pandora_lib_promethion/slurm-2556291.out

WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24': 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/part24 --region chr21:1-45090682 --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/part24/logs
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/split_beds
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/pileup_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/fa_tensor_can
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/tmp_vcf_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf
[INFO] --include_all_ctgs enabled
[INFO] Call variants in contigs: chr21
[INFO] Number of chunks for each contig: 10

[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/part24
[INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/region.bed
[INFO] GENOTYPING MODE VCF FILE PATH: None
[INFO] HYBRID MODE VCF FILE PATH: None
[INFO] REGION FOR CALLING: chr21:1-45090682
[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/part24/tmp/clair3_output/clair3_normal_output --ctg_name=chr21 --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/part24/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/part24/tmp/clair3_output/clair3_normal_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr21
[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/part24/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr21 --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/part24/tmp/clair3_output/clair3_normal_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr21
[INFO] Chunk number for each contig: 10
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr21 (chunk 1/10) : 21247
Total time elapsed: 40.19 s
Calling variants ...
Total processed positions in chr21 (chunk 2/10) : 55447
Total time elapsed: 86.41 s
Calling variants ...
Total processed positions in chr21 (chunk 5/10) : 65383
Total time elapsed: 99.76 s
Calling variants ...
Total processed positions in chr21 (chunk 6/10) : 71156
Total time elapsed: 100.33 s
Calling variants ...
Total processed positions in chr21 (chunk 4/10) : 73057
Total time elapsed: 104.96 s
Calling variants ...
Total processed positions in chr21 (chunk 3/10) : 71284
Total time elapsed: 107.34 s
Calling variants ...
Total processed positions in chr21 (chunk 7/10) : 75897
Total time elapsed: 113.52 s
Calling variants ...
Total processed positions in chr21 (chunk 9/10) : 81308
Total time elapsed: 118.65 s
Calling variants ...
Total processed positions in chr21 (chunk 8/10) : 78139
Total time elapsed: 121.89 s
Calling variants ...
Total processed positions in chr21 (chunk 10/10) : 86992
Total time elapsed: 128.36 s

real	2m15.199s
user	16m24.968s
sys	1m1.295s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
[INFO] Total heterozygous SNP positions selected: chr21: 38730

real	0m1.926s
user	0m1.806s
sys	0m0.107s

[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/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr21.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/part24/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr21
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
(chr21,5s)
parsing total:  5s
merge results ... 0s
writeResult SNP ... 0s

total process: 5s

real	0m5.642s
user	0m11.272s
sys	0m0.759s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 19.0
[INFO] Set reference calls quality cutoff 13.0
[INFO] Low quality reference calls to be processed in chr21: 57899
[INFO] Low quality variants to be processed in chr21: 69711

real	0m1.996s
user	0m1.789s
sys	0m0.182s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr21 (chunk 13/13) : 7610
Total time elapsed: 72.41 s
Calling variants ...
Total processed positions in chr21 (chunk 9/13) : 10000
Total time elapsed: 75.76 s
Calling variants ...
Total processed positions in chr21 (chunk 3/13) : 10000
Total time elapsed: 76.04 s
Calling variants ...
Total processed positions in chr21 (chunk 2/13) : 10000
Total time elapsed: 76.76 s
Calling variants ...
Total processed positions in chr21 (chunk 11/13) : 10000
Total time elapsed: 77.08 s
Calling variants ...
Total processed positions in chr21 (chunk 8/13) : 10000
Total time elapsed: 78.05 s
Calling variants ...
Total processed positions in chr21 (chunk 10/13) : 10000
Total time elapsed: 78.25 s
Calling variants ...
Total processed positions in chr21 (chunk 5/13) : 10000
Total time elapsed: 80.58 s
Calling variants ...
Total processed positions in chr21 (chunk 1/13) : 10000
Total time elapsed: 82.69 s
Calling variants ...
Total processed positions in chr21 (chunk 7/13) : 10000
Total time elapsed: 84.85 s
Calling variants ...
Total processed positions in chr21 (chunk 4/13) : 10000
Total time elapsed: 84.74 s
Calling variants ...
Total processed positions in chr21 (chunk 12/13) : 10000
Total time elapsed: 86.04 s
Calling variants ...
Total processed positions in chr21 (chunk 6/13) : 10000
Total time elapsed: 86.95 s

real	1m30.619s
user	16m49.687s
sys	1m7.751s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr21: 29908
[INFO] Full-alignment variants processed in chr21: 74068

real	0m2.641s
user	0m2.759s
sys	0m0.179s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz

