pandora_lib_promethion/slurm-2557979.out

WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20': 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/part20 --region chr2:1-113845111 --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/part20/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chr2
[INFO] Number of chunks for each contig: 49

[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/part20
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/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/part20/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chr2:1-113845111
[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/part20/tmp/clair3_output/clair3_normal_output --ctg_name=chr2 --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/part20/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/part20/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr2
[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/part20/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr2 --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/part20/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr2
[INFO] Chunk number for each contig: 49
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr2 (chunk 13/49) : 75269
Total time elapsed: 199.75 s
Calling variants ...
Total processed positions in chr2 (chunk 17/49) : 71352
Total time elapsed: 202.02 s
Calling variants ...
Total processed positions in chr2 (chunk 30/49) : 73373
Total time elapsed: 202.96 s
Calling variants ...
Total processed positions in chr2 (chunk 20/49) : 75043
Total time elapsed: 203.11 s
Calling variants ...
Total processed positions in chr2 (chunk 11/49) : 74661
Total time elapsed: 209.92 s
Calling variants ...
Total processed positions in chr2 (chunk 8/49) : 80441
Total time elapsed: 210.76 s
Calling variants ...
Total processed positions in chr2 (chunk 9/49) : 81596
Total time elapsed: 211.37 s
Calling variants ...
Total processed positions in chr2 (chunk 6/49) : 79351
Total time elapsed: 212.10 s
Calling variants ...
Total processed positions in chr2 (chunk 10/49) : 82733
Total time elapsed: 212.80 s
Calling variants ...
Total processed positions in chr2 (chunk 1/49) : 80838
Total time elapsed: 214.27 s
Calling variants ...
Total processed positions in chr2 (chunk 29/49) : 76038
Total time elapsed: 214.57 s
Calling variants ...
Total processed positions in chr2 (chunk 24/49) : 79088
Total time elapsed: 215.10 s
Calling variants ...
Total processed positions in chr2 (chunk 16/49) : 81038
Total time elapsed: 215.99 s
Calling variants ...
Total processed positions in chr2 (chunk 23/49) : 82668
Total time elapsed: 216.47 s
Calling variants ...
Total processed positions in chr2 (chunk 27/49) : 83387
Total time elapsed: 216.81 s
Calling variants ...
Total processed positions in chr2 (chunk 18/49) : 80235
Total time elapsed: 219.85 s
Calling variants ...
Total processed positions in chr2 (chunk 22/49) : 80277
Total time elapsed: 224.08 s
Calling variants ...
Total processed positions in chr2 (chunk 4/49) : 83480
Total time elapsed: 224.07 s
Calling variants ...
Total processed positions in chr2 (chunk 14/49) : 81970
Total time elapsed: 224.23 s
Calling variants ...
Total processed positions in chr2 (chunk 19/49) : 75283
Total time elapsed: 225.15 s
Calling variants ...
Total processed positions in chr2 (chunk 2/49) : 84106
Total time elapsed: 227.83 s
Calling variants ...
Total processed positions in chr2 (chunk 21/49) : 81835
Total time elapsed: 229.23 s
Calling variants ...
Total processed positions in chr2 (chunk 26/49) : 84734
Total time elapsed: 231.67 s
Calling variants ...
Total processed positions in chr2 (chunk 28/49) : 75612
Total time elapsed: 201.90 s
Calling variants ...
Total processed positions in chr2 (chunk 3/49) : 86183
Total time elapsed: 233.85 s
Calling variants ...
Total processed positions in chr2 (chunk 12/49) : 82008
Total time elapsed: 206.01 s
Calling variants ...
Total processed positions in chr2 (chunk 25/49) : 84883
Total time elapsed: 209.79 s
Calling variants ...
Total processed positions in chr2 (chunk 5/49) : 83721
Total time elapsed: 210.17 s
Calling variants ...
Total processed positions in chr2 (chunk 15/49) : 87963
Total time elapsed: 213.68 s
Calling variants ...
Total processed positions in chr2 (chunk 7/49) : 88857
Total time elapsed: 217.49 s
Calling variants ...
Total processed positions in chr2 (chunk 31/49) : 73402
Total time elapsed: 151.18 s
Calling variants ...
Total processed positions in chr2 (chunk 40/49) : 70806
Total time elapsed: 138.01 s
Calling variants ...
Total processed positions in chr2 (chunk 37/49) : 75613
Total time elapsed: 142.20 s
Calling variants ...
Total processed positions in chr2 (chunk 32/49) : 71337
Total time elapsed: 152.09 s
Calling variants ...
Total processed positions in chr2 (chunk 47/49) : 74017
Total time elapsed: 134.36 s
Calling variants ...
Total processed positions in chr2 (chunk 42/49) : 75734
Total time elapsed: 144.37 s
Calling variants ...
Total processed positions in chr2 (chunk 39/49) : 79011
Total time elapsed: 149.41 s
Calling variants ...
Total processed positions in chr2 (chunk 36/49) : 84088
Total time elapsed: 153.45 s
Calling variants ...
Total processed positions in chr2 (chunk 38/49) : 73991
Total time elapsed: 154.35 s
Calling variants ...
Total processed positions in chr2 (chunk 33/49) : 82305
Total time elapsed: 164.60 s
Calling variants ...
Total processed positions in chr2 (chunk 41/49) : 80990
Total time elapsed: 153.46 s
Calling variants ...
Total processed positions in chr2 (chunk 34/49) : 79400
Total time elapsed: 166.04 s
Calling variants ...
Total processed positions in chr2 (chunk 44/49) : 75892
Total time elapsed: 155.48 s
Calling variants ...
Total processed positions in chr2 (chunk 48/49) : 83848
Total time elapsed: 152.05 s
Calling variants ...
Total processed positions in chr2 (chunk 35/49) : 84506
Total time elapsed: 167.45 s
Calling variants ...
Total processed positions in chr2 (chunk 43/49) : 78010
Total time elapsed: 162.44 s
Calling variants ...
Total processed positions in chr2 (chunk 46/49) : 81534
Total time elapsed: 162.72 s
Calling variants ...
Total processed positions in chr2 (chunk 45/49) : 86558
Total time elapsed: 175.83 s
Calling variants ...
Total processed positions in chr2 (chunk 49/49) : 92842
Total time elapsed: 181.53 s

