pandora_lib_promethion/slurm-2536605.out

[COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_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/DUMCO/diag/ClairS/part10 --region chr14:1-14158555 --sample_name DUMCO_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/DUMCO/diag/ClairS/part10/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chr14
[INFO] Number of chunks for each contig: 21

[INFO] CALLER VERSION: 0.4.4
[INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_norm_hs1.bam
[INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_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/DUMCO/diag/ClairS/part10
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/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/DUMCO/diag/ClairS/part10/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chr14:1-14158555
[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/DUMCO/norm/DUMCO_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/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output --ctg_name=chr14 --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/DUMCO/diag/ClairS/part10/logs/clair3_log/1_CLAIR3_NORMAL.log

/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
[INFO] CLAIR3 VERSION: v1.0.8
[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_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/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr14
[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/DUMCO/norm/DUMCO_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/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr14 --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
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory

[INFO] Check environment variables
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr14
[INFO] Chunk number for each contig: 21
[INFO] 1/7 Call variants using pileup model
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 3/21) : 27087
Total time elapsed: 67.49 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 17/21) : 45594
Total time elapsed: 100.19 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 8/21) : 44012
Total time elapsed: 100.23 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 9/21) : 45077
Total time elapsed: 103.05 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 6/21) : 46771
Total time elapsed: 106.08 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 13/21) : 48523
Total time elapsed: 107.31 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 10/21) : 48629
Total time elapsed: 107.79 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 7/21) : 46998
Total time elapsed: 110.66 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 5/21) : 46930
Total time elapsed: 111.19 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 12/21) : 48751
Total time elapsed: 112.04 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 11/21) : 49628
Total time elapsed: 112.84 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 16/21) : 48404
Total time elapsed: 113.65 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 14/21) : 52138
Total time elapsed: 114.64 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 18/21) : 51792
Total time elapsed: 116.28 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 19/21) : 52771
Total time elapsed: 117.06 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 4/21) : 55960
Total time elapsed: 119.54 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 15/21) : 58588
Total time elapsed: 120.64 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 20/21) : 56358
Total time elapsed: 124.53 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 2/21) : 71708
Total time elapsed: 137.35 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 21/21) : 74382
Total time elapsed: 139.88 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 1/21) : 75522
Total time elapsed: 148.63 s

real	2m36.411s
user	36m19.108s
sys	3m11.518s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 17
[INFO] Total heterozygous SNP positions selected: chr14: 98793
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory

real	0m3.189s
user	0m3.007s
sys	0m0.160s

[INFO] 3/7 Phase VCF file using LongPhase
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr14.vcf
SV  File      : 
MOD File      : 
REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr14
Generate Dot  : False
BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/norm/DUMCO_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
(chr14,11s)
parsing total:  11s
merge results ... 0s
writeResult SNP ... 1s

total process: 14s

real	0m14.363s
user	0m28.692s
sys	0m2.098s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 21.0
[INFO] Set reference calls quality cutoff 14.0
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
[INFO] Low quality reference calls to be processed in chr14: 87036
[INFO] Low quality variants to be processed in chr14: 156699

real	0m3.580s
user	0m3.267s
sys	0m0.249s

[INFO] 6/7 Call low-quality variants using full-alignment model
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 25/25) : 3735
Total time elapsed: 40.53 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 3/25) : 10000
Total time elapsed: 91.52 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 5/25) : 10000
Total time elapsed: 93.21 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 6/25) : 10000
Total time elapsed: 95.77 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 1/25) : 10000
Total time elapsed: 99.10 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 19/25) : 10000
Total time elapsed: 102.41 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 2/25) : 10000
Total time elapsed: 103.49 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 22/25) : 10000
Total time elapsed: 103.63 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 7/25) : 10000
Total time elapsed: 104.57 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 14/25) : 10000
Total time elapsed: 105.63 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 4/25) : 10000
Total time elapsed: 105.90 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 23/25) : 10000
Total time elapsed: 105.80 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 15/25) : 10000
Total time elapsed: 106.78 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 8/25) : 10000
Total time elapsed: 108.01 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 21/25) : 10000
Total time elapsed: 108.26 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 18/25) : 10000
Total time elapsed: 108.66 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 12/25) : 10000
Total time elapsed: 109.06 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 17/25) : 10000
Total time elapsed: 109.26 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 10/25) : 10000
Total time elapsed: 110.99 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 20/25) : 10000
Total time elapsed: 112.31 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 9/25) : 10000
Total time elapsed: 113.59 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 11/25) : 10000
Total time elapsed: 113.18 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 24/25) : 10000
Total time elapsed: 113.74 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 13/25) : 10000
Total time elapsed: 114.75 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 16/25) : 10000
Total time elapsed: 117.89 s

real	2m2.215s
user	41m45.362s
sys	2m39.606s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
[INFO] Pileup variants processed in chr14: 67189
[INFO] Full-alignment variants processed in chr14: 152188

real	0m4.735s
user	0m4.953s
sys	0m0.275s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz

real	5m21.522s
user	78m59.878s
sys	5m55.410s

[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/DUMCO/diag/DUMCO_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/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output --ctg_name=chr14 --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/DUMCO/diag/ClairS/part10/logs/clair3_log/2_CLAIR3_TUMOR.log