real	4m8.696s
user	33m41.706s
sys	2m11.367s

[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/part24/tmp/clair3_output/clair3_tumor_output --ctg_name=chr21 --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/part24/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/part24/tmp/clair3_output/clair3_tumor_output
[INFO] PLATFORM: ont
[INFO] THREADS: 40
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: chr21
[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/part24/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr21 --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/part24/tmp/clair3_output/clair3_tumor_output/log
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
[INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
[INFO] Call variant in contigs: chr21
[INFO] Chunk number for each contig: 10
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in chr21 (chunk 5/10) : 11068
Total time elapsed: 44.07 s
Calling variants ...
Total processed positions in chr21 (chunk 7/10) : 9368
Total time elapsed: 44.86 s
Calling variants ...
Total processed positions in chr21 (chunk 4/10) : 10732
Total time elapsed: 45.33 s
Calling variants ...
Total processed positions in chr21 (chunk 6/10) : 10461
Total time elapsed: 45.62 s
Calling variants ...
Total processed positions in chr21 (chunk 9/10) : 11777
Total time elapsed: 48.59 s
Calling variants ...
Total processed positions in chr21 (chunk 8/10) : 11175
Total time elapsed: 50.18 s
Calling variants ...
Total processed positions in chr21 (chunk 10/10) : 15430
Total time elapsed: 53.54 s
Calling variants ...
Total processed positions in chr21 (chunk 1/10) : 36882
Total time elapsed: 81.42 s
Calling variants ...
Total processed positions in chr21 (chunk 3/10) : 32029
Total time elapsed: 89.59 s
Calling variants ...
Total processed positions in chr21 (chunk 2/10) : 75635
Total time elapsed: 132.33 s

real	2m15.749s
user	8m50.712s
sys	0m36.304s

[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: chr21: 39429

real	0m1.077s
user	0m0.967s
sys	0m0.103s

[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/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr21.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/part24/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr21
Generate Dot  : False
BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 

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

parsing VCF ... 1s
parsing SV VCF ... 0s
parsing Meth VCF ... 0s
reading reference ... 0s
(chr21,18s)
parsing total:  18s
merge results ... 0s
writeResult SNP ... 0s

total process: 19s

real	0m18.951s
user	0m46.210s
sys	0m3.036s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 21.0
[INFO] Set reference calls quality cutoff 9.0
[INFO] Low quality reference calls to be processed in chr21: 11425
[INFO] Low quality variants to be processed in chr21: 77112

real	0m1.032s
user	0m0.893s
sys	0m0.124s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in chr21 (chunk 1/9) : 10000
Total time elapsed: 85.71 s
Calling variants ...
Total processed positions in chr21 (chunk 3/9) : 10000
Total time elapsed: 89.12 s
Calling variants ...
Total processed positions in chr21 (chunk 4/9) : 10000
Total time elapsed: 98.05 s
Calling variants ...
Total processed positions in chr21 (chunk 2/9) : 10000
Total time elapsed: 101.27 s
Calling variants ...
Total processed positions in chr21 (chunk 6/9) : 10000
Total time elapsed: 103.79 s
Calling variants ...
Total processed positions in chr21 (chunk 7/9) : 10000
Total time elapsed: 105.16 s
Calling variants ...
Total processed positions in chr21 (chunk 9/9) : 8537
Total time elapsed: 105.70 s
Calling variants ...
Total processed positions in chr21 (chunk 5/9) : 10000
Total time elapsed: 110.43 s
Calling variants ...
Total processed positions in chr21 (chunk 8/9) : 10000
Total time elapsed: 110.81 s

real	1m54.184s
user	14m27.321s
sys	0m46.063s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in chr21: 33077
[INFO] Full-alignment variants processed in chr21: 73272

real	0m1.619s
user	0m1.597s
sys	0m0.153s

[INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz

real	4m38.770s
user	24m12.848s
sys	1m26.479s

[INFO] Select Heterozygous SNP for Phasing
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/1_select_hetero_snp_for_phasing.log

[INFO] Total HET SNP calls selected: chr21: 54974, not found:1251, not match:50, low_qual_count:0. Total normal:57735 Total tumor:56275, pro: 0.9769

[INFO] Phase the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/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/part24/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS

LongPhase Ver 1.7

--- File Parameter --- 
SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/vcf/chr21.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/part24/tmp/clair3_output/phased_output/tumor_phased_chr21
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
(chr21,34s)
parsing total:  34s
merge results ... 0s
writeResult SNP ... 1s

total process: 35s

[INFO] Haplotag the Tumor BAM
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/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/part24/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/part24/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/CONTIGS

phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/clair3_output/phased_output/tumor_phased_chr21.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/part24/tmp/clair3_output/phased_output/tumor_chr21.bam
number of threads: 1
write log file:    false
log file:          
-------------------------------------------
tag region:                    chr21
filter mapping quality below:  1
percentage threshold:          0.6
tag supplementary:             false
-------------------------------------------
parsing SNP VCF ... 1s
tag read start ...
chr: chr21 ... 615s
tag read 616s
-------------------------------------------
total process time:  617s
total alignment:     890148
total supplementary: 22088
total secondary:     0
total unmapped:      0
total tag alignment: 306829
total untagged:      583319

[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/part24/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/part24/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 