real	6m56.137s
user	148m38.462s
sys	7m29.296s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 16
[INFO] Total heterozygous SNP positions selected: chr2: 150142

real	0m5.569s
user	0m5.216s
sys	0m0.241s

[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/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr2.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/part20/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr2
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
(chr2,16s)
parsing total:  16s
merge results ... 0s
writeResult SNP ... 1s

total process: 18s

real	0m18.252s
user	0m39.624s
sys	0m2.736s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 20.0
[INFO] Set reference calls quality cutoff 14.0
[INFO] Low quality reference calls to be processed in chr2: 351297
[INFO] Low quality variants to be processed in chr2: 282859

real	0m6.395s
user	0m5.824s
sys	0m0.430s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr2 (chunk 19/64) : 10000
Total time elapsed: 136.19 s
Calling variants ...
Total processed positions in chr2 (chunk 9/64) : 10000
Total time elapsed: 136.95 s
Calling variants ...
Total processed positions in chr2 (chunk 30/64) : 10000
Total time elapsed: 141.06 s
Calling variants ...
Total processed positions in chr2 (chunk 17/64) : 10000
Total time elapsed: 142.38 s
Calling variants ...
Total processed positions in chr2 (chunk 6/64) : 10000
Total time elapsed: 142.84 s
Calling variants ...
Total processed positions in chr2 (chunk 16/64) : 10000
Total time elapsed: 145.46 s
Calling variants ...
Total processed positions in chr2 (chunk 10/64) : 10000
Total time elapsed: 145.78 s
Calling variants ...
Total processed positions in chr2 (chunk 21/64) : 10000
Total time elapsed: 145.87 s
Calling variants ...
Total processed positions in chr2 (chunk 2/64) : 10000
Total time elapsed: 146.26 s
Calling variants ...
Total processed positions in chr2 (chunk 11/64) : 10000
Total time elapsed: 146.61 s
Calling variants ...
Total processed positions in chr2 (chunk 28/64) : 10000
Total time elapsed: 147.30 s
Calling variants ...
Total processed positions in chr2 (chunk 3/64) : 10000
Total time elapsed: 148.00 s
Calling variants ...
Total processed positions in chr2 (chunk 5/64) : 10000
Total time elapsed: 148.47 s
Calling variants ...
Total processed positions in chr2 (chunk 27/64) : 10000
Total time elapsed: 149.41 s
Calling variants ...
Total processed positions in chr2 (chunk 7/64) : 10000
Total time elapsed: 149.28 s
Calling variants ...
Total processed positions in chr2 (chunk 29/64) : 10000
Total time elapsed: 149.50 s
Calling variants ...
Total processed positions in chr2 (chunk 26/64) : 10000
Total time elapsed: 149.59 s
Calling variants ...
Total processed positions in chr2 (chunk 18/64) : 10000
Total time elapsed: 150.10 s
Calling variants ...
Total processed positions in chr2 (chunk 8/64) : 10000
Total time elapsed: 151.30 s
Calling variants ...
Total processed positions in chr2 (chunk 23/64) : 10000
Total time elapsed: 152.13 s
Calling variants ...
Total processed positions in chr2 (chunk 4/64) : 10000
Total time elapsed: 153.23 s
Calling variants ...
Total processed positions in chr2 (chunk 25/64) : 10000
Total time elapsed: 154.11 s
Calling variants ...
Total processed positions in chr2 (chunk 15/64) : 10000
Total time elapsed: 153.49 s
Calling variants ...
Total processed positions in chr2 (chunk 12/64) : 10000
Total time elapsed: 154.56 s
Calling variants ...
Total processed positions in chr2 (chunk 20/64) : 10000
Total time elapsed: 154.74 s
Calling variants ...
Total processed positions in chr2 (chunk 22/64) : 10000
Total time elapsed: 156.87 s
Calling variants ...
Total processed positions in chr2 (chunk 14/64) : 10000
Total time elapsed: 157.18 s
Calling variants ...
Total processed positions in chr2 (chunk 13/64) : 10000
