Thomas
/
pandora_lib_promethion


			
				
					
						
						
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							WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6': 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/part6 --region chr11:84448351-135127769 --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/part6/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chr11
[INFO] Number of chunks for each contig: 28

[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/part6
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/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/part6/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chr11:84448351-135127769
[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/part6/tmp/clair3_output/clair3_normal_output --ctg_name=chr11 --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/part6/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/part6/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr11
[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/part6/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr11 --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/part6/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part6/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr11
[INFO] Chunk number for each contig: 28
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr11 (chunk 11/28) : 49165
Total time elapsed: 178.48 s
Calling variants ...
Total processed positions in chr11 (chunk 12/28) : 56920
Total time elapsed: 181.36 s
Calling variants ...
Total processed positions in chr11 (chunk 22/28) : 75977
Total time elapsed: 209.99 s
Calling variants ...
Total processed positions in chr11 (chunk 19/28) : 71613
Total time elapsed: 214.42 s
Calling variants ...
Total processed positions in chr11 (chunk 9/28) : 70940
Total time elapsed: 222.08 s
Calling variants ...
Total processed positions in chr11 (chunk 6/28) : 73742
Total time elapsed: 222.47 s
Calling variants ...
Total processed positions in chr11 (chunk 5/28) : 75204
Total time elapsed: 224.15 s
Calling variants ...
Total processed positions in chr11 (chunk 21/28) : 71045
Total time elapsed: 224.79 s
Calling variants ...
Total processed positions in chr11 (chunk 7/28) : 73918
Total time elapsed: 227.41 s
Calling variants ...
Total processed positions in chr11 (chunk 17/28) : 78578
Total time elapsed: 229.56 s
Calling variants ...
Total processed positions in chr11 (chunk 18/28) : 73703
Total time elapsed: 234.10 s
Calling variants ...
Total processed positions in chr11 (chunk 4/28) : 81512
Total time elapsed: 236.81 s
Calling variants ...
Total processed positions in chr11 (chunk 14/28) : 83931
Total time elapsed: 237.93 s
Calling variants ...
Total processed positions in chr11 (chunk 16/28) : 82083
Total time elapsed: 240.35 s
Calling variants ...
Total processed positions in chr11 (chunk 3/28) : 82458
Total time elapsed: 241.23 s
Calling variants ...
Total processed positions in chr11 (chunk 13/28) : 79284
Total time elapsed: 243.04 s
Calling variants ...
Total processed positions in chr11 (chunk 2/28) : 79749
Total time elapsed: 243.40 s
Calling variants ...
Total processed positions in chr11 (chunk 15/28) : 84644
Total time elapsed: 247.06 s
Calling variants ...
Total processed positions in chr11 (chunk 20/28) : 78075
Total time elapsed: 249.18 s
Calling variants ...
Total processed positions in chr11 (chunk 26/28) : 89044
Total time elapsed: 249.72 s
Calling variants ...
Total processed positions in chr11 (chunk 24/28) : 84661
Total time elapsed: 253.22 s
Calling variants ...
Total processed positions in chr11 (chunk 10/28) : 85066
Total time elapsed: 253.66 s
Calling variants ...
Total processed positions in chr11 (chunk 28/28) : 83894
Total time elapsed: 253.82 s
Calling variants ...
Total processed positions in chr11 (chunk 23/28) : 77217
Total time elapsed: 229.34 s
Calling variants ...
Total processed positions in chr11 (chunk 8/28) : 83397
Total time elapsed: 256.16 s
Calling variants ...
Total processed positions in chr11 (chunk 25/28) : 85368
Total time elapsed: 235.94 s
Calling variants ...
Total processed positions in chr11 (chunk 1/28) : 94486
Total time elapsed: 265.61 s
Calling variants ...
Total processed positions in chr11 (chunk 27/28) : 84745
Total time elapsed: 246.95 s

real	4m41.889s
user	104m58.241s
sys	4m37.088s

[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: chr11: 85688

real	0m4.179s
user	0m3.753s
sys	0m0.321s

[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/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr11.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/part6/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr11
Generate Dot  : False
BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 