[INFO] chr21 chunk 0/10: Total snv candidates found: 5072, total indel candidates found: 757
[INFO] chr21 chunk 1/10: Total snv candidates found: 20319, total indel candidates found: 4282
[INFO] chr21 chunk 2/10: Total snv candidates found: 6136, total indel candidates found: 1125
[INFO] chr21 chunk 8/10: Total snv candidates found: 912, total indel candidates found: 1199
[INFO] chr21 chunk 9/10: Total snv candidates found: 3112, total indel candidates found: 2027
[faidx] Truncated sequence: chr21:40580649-45091721
[INFO] chr21 chunk 6/10: Total snv candidates found: 736, total indel candidates found: 1237
[INFO] chr21 chunk 7/10: Total snv candidates found: 1248, total indel candidates found: 1555
[INFO] chr21 chunk 3/10: Total snv candidates found: 616, total indel candidates found: 964
[INFO] chr21 chunk 4/10: Total snv candidates found: 805, total indel candidates found: 947
[INFO] chr21 chunk 5/10: Total snv candidates found: 741, total indel candidates found: 1069

[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/part24/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/part24/tmp/pileup_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/2-1_CPT.log

[INFO] chr21 chunk 3-3/1 Tensors generated: 318
[INFO] chr21 chunk 1-1/3 Tensors generated: 616
[INFO] chr21 chunk 1-1/5 Tensors generated: 741
[INFO] chr21 chunk 1-1/4 Tensors generated: 805
[INFO] chr21 chunk 1-1/6 Tensors generated: 729
[INFO] chr21 chunk 1-1/8 Tensors generated: 912
[INFO] chr21 chunk 1-1/0 Tensors generated: 5057
[INFO] chr21 chunk 1-1/7 Tensors generated: 1248
[INFO] chr21 chunk 2-3/1 Tensors generated: 9316
[INFO] chr21 chunk 1-1/9 Tensors generated: 3109
[faidx] Truncated sequence: chr21:40603737-45091575
[INFO] chr21 chunk 1-3/1 Tensors generated: 9761
[INFO] chr21 chunk 1-1/2 Tensors generated: 6135

[INFO] Pileup Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/pileup_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/2-2_PREDICT.log

[INFO] chr21 total processed positions: 318, time elapsed: 1.2s
[INFO] chr21 total processed positions: 616, time elapsed: 1.7s
[INFO] chr21 total processed positions: 729, time elapsed: 2.0s
[INFO] chr21 total processed positions: 741, time elapsed: 2.0s
[INFO] chr21 total processed positions: 805, time elapsed: 2.2s
[INFO] chr21 total processed positions: 912, time elapsed: 2.4s
[INFO] chr21 total processed positions: 1248, time elapsed: 3.0s
[INFO] chr21 total processed positions: 3109, time elapsed: 6.7s
[INFO] chr21 total processed positions: 5057, time elapsed: 10.3s
[INFO] chr21 total processed positions: 6135, time elapsed: 12.9s
[INFO] chr21 total processed positions: 9316, time elapsed: 18.5s
[INFO] chr21 total processed positions: 9761, time elapsed: 20.0s

[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/part24/tmp/CONTIGS --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/vcf_output --vcf_fn_prefix p_ --output_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/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/part24/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/part24/tmp/fa_tensor_can/{1/}  --platform ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/3-1_CPT.log

[INFO] chr21 chunk 3-3/1 Tensors generated: 316
[INFO] chr21 chunk 1-1/3 Tensors generated: 616
[INFO] chr21 chunk 1-1/6 Tensors generated: 729
[INFO] chr21 chunk 1-1/5 Tensors generated: 741
[INFO] chr21 chunk 1-1/4 Tensors generated: 805
[INFO] chr21 chunk 1-1/8 Tensors generated: 912
[INFO] chr21 chunk 1-1/7 Tensors generated: 1248
[INFO] chr21 chunk 1-1/0 Tensors generated: 4472
[INFO] chr21 chunk 2-3/1 Tensors generated: 8494
[INFO] chr21 chunk 1-1/9 Tensors generated: 3109
[faidx] Truncated sequence: chr21:40603737-45091575
[INFO] chr21 chunk 1-1/2 Tensors generated: 6067
[INFO] chr21 chunk 1-3/1 Tensors generated: 9502

[INFO] Full-alignment Model Prediction
[INFO] RUN THE FOLLOWING COMMAND:
( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/fa_tensor_can/{1/}  --call_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/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/part24/tmp/candidates/CANDIDATES_FILES ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part24/logs/3-2_PREDICT.log

[INFO] chr21 total processed positions: 316, time elapsed: 37.3s
[INFO] chr21 total processed positions: 616, time elapsed: 71.5s
slurmstepd: error: *** JOB 2556291 ON n01 CANCELLED AT 2025-12-08T16:49:54 ***

----------------------------------------------
|                SLURM EPILOG                |
----------------------------------------------
Job ID: 2556291
Cluster: flamingo
User/Group: t_steimle/gs_hpc_biopath
Nodelist: n01
Nodes: 1
Cores per node: 40
Job started at: 2025-12-08 16:24:11
Job ended at:   2025-12-08 16:49:54
Job Wall-clock time: 00:25:43
CPU Utilized: 02:07:35
CPU Efficiency: 12.40% of 17:08:40 core-walltime
Memory Utilized: 16.69 GB
Memory Efficiency: 41.71% of 40.00 GB