Total time elapsed: 158.06 s
Calling variants ...
Total processed positions in chr2 (chunk 24/64) : 10000
Total time elapsed: 159.71 s
Calling variants ...
Total processed positions in chr2 (chunk 1/64) : 10000
Total time elapsed: 162.45 s
Calling variants ...
Total processed positions in chr2 (chunk 31/64) : 10000
Total time elapsed: 139.95 s
Calling variants ...
Total processed positions in chr2 (chunk 32/64) : 10000
Total time elapsed: 149.41 s
Calling variants ...
Total processed positions in chr2 (chunk 44/64) : 10000
Total time elapsed: 140.36 s
Calling variants ...
Total processed positions in chr2 (chunk 41/64) : 10000
Total time elapsed: 142.69 s
Calling variants ...
Total processed positions in chr2 (chunk 49/64) : 10000
Total time elapsed: 140.69 s
Calling variants ...
Total processed positions in chr2 (chunk 56/64) : 10000
Total time elapsed: 134.70 s
Calling variants ...
Total processed positions in chr2 (chunk 45/64) : 10000
Total time elapsed: 141.91 s
Calling variants ...
Total processed positions in chr2 (chunk 38/64) : 10000
Total time elapsed: 147.31 s
Calling variants ...
Total processed positions in chr2 (chunk 37/64) : 10000
Total time elapsed: 148.15 s
Calling variants ...
Total processed positions in chr2 (chunk 42/64) : 10000
Total time elapsed: 144.90 s
Calling variants ...
Total processed positions in chr2 (chunk 50/64) : 10000
Total time elapsed: 143.17 s
Calling variants ...
Total processed positions in chr2 (chunk 35/64) : 10000
Total time elapsed: 153.02 s
Calling variants ...
Total processed positions in chr2 (chunk 51/64) : 10000
Total time elapsed: 142.60 s
Calling variants ...
Total processed positions in chr2 (chunk 46/64) : 10000
Total time elapsed: 147.12 s
Calling variants ...
Total processed positions in chr2 (chunk 52/64) : 10000
Total time elapsed: 145.77 s
Calling variants ...
Total processed positions in chr2 (chunk 57/64) : 10000
Total time elapsed: 142.08 s
Calling variants ...
Total processed positions in chr2 (chunk 33/64) : 10000
Total time elapsed: 158.96 s
Calling variants ...
Total processed positions in chr2 (chunk 59/64) : 10000
Total time elapsed: 140.68 s
Calling variants ...
Total processed positions in chr2 (chunk 53/64) : 10000
Total time elapsed: 146.33 s
Calling variants ...
Total processed positions in chr2 (chunk 39/64) : 10000
Total time elapsed: 154.28 s
Calling variants ...
Total processed positions in chr2 (chunk 36/64) : 10000
Total time elapsed: 154.64 s
Calling variants ...
Total processed positions in chr2 (chunk 40/64) : 10000
Total time elapsed: 153.95 s
Calling variants ...
Total processed positions in chr2 (chunk 34/64) : 10000
Total time elapsed: 158.39 s
Calling variants ...
Total processed positions in chr2 (chunk 55/64) : 10000
Total time elapsed: 146.24 s
Calling variants ...
Total processed positions in chr2 (chunk 58/64) : 10000
Total time elapsed: 143.60 s
Calling variants ...
Total processed positions in chr2 (chunk 48/64) : 10000
Total time elapsed: 151.82 s
Calling variants ...
Total processed positions in chr2 (chunk 43/64) : 10000
Total time elapsed: 154.28 s
Calling variants ...
Total processed positions in chr2 (chunk 47/64) : 10000
Total time elapsed: 155.12 s
Calling variants ...
Total processed positions in chr2 (chunk 54/64) : 10000
Total time elapsed: 152.51 s
Calling variants ...
Total processed positions in chr2 (chunk 60/64) : 10000
Total time elapsed: 147.03 s
Calling variants ...
Total processed positions in chr2 (chunk 64/64) : 4156
Total time elapsed: 40.98 s
Calling variants ...
Total processed positions in chr2 (chunk 61/64) : 10000
Total time elapsed: 96.41 s
Calling variants ...
Total processed positions in chr2 (chunk 62/64) : 10000
Total time elapsed: 90.96 s
Calling variants ...
Total processed positions in chr2 (chunk 63/64) : 10000
Total time elapsed: 91.35 s