/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
[INFO] CLAIR3 VERSION: v1.0.8
[INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_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/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr14
[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/DUMCO/diag/DUMCO_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/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr14 --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
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory

[INFO] Check environment variables
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr14
[INFO] Chunk number for each contig: 21
[INFO] 1/7 Call variants using pileup model
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 13/21) : 9272
Total time elapsed: 83.25 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 16/21) : 10505
Total time elapsed: 83.09 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 9/21) : 9874
Total time elapsed: 83.84 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 12/21) : 10329
Total time elapsed: 84.85 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 10/21) : 10784
Total time elapsed: 84.83 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 11/21) : 10970
Total time elapsed: 85.64 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 8/21) : 11132
Total time elapsed: 85.34 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 5/21) : 10500
Total time elapsed: 86.17 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 7/21) : 11262
Total time elapsed: 86.28 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 15/21) : 11428
Total time elapsed: 88.28 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 3/21) : 24051
Total time elapsed: 107.75 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 14/21) : 9848
Total time elapsed: 54.85 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 20/21) : 10535
Total time elapsed: 56.16 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 18/21) : 10561
Total time elapsed: 56.64 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 6/21) : 11505
Total time elapsed: 57.66 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 17/21) : 10878
Total time elapsed: 59.43 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 19/21) : 10682
Total time elapsed: 59.99 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 4/21) : 13820
Total time elapsed: 60.94 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 21/21) : 21301
Total time elapsed: 70.54 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 2/21) : 49177
Total time elapsed: 151.29 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 1/21) : 56135
Total time elapsed: 123.51 s

real	3m36.782s
user	21m31.870s
sys	2m35.445s

[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: chr14: 92503
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory

real	0m1.739s
user	0m1.463s
sys	0m0.206s

[INFO] 3/7 Phase VCF file using LongPhase
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr14.vcf
SV  File      : 
MOD File      : 
REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr14
Generate Dot  : False
BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_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
(chr14,46s)
parsing total:  46s
merge results ... 0s
writeResult SNP ... 1s

total process: 49s

real	0m49.025s
user	1m52.723s
sys	0m7.403s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 21.0
[INFO] Set reference calls quality cutoff 8.0
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
[INFO] Low quality reference calls to be processed in chr14: 12071
[INFO] Low quality variants to be processed in chr14: 149419

real	0m1.560s
user	0m1.344s
sys	0m0.181s

[INFO] 6/7 Call low-quality variants using full-alignment model
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 17/17) : 1490
Total time elapsed: 17.69 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 2/17) : 10000
Total time elapsed: 77.45 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 3/17) : 10000
Total time elapsed: 85.49 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 4/17) : 10000
Total time elapsed: 108.69 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 16/17) : 10000
Total time elapsed: 111.72 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 5/17) : 10000
Total time elapsed: 111.92 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 6/17) : 10000
Total time elapsed: 113.19 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 1/17) : 10000
Total time elapsed: 116.51 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 7/17) : 10000
Total time elapsed: 118.51 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 9/17) : 10000
Total time elapsed: 120.23 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 8/17) : 10000
Total time elapsed: 120.33 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 15/17) : 10000
Total time elapsed: 120.91 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 12/17) : 10000
Total time elapsed: 121.70 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 10/17) : 10000
Total time elapsed: 125.60 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 11/17) : 10000
Total time elapsed: 132.71 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 13/17) : 10000
Total time elapsed: 133.62 s
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Calling variants ...
Total processed positions in chr14 (chunk 14/17) : 10000
Total time elapsed: 137.02 s

real	2m20.809s
user	29m25.734s
sys	1m36.544s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
[INFO] Pileup variants processed in chr14: 64294
[INFO] Full-alignment variants processed in chr14: 125164

real	0m2.550s
user	0m2.580s
sys	0m0.179s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz

real	7m1.826s
user	53m3.431s
sys	4m21.166s

[INFO] Select Heterozygous SNP for Phasing
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/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/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/1_select_hetero_snp_for_phasing.log

[INFO] Total HET SNP calls selected: chr14: 109551, not found:498, not match:37, low_qual_count:0. Total normal:129319 Total tumor:110086, pro: 0.9951

[INFO] Phase the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/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/DUMCO/diag/ClairS/part10/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS

LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/vcf/chr14.vcf
SV  File      : 
MOD File      : 
REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_chr14
Generate Dot  : False
BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_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
(chr14,62s)
parsing total:  62s
merge results ... 0s
writeResult SNP ... 1s

total process: 65s

[INFO] Haplotag the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/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/DUMCO/diag/ClairS/part10/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/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/DUMCO_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part10/tmp/CONTIGS