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

parsing VCF ... 0s
parsing SV VCF ... 0s
parsing Meth VCF ... 0s
reading reference ... 2s
(chr11,10s)
parsing total:  10s
merge results ... 0s
writeResult SNP ... 1s

total process: 13s

real	0m13.103s
user	0m44.278s
sys	0m3.402s

[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 chr11: 195328
[INFO] Low quality variants to be processed in chr11: 162732

real	0m4.471s
user	0m4.035s
sys	0m0.344s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr11 (chunk 4/36) : 10000
Total time elapsed: 143.44 s
Calling variants ...
Total processed positions in chr11 (chunk 22/36) : 10000
Total time elapsed: 143.91 s
Calling variants ...
Total processed positions in chr11 (chunk 2/36) : 10000
Total time elapsed: 145.31 s
Calling variants ...
Total processed positions in chr11 (chunk 10/36) : 10000
Total time elapsed: 148.91 s
Calling variants ...
Total processed positions in chr11 (chunk 9/36) : 10000
Total time elapsed: 158.77 s
Calling variants ...
Total processed positions in chr11 (chunk 16/36) : 10000
Total time elapsed: 160.86 s
Calling variants ...
Total processed positions in chr11 (chunk 13/36) : 10000
Total time elapsed: 161.73 s
Calling variants ...
Total processed positions in chr11 (chunk 26/36) : 10000
Total time elapsed: 162.70 s
Calling variants ...
Total processed positions in chr11 (chunk 5/36) : 10000
Total time elapsed: 163.82 s
Calling variants ...
Total processed positions in chr11 (chunk 25/36) : 10000
Total time elapsed: 164.25 s
Calling variants ...
Total processed positions in chr11 (chunk 21/36) : 10000
Total time elapsed: 165.81 s
Calling variants ...
Total processed positions in chr11 (chunk 19/36) : 10000
Total time elapsed: 166.75 s
Calling variants ...
Total processed positions in chr11 (chunk 7/36) : 10000
Total time elapsed: 172.07 s
Calling variants ...
Total processed positions in chr11 (chunk 18/36) : 10000
Total time elapsed: 172.46 s
Calling variants ...
Total processed positions in chr11 (chunk 30/36) : 10000
Total time elapsed: 178.30 s
Calling variants ...
Total processed positions in chr11 (chunk 1/36) : 10000
Total time elapsed: 179.50 s
Calling variants ...
Total processed positions in chr11 (chunk 15/36) : 10000
Total time elapsed: 179.65 s
Calling variants ...
Total processed positions in chr11 (chunk 24/36) : 10000
Total time elapsed: 179.97 s
Calling variants ...
Total processed positions in chr11 (chunk 12/36) : 10000
Total time elapsed: 179.65 s
Calling variants ...
Total processed positions in chr11 (chunk 8/36) : 10000
Total time elapsed: 181.87 s
Calling variants ...
Total processed positions in chr11 (chunk 3/36) : 10000
Total time elapsed: 182.80 s
Calling variants ...
Total processed positions in chr11 (chunk 29/36) : 10000
Total time elapsed: 183.85 s
Calling variants ...
Total processed positions in chr11 (chunk 27/36) : 10000
Total time elapsed: 183.49 s
Calling variants ...
Total processed positions in chr11 (chunk 17/36) : 10000
Total time elapsed: 184.91 s
Calling variants ...
Total processed positions in chr11 (chunk 11/36) : 10000
Total time elapsed: 185.82 s
Calling variants ...
Total processed positions in chr11 (chunk 28/36) : 10000
Total time elapsed: 186.43 s
Calling variants ...
Total processed positions in chr11 (chunk 6/36) : 10000
Total time elapsed: 187.85 s
Calling variants ...
Total processed positions in chr11 (chunk 14/36) : 10000
Total time elapsed: 188.97 s
Calling variants ...
Total processed positions in chr11 (chunk 23/36) : 10000
Total time elapsed: 189.86 s
Calling variants ...
Total processed positions in chr11 (chunk 20/36) : 10000
Total time elapsed: 191.75 s