search

CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
Apache License 2.0
52 stars 19 forks source link

[BUG] - check mlst failure #102

Closed erinyoung closed 1 year ago

erinyoung commented 1 year ago

Describe the bug I encountered an error when running phoenix.

Impact Please describe the impact this bug is causing.

To Reproduce This the command that I used

nextflow run CDCgov/phoenix
         -profile singularity
         --input phoenix_input.csv
         --kraken2db /Volumes/IDGenomics_NAS/Data/kraken2_db/phoenix/
         -entry PHOENIX
         -with-tower
         -resume

And sample 2020CK-00232 was part of the sample sheet (Also known as SRR12519092)

Expected behavior No error

Screenshots

The exit status of the task that caused the workflow execution to fail was: 1

Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST (2020CK-00232)'

Caused by:
  Process `PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST (2020CK-00232)` terminated with an error exit status (1)

Command executed:

  wget  --secure-protocol=TLSv1_3 "https://pubmlst.org/data/dbases.xml"

  check_and_fix_MLST2_new2.py --input 2020CK-00232.tsv --taxonomy 2020CK-00232.tax --docfile dbases.xml

  cat <<-END_VERSIONS > versions.yml
  "PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST":
      check_mlst: 1.1
      pubMLST_db_download_date:
  END_VERSIONS

Command exit status:
  1

Command output:
  Array of original itmes 2020CK-00232.filtered.scaffolds.fa
  klebsiella
  -
  gapA(4,144)
  infB(1,123)
  mdh(2)
  pgi(52,168)
  phoE(1)
  rpoB(1,146)
  tonB(7)
  More than one found for  ['4', '144'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], [], 'standard', '2023-03-08']]
  More than one found for  ['1', '123'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144'], 'standard', '2023-03-08']]
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1'], 'standard', '2023-03-08'] ['2'] 2
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1'], 'standard', '2023-03-08'] ['2'] 2
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123'], 'standard', '2023-03-08'] ['2'] 2
  More than one found for  ['52', '168'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2'], 'standard', '2023-03-08']]
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52'], 'standard', '2023-03-08'] ['1'] 1
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52'], 'standard', '2023-03-08'] ['1'] 1
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52'], 'standard', '2023-03-08'] ['1'] 1
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168'], 'standard', '2023-03-08'] ['1'] 1
  More than one found for  ['1', '146'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1'], 'standard', '2023-03-08']]
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146'], 'standard', '2023-03-08'] ['7'] 7
  Schemes found: 1
  [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE'hoE', 'rpoB', 'tonB'], ['4', '123', '2', '52'], 'standard', '2023-03-08'] ['1'] 1
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168'], 'standard', '2023-03-08'] ['1'] 1
  More than one found for  ['1', '146'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1'], 'standard', '2023-03-08']]
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146'], 'standard', '2023-03-08'] ['7'] 7
  Schemes found: 1
  [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146', '7'], 'standard', '2023-03-08']]
  # of catted schemes found: 5
  0 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08']
  1 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08']
  2 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1', '7'], 'standard', '2023-03-08']
  3 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1', '7'], 'standard', '2023-03-08']
  4 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146', '7'], 'standard', '2023-03-08']
  Trimmed catted:  [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146', '7'], 'standard', '2023-03-08']]
  - ['4', '1', '2', '52', '1', '1', '7']
  About to look into ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', 'Novel_profile', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08']
  Looking to convert: klebsiella
  No match found
  Downloading profile file for: No match found
  No species matched your query.