real	6m32.438s
user	149m33.204s
sys	6m35.289s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr2: 121260
[INFO] Full-alignment variants processed in chr2: 298027

real	0m7.682s
user	0m8.986s
sys	0m0.390s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz

real	14m39.872s
user	299m42.740s
sys	14m11.207s

[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/part20/tmp/clair3_output/clair3_tumor_output --ctg_name=chr2 --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/part20/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/part20/tmp/clair3_output/clair3_tumor_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr2
[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/part20/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr2 --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/part20/tmp/clair3_output/clair3_tumor_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr2
[INFO] Chunk number for each contig: 49
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr2 (chunk 17/49) : 7627
Total time elapsed: 101.22 s
Calling variants ...
Total processed positions in chr2 (chunk 5/49) : 8455
Total time elapsed: 103.54 s
Calling variants ...
Total processed positions in chr2 (chunk 21/49) : 9171
Total time elapsed: 104.85 s
Calling variants ...
Total processed positions in chr2 (chunk 6/49) : 9236
Total time elapsed: 104.97 s
Calling variants ...
Total processed positions in chr2 (chunk 23/49) : 8909
Total time elapsed: 105.24 s
Calling variants ...
Total processed positions in chr2 (chunk 22/49) : 9821
Total time elapsed: 106.19 s
Calling variants ...
Total processed positions in chr2 (chunk 24/49) : 9129
Total time elapsed: 106.40 s
Calling variants ...
Total processed positions in chr2 (chunk 29/49) : 10495
Total time elapsed: 108.59 s
Calling variants ...
Total processed positions in chr2 (chunk 18/49) : 11980
Total time elapsed: 108.93 s
Calling variants ...
Total processed positions in chr2 (chunk 7/49) : 11591
Total time elapsed: 109.33 s
Calling variants ...
Total processed positions in chr2 (chunk 11/49) : 11806
Total time elapsed: 109.32 s
Calling variants ...
Total processed positions in chr2 (chunk 4/49) : 10602
Total time elapsed: 109.98 s
Calling variants ...
Total processed positions in chr2 (chunk 26/49) : 11900
Total time elapsed: 112.11 s
Calling variants ...
Total processed positions in chr2 (chunk 12/49) : 12287
Total time elapsed: 112.73 s
Calling variants ...
Total processed positions in chr2 (chunk 3/49) : 13938
Total time elapsed: 114.59 s
Calling variants ...
Total processed positions in chr2 (chunk 27/49) : 14692
Total time elapsed: 115.74 s
Calling variants ...
Total processed positions in chr2 (chunk 20/49) : 24047
Total time elapsed: 131.50 s
Calling variants ...
Total processed positions in chr2 (chunk 28/49) : 7473
Total time elapsed: 66.78 s
Calling variants ...
Total processed positions in chr2 (chunk 9/49) : 10082
Total time elapsed: 69.67 s
Calling variants ...
Total processed positions in chr2 (chunk 2/49) : 10653
Total time elapsed: 71.83 s
Calling variants ...
Total processed positions in chr2 (chunk 13/49) : 10312
Total time elapsed: 73.61 s
Calling variants ...
Total processed positions in chr2 (chunk 16/49) : 11769
Total time elapsed: 76.02 s
Calling variants ...
Total processed positions in chr2 (chunk 15/49) : 11490
Total time elapsed: 77.23 s
Calling variants ...
Total processed positions in chr2 (chunk 14/49) : 12324
Total time elapsed: 76.89 s
Calling variants ...
Total processed positions in chr2 (chunk 8/49) : 13128
