Error executing process > 'SEQTOOL (dna_s1343)'

Caused by:
  Process `SEQTOOL (dna_s1343)` 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 dna_s1343.bam \
      -reference Homo_sapiens_assembly38.fasta \
      -beds altera_v2_targets_effective_coding_hg38.bed altera_v2_targets_effective_noncoding_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v2.bed altera_v2_targets_coding_hg38.bed altera_v2_targets_noncoding_hg38.bed altera_v2_probes_noncoding_postQC_hg38.bed altera_v2_probes_coding_postQC_hg38.bed \
      -dbsnp_bed dbsnp138_hg38_common.bed \
      -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz \
      -contamination_bed dbsnp_hg38_contam_sites.bed \
      -output_folder qc \
      -threads 31 \
  
  
  merge_qc -folders qc/* -output qc/dna_s1343_full_basic_stats.tsv
  
  head -n1 qc/dna_s1343_full_basic_stats.tsv > qc/dna_s1343_basic_stats.tsv
  grep -e "$(basename altera_v2_targets_effective_coding_hg38.bed)" qc/dna_s1343_full_basic_stats.tsv >> qc/dna_s1343_basic_stats.tsv
  
  cat <<-END_VERSIONS > versions.yml
  "SEQTOOL":
      seqtool: 1.5.1
  END_VERSIONS

Command exit status:
  1

Command output:
  mkdir -p qc/dna_s1343/
  
  
  cat altera_v2_targets_effective_coding_hg38.bed altera_v2_targets_effective_noncoding_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v2.bed altera_v2_targets_coding_hg38.bed altera_v2_targets_noncoding_hg38.bed altera_v2_probes_noncoding_postQC_hg38.bed altera_v2_probes_coding_postQC_hg38.bed | cut -f 1-3 | bedtools sort -g Homo_sapiens_assembly38.fasta.fai | bedtools merge > qc/dna_s1343/full_bed.bed
  
  
  saturation_plot       -bams dna_s1343.bam       -region chr20       -output qc/dna_s1343/saturation_plot.png       -threads 1 
  seqtool qc_all     -bam dna_s1343.bam     -depth_bed qc/dna_s1343/full_bed.bed     -reference Homo_sapiens_assembly38.fasta     -output_dir qc/dna_s1343     -bam_threads 4     altera_v2_targets_effective_coding_hg38.bed altera_v2_targets_effective_noncoding_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v2.bed altera_v2_targets_coding_hg38.bed altera_v2_targets_noncoding_hg38.bed altera_v2_probes_noncoding_postQC_hg38.bed altera_v2_probes_coding_postQC_hg38.bed
  seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       dna_s1343.bam > qc/dna_s1343/saturation_qc.tsv 
  fragment_size       -bams dna_s1343.bam       -region chr20       -output_prefix qc/dna_s1343/fragsize       -threads 1 
  samtools mpileup   -B --min-MQ 60 --min-BQ 30    -f Homo_sapiens_assembly38.fasta   -l dbsnp_hg38_contam_sites.bed   dna_s1343.bam > dna_s1343.mpileup && contamination -input dna_s1343.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > qc/dna_s1343/contamination.tsv 
  seqtool noise   -bam dna_s1343.bam   -ref Homo_sapiens_assembly38.fasta   -region chr20   -include_bed qc/dna_s1343/full_bed.bed   -exclude_bed dbsnp138_hg38_common.bed   -threads 1 > qc/dna_s1343/dna_s1343.noise_summary.tsv 
  
  
  
  
  
  
  
  
  

Command error:
  [qc_all] Processed 580000000 reads (3669.38s, 0.16M reads/s)...
  [qc_all] Processed 590000000 reads (3732.82s, 0.16M reads/s)...
  [qc_all] Processed 600000000 reads (3798.86s, 0.16M reads/s)...
  [qc_all] Processed 610000000 reads (3871.99s, 0.16M reads/s)...
  [qc_all] Processed 620000000 reads (3950.03s, 0.16M reads/s)...
  [qc_all] Processed 630000000 reads (4021.19s, 0.16M reads/s)...
  [qc_all] Processed 640000000 reads (4091.10s, 0.16M reads/s)...
  [qc_all] Processed 650000000 reads (4158.56s, 0.16M reads/s)...
  [qc_all] Processed 660000000 reads (4229.59s, 0.16M reads/s)...
  [qc_all] Processed 670000000 reads (4304.94s, 0.16M reads/s)...
  [qc_all] Processed 680000000 reads (4373.88s, 0.16M reads/s)...
  [qc_all] Processed 690000000 reads (4449.19s, 0.16M reads/s)...
  [qc_all] Processed 700000000 reads (4521.83s, 0.15M reads/s)...
  [qc_all] Processed 710000000 reads (4588.45s, 0.15M reads/s)...
  [qc_all] Processed 720000000 reads (4661.36s, 0.15M reads/s)...
  [qc_all] Processed 730000000 reads (4731.01s, 0.15M reads/s)...
  [qc_all] Processed 740000000 reads (4809.21s, 0.15M reads/s)...
  [qc_all] Processed 750000000 reads (4884.70s, 0.15M reads/s)...
  Error: signal 11:
  seqtool(+0x9d30)[0x56183c6ebd30]
  /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f8720a1f520]
  /lib/x86_64-linux-gnu/libc.so.6(+0x1b20bc)[0x7f8720b8f0bc]
  seqtool(+0x37f76)[0x56183c719f76]
  seqtool(+0x216d8)[0x56183c7036d8]
  seqtool(+0x9a4a)[0x56183c6eba4a]
  /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f8720a06d90]
  /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f8720a06e40]
  seqtool(+0x9c35)[0x56183c6ebc35]
  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 221, in run_qc_all
      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 288, 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/76/2dc06ffbc7afe63ed7776befb679cd

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/seqtool:ultra1-5334e0c

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`