pandora_lib_promethion/slurm-2536606.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/part15 --region chr17:1-28642702 --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/part15/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chr17
[INFO] Number of chunks for each contig: 17

[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/part15
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/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/part15/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chr17:1-28642702
[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/part15/tmp/clair3_output/clair3_normal_output --ctg_name=chr17 --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/part15/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/part15/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr17
[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/part15/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr17 --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/part15/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr17
[INFO] Chunk number for each contig: 17
[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 chr17 (chunk 6/17) : 27914
Total time elapsed: 56.65 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 chr17 (chunk 13/17) : 50335
Total time elapsed: 84.56 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 chr17 (chunk 15/17) : 51403
Total time elapsed: 90.68 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 chr17 (chunk 5/17) : 55409
Total time elapsed: 96.01 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 chr17 (chunk 4/17) : 58603
Total time elapsed: 98.13 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 chr17 (chunk 7/17) : 54606
Total time elapsed: 98.11 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 chr17 (chunk 8/17) : 59803
Total time elapsed: 98.55 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 chr17 (chunk 14/17) : 55106
Total time elapsed: 100.54 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 chr17 (chunk 3/17) : 57778
Total time elapsed: 100.70 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 chr17 (chunk 11/17) : 57487
Total time elapsed: 102.90 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 chr17 (chunk 12/17) : 57337
Total time elapsed: 103.47 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 chr17 (chunk 10/17) : 57826
Total time elapsed: 104.26 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 chr17 (chunk 2/17) : 59536
Total time elapsed: 105.58 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 chr17 (chunk 16/17) : 65379
Total time elapsed: 111.75 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 chr17 (chunk 1/17) : 66124
Total time elapsed: 112.58 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 chr17 (chunk 9/17) : 65558
Total time elapsed: 114.98 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 chr17 (chunk 17/17) : 74166
Total time elapsed: 122.34 s

real	2m9.004s
user	26m3.068s
sys	2m5.460s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 18
[INFO] Total heterozygous SNP positions selected: chr17: 61710
/mnt/beegfs02/software/tools/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory

real	0m2.565s
user	0m2.421s
sys	0m0.123s

[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/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr17.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/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr17
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 ... 1s
(chr17,7s)
parsing total:  7s
merge results ... 0s
writeResult SNP ... 0s

total process: 8s

real	0m8.670s
user	0m18.510s
sys	0m1.250s
/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 chr17: 80349
[INFO] Low quality variants to be processed in chr17: 119468

real	0m2.724s
user	0m2.475s
sys	0m0.198s

[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 chr17 (chunk 10/20) : 10000
Total time elapsed: 82.58 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 chr17 (chunk 13/20) : 10000
Total time elapsed: 82.82 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 chr17 (chunk 11/20) : 10000
Total time elapsed: 82.94 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 chr17 (chunk 7/20) : 10000
Total time elapsed: 84.01 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 chr17 (chunk 5/20) : 10000
Total time elapsed: 84.06 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 chr17 (chunk 14/20) : 10000
Total time elapsed: 84.91 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 chr17 (chunk 12/20) : 10000
Total time elapsed: 85.09 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 chr17 (chunk 8/20) : 10000
Total time elapsed: 85.29 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 chr17 (chunk 2/20) : 10000
Total time elapsed: 86.07 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 chr17 (chunk 6/20) : 10000
Total time elapsed: 86.76 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 chr17 (chunk 15/20) : 10000
Total time elapsed: 87.23 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 chr17 (chunk 18/20) : 10000
Total time elapsed: 87.28 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 chr17 (chunk 3/20) : 10000
Total time elapsed: 87.72 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 chr17 (chunk 4/20) : 10000
Total time elapsed: 87.77 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 chr17 (chunk 17/20) : 10000
Total time elapsed: 87.96 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 chr17 (chunk 9/20) : 10000
Total time elapsed: 88.04 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 chr17 (chunk 16/20) : 10000
Total time elapsed: 88.27 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 chr17 (chunk 19/20) : 10000
Total time elapsed: 90.27 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 chr17 (chunk 1/20) : 10000
Total time elapsed: 90.39 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 chr17 (chunk 20/20) : 9817
Total time elapsed: 93.15 s

real	1m36.429s
user	27m51.849s
sys	1m41.958s

[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 chr17: 51317
[INFO] Full-alignment variants processed in chr17: 125849

real	0m3.646s
user	0m3.834s
sys	0m0.179s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz

real	4m17.319s
user	54m35.144s
sys	3m50.375s

[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/part15/tmp/clair3_output/clair3_tumor_output --ctg_name=chr17 --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/part15/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/part15/tmp/clair3_output/clair3_tumor_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr17
[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/part15/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr17 --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/part15/tmp/clair3_output/clair3_tumor_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/DUMCO/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr17
[INFO] Chunk number for each contig: 17
[INFO] 1/7 Call variants using pileup model