased_chr9
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
(chr9,49s)
parsing total:  49s
merge results ... 0s
writeResult SNP ... 1s

total process: 52s

[INFO] Haplotag the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/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/part40/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/part40/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/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS

phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_chr9.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/part40/tmp/clair3_output/phased_output/tumor_chr9.bam
number of threads: 1
write log file:    false
log file:          
-------------------------------------------
tag region:                    chr9
filter mapping quality below:  1
percentage threshold:          0.6
tag supplementary:             false
-------------------------------------------
parsing SNP VCF ... 1s
tag read start ...
chr: chr9 ... 1322s
tag read 1325s
-------------------------------------------
total process time:  1326s
total alignment:     1870680
total supplementary: 62722
total secondary:     0
total unmapped:      0
total tag alignment: 709540
total untagged:      1161140

[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/part40/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/part40/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/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/part40/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 

[INFO] chr9 chunk 0/31: Total snv candidates found: 74, total indel candidates found: 46
[INFO] chr9 chunk 1/31: Total snv candidates found: 1194, total indel candidates found: 371
[INFO] chr9 chunk 4/31: Total snv candidates found: 656, total indel candidates found: 215