pandora_lib_promethion/slurm-2557980.out

WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44': 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/part44 --region chrY:1-62460029 --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/part44/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chrY
[INFO] Number of chunks for each contig: 13

[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/part44
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chrY:1-62460029
[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/part44/tmp/clair3_output/clair3_normal_output --ctg_name=chrY --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/part44/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/part44/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chrY
[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/part44/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chrY --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/part44/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chrY
[INFO] Chunk number for each contig: 13
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chrY (chunk 10/13) : 2510
Total time elapsed: 14.69 s
Calling variants ...
Total processed positions in chrY (chunk 8/13) : 3198
Total time elapsed: 15.01 s
Calling variants ...
Total processed positions in chrY (chunk 9/13) : 5363
Total time elapsed: 19.82 s
Calling variants ...
Total processed positions in chrY (chunk 7/13) : 13555
Total time elapsed: 31.66 s
Calling variants ...
Total processed positions in chrY (chunk 13/13) : 20440
Total time elapsed: 40.73 s
Calling variants ...
Total processed positions in chrY (chunk 12/13) : 19252
Total time elapsed: 41.61 s
Calling variants ...
Total processed positions in chrY (chunk 6/13) : 20091
Total time elapsed: 46.89 s
Calling variants ...
Total processed positions in chrY (chunk 11/13) : 23275
Total time elapsed: 48.80 s
Calling variants ...
Total processed positions in chrY (chunk 4/13) : 37911
Total time elapsed: 64.24 s
Calling variants ...
Total processed positions in chrY (chunk 5/13) : 36533
Total time elapsed: 65.91 s
Calling variants ...
Total processed positions in chrY (chunk 3/13) : 38723
Total time elapsed: 66.37 s
Calling variants ...
Total processed positions in chrY (chunk 2/13) : 43770
Total time elapsed: 72.50 s
Calling variants ...
Total processed positions in chrY (chunk 1/13) : 47658
Total time elapsed: 80.74 s

real	1m26.989s
user	9m48.882s
sys	0m30.243s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 11
[INFO] Total heterozygous SNP positions selected: chrY: 21687

real	0m0.762s
user	0m0.656s
sys	0m0.088s

[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/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chrY.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/part44/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chrY
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 ... 0s
(chrY,3s)
parsing total:  3s
merge results ... 0s
writeResult SNP ... 0s

total process: 3s

real	0m3.472s
user	0m8.235s
sys	0m0.764s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 17.0
[INFO] Set reference calls quality cutoff 11.0
[INFO] Low quality reference calls to be processed in chrY: 26213
[INFO] Low quality variants to be processed in chrY: 34866

real	0m0.792s
user	0m0.667s
sys	0m0.106s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chrY (chunk 7/7) : 1079
Total time elapsed: 11.23 s
Calling variants ...
Total processed positions in chrY (chunk 2/7) : 10000
Total time elapsed: 91.05 s
Calling variants ...
Total processed positions in chrY (chunk 1/7) : 10000
Total time elapsed: 91.43 s
Calling variants ...
Total processed positions in chrY (chunk 3/7) : 10000
Total time elapsed: 92.16 s
Calling variants ...
Total processed positions in chrY (chunk 5/7) : 10000
Total time elapsed: 92.18 s
Calling variants ...
Total processed positions in chrY (chunk 4/7) : 10000
Total time elapsed: 93.21 s
Calling variants ...
Total processed positions in chrY (chunk 6/7) : 10000
Total time elapsed: 93.30 s

real	1m35.777s
user	9m8.817s
sys	0m28.111s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chrY: 14986
[INFO] Full-alignment variants processed in chrY: 38380

real	0m1.052s
user	0m1.067s
sys	0m0.117s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz

real	3m13.768s
user	19m12.062s
sys	1m0.250s

[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/part44/tmp/clair3_output/clair3_tumor_output --ctg_name=chrY --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/part44/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/part44/tmp/clair3_output/clair3_tumor_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chrY
[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/part44/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chrY --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/part44/tmp/clair3_output/clair3_tumor_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chrY
[INFO] Chunk number for each contig: 13
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chrY (chunk 8/13) : 7329
Total time elapsed: 39.08 s
Calling variants ...
Total processed positions in chrY (chunk 4/13) : 9532
Total time elapsed: 43.30 s
Calling variants ...
Total processed positions in chrY (chunk 2/13) : 7989
Total time elapsed: 44.10 s
Calling variants ...
Total processed positions in chrY (chunk 10/13) : 9348
Total time elapsed: 46.20 s
Calling variants ...
Total processed positions in chrY (chunk 9/13) : 13536
Total time elapsed: 51.94 s
Calling variants ...
Total processed positions in chrY (chunk 5/13) : 15812
Total time elapsed: 52.23 s
Calling variants ...
Total processed positions in chrY (chunk 3/13) : 16514
Total time elapsed: 54.48 s
Calling variants ...
Total processed positions in chrY (chunk 7/13) : 20564
Total time elapsed: 59.94 s
Calling variants ...
Total processed positions in chrY (chunk 13/13) : 23851
Total time elapsed: 66.40 s
Calling variants ...
Total processed positions in chrY (chunk 1/13) : 25344
Total time elapsed: 67.41 s
Calling variants ...
Total processed positions in chrY (chunk 6/13) : 27005
Total time elapsed: 70.73 s
Calling variants ...
Total processed positions in chrY (chunk 12/13) : 27326
Total time elapsed: 75.58 s
Calling variants ...
Total processed positions in chrY (chunk 11/13) : 32618
Total time elapsed: 80.59 s