Total time elapsed: 77.71 s
Calling variants ...
Total processed positions in chr2 (chunk 31/49) : 7977
Total time elapsed: 61.62 s
Calling variants ...
Total processed positions in chr2 (chunk 1/49) : 15284
Total time elapsed: 81.62 s
Calling variants ...
Total processed positions in chr2 (chunk 36/49) : 9813
Total time elapsed: 64.59 s
Calling variants ...
Total processed positions in chr2 (chunk 34/49) : 10438
Total time elapsed: 66.29 s
Calling variants ...
Total processed positions in chr2 (chunk 37/49) : 9564
Total time elapsed: 64.73 s
Calling variants ...
Total processed positions in chr2 (chunk 39/49) : 7943
Total time elapsed: 62.60 s
Calling variants ...
Total processed positions in chr2 (chunk 44/49) : 8253
Total time elapsed: 58.74 s
Calling variants ...
Total processed positions in chr2 (chunk 35/49) : 11348
Total time elapsed: 67.32 s
Calling variants ...
Total processed positions in chr2 (chunk 38/49) : 8387
Total time elapsed: 63.79 s
Calling variants ...
Total processed positions in chr2 (chunk 42/49) : 9050
Total time elapsed: 63.53 s
Calling variants ...
Total processed positions in chr2 (chunk 41/49) : 9364
Total time elapsed: 64.39 s
Calling variants ...
Total processed positions in chr2 (chunk 43/49) : 9185
Total time elapsed: 62.50 s
Calling variants ...
Total processed positions in chr2 (chunk 46/49) : 10647
Total time elapsed: 61.22 s
Calling variants ...
Total processed positions in chr2 (chunk 45/49) : 9880
Total time elapsed: 62.34 s
Calling variants ...
Total processed positions in chr2 (chunk 30/49) : 6472
Total time elapsed: 50.40 s
Calling variants ...
Total processed positions in chr2 (chunk 25/49) : 10438
Total time elapsed: 54.55 s
Calling variants ...
Total processed positions in chr2 (chunk 47/49) : 11754
Total time elapsed: 56.15 s
Calling variants ...
Total processed positions in chr2 (chunk 10/49) : 12602
Total time elapsed: 57.65 s
Calling variants ...
Total processed positions in chr2 (chunk 32/49) : 8410
Total time elapsed: 45.98 s
Calling variants ...
Total processed positions in chr2 (chunk 33/49) : 10165
Total time elapsed: 49.23 s
Calling variants ...
Total processed positions in chr2 (chunk 40/49) : 8407
Total time elapsed: 44.81 s
Calling variants ...
Total processed positions in chr2 (chunk 48/49) : 12378
Total time elapsed: 48.29 s
Calling variants ...
Total processed positions in chr2 (chunk 19/49) : 64666
Total time elapsed: 214.06 s
Calling variants ...
Total processed positions in chr2 (chunk 49/49) : 16414
Total time elapsed: 54.77 s

real	3m38.990s
user	49m2.698s
sys	12m29.771s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 20
[INFO] Total heterozygous SNP positions selected: chr2: 154655

real	0m1.575s
user	0m1.297s
sys	0m0.177s

[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/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr2.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/part20/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr2
Generate Dot  : False
BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 

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

parsing VCF ... 0s
parsing SV VCF ... 0s
parsing Meth VCF ... 0s
reading reference ... 2s
(chr2,60s)
parsing total:  60s
merge results ... 0s
writeResult SNP ... 1s

total process: 63s

real	1m3.199s
user	3m4.039s
sys	0m11.635s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 22.0
[INFO] Set reference calls quality cutoff 7.0
[INFO] Low quality reference calls to be processed in chr2: 18408
[INFO] Low quality variants to be processed in chr2: 277651