Command error:
  reg:1 2020CK-00232.filtered.scaffolds.fa  klebsiella  -   gapA(4,144) infB(1,123) mdh(2)  pgi(52,168) phoE(1) rpoB(1,146) tonB(7)
  appending - 2020CK-00232.filtered.scaffolds.fa    klebsiella  -   gapA(4,144) infB(1,123) mdh(2)  pgi(52,168) phoE(1) rpoB(1,146) tonB(7)
  No srst2 input file provided
  Taxonomy: Escherichia coli
  [['2020CK-00232.filtered.scaffolds.fa\tklebsiella\t-\tgapA(4,144)\tinfB(1,123)\tmdh(2)\tpgi(52,168)\tphoE(1)\trpoB(1,146)\ttonB(7)', 'mlst', '2020CK-00232.tsv']]
  2020CK-00232.filtered.scaffolds.fa    klebsiella  -   gapA(4,144) infB(1,123) mdh(2)  pgi(52,168) phoE(1) rpoB(1,146) tonB(7)
  Array of original itmes 2020CK-00232.filtered.scaffolds.fa
  klebsiella
  -
  gapA(4,144)
  infB(1,123)
  mdh(2)
  pgi(52,168)
  phoE(1)
  rpoB(1,146)
  tonB(7)
  More than one found for  ['4', '144'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], [], 'standard', '2023-03-08']]
  More than one found for  ['1', '123'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144'], 'standard', '2023-03-08']]
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1'], 'standard', '2023-03-08'] ['2'] 2
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1'], 'standard', '2023-03-08'] ['2'] 2
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123'], 'standard', '2023-03-08'] ['2'] 2
  More than one found for  ['52', '168'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2'], 'standard', '2023-03-08']]
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52'], 'standard', '2023-03-08'] ['1'] 1
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52'], 'standard', '2023-03-08'] ['1'] 1
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52'], 'standard', '2023-03-08'] ['1'] 1
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168'], 'standard', '2023-03-08'] ['1'] 1
  More than one found for  ['1', '146'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1'], 'standard', '2023-03-08']]
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1'], 'standard', '2hoE', 'rpoB', 'tonB'], ['4', '123', '2', '52'], 'standard', '2023-03-08'] ['1'] 1
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168'], 'standard', '2023-03-08'] ['1'] 1
  More than one found for  ['1', '146'] template= [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1'], 'standard', '2023-03-08']]
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1'], 'standard', '2023-03-08'] ['7'] 7
  ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146'], 'standard', '2023-03-08'] ['7'] 7
  Schemes found: 1
  [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146', '7'], 'standard', '2023-03-08']]
  # of catted schemes found: 5
  0 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08']
  1 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08']
  2 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1', '7'], 'standard', '2023-03-08']
  3 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1', '7'], 'standard', '2023-03-08']
  4 ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146', '7'], 'standard', '2023-03-08']
  Trimmed catted:  [['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['144', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '123', '2', '52', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '168', '1', '1', '7'], 'standard', '2023-03-08'], ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', '-', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '146', '7'], 'standard', '2023-03-08']]
  - ['4', '1', '2', '52', '1', '1', '7']
  About to look into ['2020CK-00232.filtered.scaffolds.fa', 'klebsiella', 'Novel_profile', 7, ['gapA', 'infB', 'mdh', 'pgi', 'phoE', 'rpoB', 'tonB'], ['4', '1', '2', '52', '1', '1', '7'], 'standard', '2023-03-08']
  Looking to convert: klebsiella
  No match found
  Downloading profile file for: No match found
  No species matched your query.

Work dir:
  /Volumes/IDGenomics_NAS/testing_phoenix/2023-03-07/work/eb/7486f564181f28ea8bab85736e78d8

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`

Logs If applicable, please attach logs to help describe your problem. These would be the .command.err, .command.out, .command.sh and/or the .nextflow.log files associated with the run/process that failed. The .nextflow.log file is in directory you ran the pipeline from. The .command.XXX files are found in <directory you ran pipeline from>/work/XX/xxxxxxxxxxxxxx here the x and X are a random string of letters/numbers associated with the process. As the pipeline runs on CLI you will see the beginning of these strings to the left of the process that is running.

I have attached the logs here. I have renamed them so they could uploaded into github issues.

command.begin.txt command.err.txt command.log.txt command.out.txt command.run.txt command.sh.txt command.trace.txt

Additional context Add any other context about the problem here. If you have done any internet sleuthing already please link to any relevant posts on the topic.

erinyoung commented 1 year ago

Closing this issue since it's a duplicate of https://github.com/CDCgov/phoenix/issues/91. Sorry!