real	1m23.256s
user	9m43.700s
sys	0m39.007s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 12
[INFO] Total heterozygous SNP positions selected: chrY: 31855

real	0m0.720s
user	0m0.592s
sys	0m0.097s

[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/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chrY.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/part44/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chrY
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 ... 1s
(chrY,13s)
parsing total:  13s
merge results ... 0s
writeResult SNP ... 0s

total process: 14s

real	0m13.758s
user	0m41.538s
sys	0m2.887s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 20.0
[INFO] Set reference calls quality cutoff 10.0
[INFO] Low quality reference calls to be processed in chrY: 15293
[INFO] Low quality variants to be processed in chrY: 58497

real	0m0.761s
user	0m0.602s
sys	0m0.098s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chrY (chunk 8/8) : 3790
Total time elapsed: 41.07 s
Calling variants ...
Total processed positions in chrY (chunk 3/8) : 10000
Total time elapsed: 100.57 s
Calling variants ...
Total processed positions in chrY (chunk 5/8) : 10000
Total time elapsed: 102.89 s
Calling variants ...
Total processed positions in chrY (chunk 6/8) : 10000
Total time elapsed: 103.29 s
Calling variants ...
Total processed positions in chrY (chunk 7/8) : 10000
Total time elapsed: 103.39 s
Calling variants ...
Total processed positions in chrY (chunk 1/8) : 10000
Total time elapsed: 110.52 s
Calling variants ...
Total processed positions in chrY (chunk 4/8) : 10000
Total time elapsed: 111.71 s
Calling variants ...
Total processed positions in chrY (chunk 2/8) : 10000
Total time elapsed: 113.96 s

real	1m56.455s
user	12m24.097s
sys	0m37.720s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chrY: 25148
[INFO] Full-alignment variants processed in chrY: 60787

real	0m1.113s
user	0m1.054s
sys	0m0.123s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz

real	3m40.589s
user	22m55.153s
sys	1m20.559s

[INFO] Select Heterozygous SNP for Phasing
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/1_select_hetero_snp_for_phasing.log

[INFO] Total HET SNP calls selected: chrY: 51398, not found:568, not match:45, low_qual_count:0. Total normal:36068 Total tumor:52011, pro: 0.9882

[INFO] Phase the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/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/part44/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS

LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/vcf/chrY.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/part44/tmp/clair3_output/phased_output/tumor_phased_chrY
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 ... 0s
(chrY,23s)
parsing total:  23s
merge results ... 0s
writeResult SNP ... 0s

total process: 23s

[INFO] Haplotag the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/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/part44/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/part44/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/part44/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS

phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_phased_chrY.vcf.gz
phased SV file:    
phased MOD file:   
input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_chrY.bam
number of threads: 1
write log file:    false
log file:          
-------------------------------------------
tag region:                    chrY
filter mapping quality below:  1
percentage threshold:          0.6
tag supplementary:             false
-------------------------------------------
parsing SNP VCF ... 0s
tag read start ...
chr: chrY ... 723s
tag read 724s
-------------------------------------------
total process time:  724s
total alignment:     1029125
total supplementary: 12705
total secondary:     0
total unmapped:      0
total tag alignment: 118794
total untagged:      910331

[INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 

[INFO] chrY chunk 7/13: Total snv candidates found: 761, total indel candidates found: 37
[INFO] chrY chunk 9/13: Total snv candidates found: 309, total indel candidates found: 16
[INFO] chrY chunk 8/13: Total snv candidates found: 821, total indel candidates found: 52
[INFO] chrY chunk 6/13: Total snv candidates found: 3048, total indel candidates found: 258
[INFO] chrY chunk 5/13: Total snv candidates found: 2009, total indel candidates found: 445
[INFO] chrY chunk 11/13: Total snv candidates found: 4319, total indel candidates found: 270
[INFO] chrY chunk 12/13: Total snv candidates found: 5416, total indel candidates found: 610
[faidx] Truncated sequence: chrY:57654453-62461074
[INFO] chrY chunk 10/13: Total snv candidates found: 5980, total indel candidates found: 374
[INFO] chrY chunk 4/13: Total snv candidates found: 2127, total indel candidates found: 1355
[INFO] chrY chunk 0/13: Total snv candidates found: 4192, total indel candidates found: 3001
[INFO] chrY chunk 2/13: Total snv candidates found: 2871, total indel candidates found: 1731
[INFO] chrY chunk 3/13: Total snv candidates found: 357, total indel candidates found: 1566
[INFO] chrY chunk 1/13: Total snv candidates found: 421, total indel candidates found: 1763

