Error executing process > 'DAQ:BAM_POSTDEDUP_QC:SEQTOOL (1029_GW0-N1-BDNA-1_2375WFLT3_s72)'

Caused by:
  Process `DAQ:BAM_POSTDEDUP_QC:SEQTOOL (1029_GW0-N1-BDNA-1_2375WFLT3_s72)` terminated with an error exit status (1)


Command executed:

  # Matplotlib cache dir must be writable; default location may not be
  export MPLCONFIGDIR=/tmp/matplotlib
  
  all_qc \
      -bam 1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.bam \
      -reference Homo_sapiens_assembly38.fasta \
      -beds xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed altera_v3_targets_postQC_hg38.bed altera_v3_targets_coding_postQC_hg38.bed altera_v3_targets_noncoding_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_footprint.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38.bed FINAL_hotspot_list_07302025_hg38_sorted.bed \
      -dbsnp_bed dbsnp138_hg38_common.bed \
      -dbsnp_vcf dbsnp_146.hg38.vcf.gz \
      -contamination_bed dbsnp_hg38_contam_sites.bed \
      -output_folder 1029_GW0-N1-BDNA-1_2375WFLT3_s72 \
      -threads 31 \
  
  
  merge_qc -folders 1029_GW0-N1-BDNA-1_2375WFLT3_s72/* -output 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72_full_basic_stats.tsv
  
  head -n1 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72_full_basic_stats.tsv > 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72_basic_stats.tsv
  grep -e "$(basename xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed)" 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72_full_basic_stats.tsv >> 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72_basic_stats.tsv
  
  cat <<-END_VERSIONS > versions.yml
  "DAQ:BAM_POSTDEDUP_QC:SEQTOOL":
      seqtool: 1.5.1
  END_VERSIONS

Command exit status:
  1

Command output:
  mkdir -p 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/
  
  
  cat xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed altera_v3_targets_postQC_hg38.bed altera_v3_targets_coding_postQC_hg38.bed altera_v3_targets_noncoding_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_footprint.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38.bed FINAL_hotspot_list_07302025_hg38_sorted.bed | cut -f 1-3 | bedtools sort -g Homo_sapiens_assembly38.fasta.fai | bedtools merge > 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/full_bed.bed
  
  
  seqtool depth -bam 1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.bam -bed 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/full_bed.bed -threads 6 | bgzip -c > 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.depth.gz
  saturation_plot       -bams 1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.bam       -region chr20       -output 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/saturation_plot.png       -threads 1 
  seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.bam > 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/saturation_qc.tsv 
  fragment_size       -bams 1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.bam       -region chr20       -output_prefix 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/fragsize       -threads 1 
  samtools mpileup   -B --min-MQ 60 --min-BQ 30    -f Homo_sapiens_assembly38.fasta   -l dbsnp_hg38_contam_sites.bed   1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.bam > 1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.mpileup && contamination -input 1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.mpileup -dbsnp_vcf dbsnp_146.hg38.vcf.gz > 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/contamination.tsv 
  seqtool noise   -bam 1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.bam   -ref Homo_sapiens_assembly38.fasta   -region chr20   -include_bed 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/full_bed.bed   -exclude_bed dbsnp138_hg38_common.bed   -threads 1 > 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.noise_summary.tsv 
  
  
  
  
  
  
  
  
  
  
  tabix -s 1 -b 2 -e 2 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.depth.gz
  
  
  seqtool depth_hist     -nbins 500     1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.depth.gz     > 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.depth_hist.tsv
  
  
  cat 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title 1029_GW0-N1-BDNA-1_2375WFLT3_s72.md         -output 1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md/1029_GW0-N1-BDNA-1_2375WFLT3_s72.md.depth.png
  

Command error:
  2477634it [00:02, 1137635.32it/s]
  2591924it [00:02, 1139187.51it/s]
  2705854it [00:02, 1135889.48it/s]
  2819739it [00:02, 1136748.08it/s]
  2934450it [00:02, 1139828.87it/s]
  3048845it [00:02, 1141039.73it/s]
  3162954it [00:02, 1139862.21it/s]
  3276944it [00:02, 1138995.42it/s]
  3390846it [00:03, 1132789.25it/s]
  3504134it [00:03, 1125620.46it/s]
  3618088it [00:03, 1129663.28it/s]
  3731067it [00:03, 1128433.34it/s]
  3844833it [00:03, 1131164.40it/s]
  3958656it [00:03, 1133250.67it/s]
  4072526it [00:03, 1134859.27it/s]
  4186696it [00:03, 1136802.88it/s]
  4192441it [00:03, 1124566.37it/s]
  done loading BEDs.
  [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
  Traceback (most recent call last):
    File "/opt/conda/bin/contamination", line 7, in <module>
      sys.exit(main())
    File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/contamination.py", line 66, in main
      gmaf = dbsnp_get_gmaf(dbsnp_records[0])
    File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/contamination.py", line 27, in dbsnp_get_gmaf
      fields = [re.sub("[\[\]]", "", af) for af in variant.info["CAF"]]
    File "pysam/libcbcf.pyx", line 2608, in pysam.libcbcf.VariantRecordInfo.__getitem__
  KeyError: 'Invalid INFO field: CAF'
  multiprocessing.pool.RemoteTraceback: 
  """
  Traceback (most recent call last):
    File "/opt/conda/lib/python3.9/multiprocessing/pool.py", line 125, in worker
      result = (True, func(*args, **kwds))
    File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/all_qc.py", line 74, in run_contamination
      safe_system((
    File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/all_qc.py", line 12, in safe_system
      assert(os.system(cmd) == 0)
  AssertionError
  """
  
  The above exception was the direct cause of the following exception:
  
  Traceback (most recent call last):
    File "/opt/conda/bin/all_qc", line 7, in <module>
      sys.exit(main())
    File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/all_qc.py", line 264, in main
      r.get()
    File "/opt/conda/lib/python3.9/multiprocessing/pool.py", line 771, in get
      raise self._value
  AssertionError

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/d325a35fe33b7950388a0749ac2420

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/seqtool:speedup-6873c4b

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line