real	0m1.581s
user	0m1.339s
sys	0m0.173s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr2 (chunk 30/30) : 6059
Total time elapsed: 102.23 s
Calling variants ...
Total processed positions in chr2 (chunk 13/30) : 10000
Total time elapsed: 154.87 s
Calling variants ...
Total processed positions in chr2 (chunk 2/30) : 10000
Total time elapsed: 176.62 s
Calling variants ...
Total processed positions in chr2 (chunk 29/30) : 10000
Total time elapsed: 177.89 s
Calling variants ...
Total processed positions in chr2 (chunk 14/30) : 10000
Total time elapsed: 180.12 s
Calling variants ...
Total processed positions in chr2 (chunk 25/30) : 10000
Total time elapsed: 181.74 s
Calling variants ...
Total processed positions in chr2 (chunk 3/30) : 10000
Total time elapsed: 182.47 s
Calling variants ...
Total processed positions in chr2 (chunk 11/30) : 10000
Total time elapsed: 185.54 s
Calling variants ...
Total processed positions in chr2 (chunk 9/30) : 10000
Total time elapsed: 186.85 s
Calling variants ...
Total processed positions in chr2 (chunk 6/30) : 10000
Total time elapsed: 186.98 s
Calling variants ...
Total processed positions in chr2 (chunk 18/30) : 10000
Total time elapsed: 186.71 s
Calling variants ...
Total processed positions in chr2 (chunk 5/30) : 10000
Total time elapsed: 187.14 s
Calling variants ...
Total processed positions in chr2 (chunk 23/30) : 10000
Total time elapsed: 189.44 s
Calling variants ...
Total processed positions in chr2 (chunk 22/30) : 10000
Total time elapsed: 189.09 s
Calling variants ...
Total processed positions in chr2 (chunk 15/30) : 10000
Total time elapsed: 189.34 s
Calling variants ...
Total processed positions in chr2 (chunk 16/30) : 10000
Total time elapsed: 189.71 s
Calling variants ...
Total processed positions in chr2 (chunk 28/30) : 10000
Total time elapsed: 190.87 s
Calling variants ...
Total processed positions in chr2 (chunk 7/30) : 10000
Total time elapsed: 191.68 s
Calling variants ...
Total processed positions in chr2 (chunk 12/30) : 10000
Total time elapsed: 190.92 s
Calling variants ...
Total processed positions in chr2 (chunk 19/30) : 10000
Total time elapsed: 192.52 s
Calling variants ...
Total processed positions in chr2 (chunk 8/30) : 10000
Total time elapsed: 193.53 s
Calling variants ...
Total processed positions in chr2 (chunk 10/30) : 10000
Total time elapsed: 194.41 s
Calling variants ...
Total processed positions in chr2 (chunk 17/30) : 10000
Total time elapsed: 196.52 s
Calling variants ...
Total processed positions in chr2 (chunk 1/30) : 10000
Total time elapsed: 198.59 s
Calling variants ...
Total processed positions in chr2 (chunk 24/30) : 10000
Total time elapsed: 198.82 s
Calling variants ...
Total processed positions in chr2 (chunk 4/30) : 10000
Total time elapsed: 200.41 s
Calling variants ...
Total processed positions in chr2 (chunk 27/30) : 10000
Total time elapsed: 203.01 s
Calling variants ...
Total processed positions in chr2 (chunk 20/30) : 10000
Total time elapsed: 202.15 s
Calling variants ...
Total processed positions in chr2 (chunk 26/30) : 10000
Total time elapsed: 204.48 s
Calling variants ...
Total processed positions in chr2 (chunk 21/30) : 10000
Total time elapsed: 206.71 s

real	3m31.628s
user	86m24.557s
sys	3m59.700s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr2: 119513
[INFO] Full-alignment variants processed in chr2: 256477

real	0m2.788s
user	0m2.943s
sys	0m0.205s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz

real	8m30.472s
user	138m45.707s
sys	16m43.041s

[INFO] Select Heterozygous SNP for Phasing
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/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/part20/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/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/part20/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/1_select_hetero_snp_for_phasing.log

[INFO] Total HET SNP calls selected: chr2: 199643, not found:792, not match:54, low_qual_count:0. Total normal:208641 Total tumor:200489, pro: 0.9958

[INFO] Phase the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/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/part20/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/part20/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS

LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/vcf/chr2.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/part20/tmp/clair3_output/phased_output/tumor_phased_chr2
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
(chr2,93s)
parsing total:  93s
merge results ... 1s
writeResult SNP ... 1s

total process: 97s

[INFO] Haplotag the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/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/part20/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/part20/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/part20/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part20/tmp/CONTIGS