[INFO] STEP 2: Pileup Model Calling
[INFO] Create Paired Tensors
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_2-1_create_pair_tensor.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor_pileup --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_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 --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/2-1_CPT.log

[INFO] chrY chunk 1-1/3 Tensors generated: 352
[INFO] chrY chunk 1-1/1 Tensors generated: 405
[INFO] chrY chunk 1-1/7 Tensors generated: 758
[INFO] chrY chunk 1-1/9 Tensors generated: 309
[INFO] chrY chunk 1-1/8 Tensors generated: 812
[INFO] chrY chunk 1-1/2 Tensors generated: 2762
[INFO] chrY chunk 1-1/5 Tensors generated: 1950
[INFO] chrY chunk 1-1/0 Tensors generated: 4115
[INFO] chrY chunk 1-1/4 Tensors generated: 2055
[INFO] chrY chunk 1-1/6 Tensors generated: 3015
[INFO] chrY chunk 1-1/11 Tensors generated: 4309
[INFO] chrY chunk 1-1/10 Tensors generated: 5972
[INFO] chrY chunk 1-1/12 Tensors generated: 5342

[INFO] Pileup Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_2-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output/p_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl --use_gpu False --platform ont --ctg_name {1/.} --pileup  --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/2-2_PREDICT.log

[INFO] chrY total processed positions: 309, time elapsed: 0.7s
[INFO] No variant output for p_chrY.9_0_1.vcf, remove empty VCF
[INFO] chrY total processed positions: 352, time elapsed: 1.0s
[INFO] chrY total processed positions: 405, time elapsed: 1.0s
[INFO] chrY total processed positions: 758, time elapsed: 1.4s
[INFO] No variant output for p_chrY.7_0_1.vcf, remove empty VCF
[INFO] chrY total processed positions: 812, time elapsed: 1.5s
[INFO] chrY total processed positions: 1950, time elapsed: 3.2s
[INFO] chrY total processed positions: 2055, time elapsed: 3.6s
[INFO] chrY total processed positions: 2762, time elapsed: 4.7s
[INFO] chrY total processed positions: 3015, time elapsed: 5.0s
[INFO] chrY total processed positions: 4115, time elapsed: 6.7s
[INFO] chrY total processed positions: 4309, time elapsed: 7.2s
[INFO] chrY total processed positions: 5342, time elapsed: 8.5s
[INFO] chrY total processed positions: 5972, time elapsed: 9.5s

[INFO] Merge Pileup VCFs
[INFO] RUN THE FOLLOWING COMMAND:
pypy3 /opt/bin/clairs.py sort_vcf --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --contigs_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output/pileup.vcf

[INFO] Sorting VCFs...
[INFO] Finished VCF sorting!

[INFO] STEP 3: Full-alignment Model Calling
[INFO] Create Full-alignment Paired Tensors
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_3-1_create_pair_tensor_fa.log -j 40 pypy3 /opt/bin/clairs.py create_pair_tensor --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/clair3_output/phased_output/tumor_{1/.}.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --ctg_name {1/.} --samtools samtools --candidates_bed_regions {1} --tensor_can_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/3-1_CPT.log

[INFO] chrY chunk 1-1/3 Tensors generated: 347
[INFO] chrY chunk 1-1/9 Tensors generated: 173
[INFO] chrY chunk 1-1/1 Tensors generated: 399
[INFO] chrY chunk 1-1/8 Tensors generated: 396
[INFO] chrY chunk 1-1/7 Tensors generated: 588
[INFO] chrY chunk 1-1/5 Tensors generated: 1815
[INFO] chrY chunk 1-1/6 Tensors generated: 2359
[INFO] chrY chunk 1-1/2 Tensors generated: 2616
[INFO] chrY chunk 1-1/0 Tensors generated: 3907
[INFO] chrY chunk 1-1/4 Tensors generated: 2046
[INFO] chrY chunk 1-1/11 Tensors generated: 3394
[INFO] chrY chunk 1-1/12 Tensors generated: 4768
[INFO] chrY chunk 1-1/10 Tensors generated: 5087

[INFO] Full-alignment Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/parallel_3-2_predict.log -j 40 python3 /opt/bin/clairs.py predict --tensor_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/vcf_output/fa_{1/}.vcf --chkpnt_fn /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl --use_gpu False --platform ont --ctg_name {1/.} --show_germline  :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part44/logs/3-2_PREDICT.log

[INFO] chrY total processed positions: 173, time elapsed: 30.6s
[INFO] chrY total processed positions: 347, time elapsed: 61.0s
[INFO] chrY total processed positions: 396, time elapsed: 69.7s
[INFO] chrY total processed positions: 399, time elapsed: 70.2s
[INFO] chrY total processed positions: 588, time elapsed: 104.2s