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bigbio / pmultiqc

A library for QC report based on MultiQC framework
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Another CPTAC error in pmultiqc #83

Closed ypriverol closed 11 months ago

ypriverol commented 12 months ago

Here another CPTAC error similar to the previous ones:


nf-core/quantms execution completed unsuccessfully!

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

The full error message was:

Error executing process > 'NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE (1)'

Caused by:
  Process `NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE (1)` terminated with an error exit status (1)

Command executed:

  multiqc \
      -f \
      --config ./results/multiqc_config.yml \
       \
       \
       \
      --quantification_method feature_intensity \
      ./results \
      -o .

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE":
      pmultiqc: $(multiqc --pmultiqc_version | sed -e "s/pmultiqc, version //g")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  │     output = mod()                                                           │
  │   File "/usr/local/lib/python3.10/site-packages/pmultiqc/modules/quantms/qua │
  │     self.parse_idxml(mt)                                                     │
  │   File "/usr/local/lib/python3.10/site-packages/pmultiqc/modules/quantms/qua │
  │     mzml_table[mzML_name]['Comet'] = identified_num                          │
  │ KeyError: 'TCGA_114C_13-1409-01A-01_24-1416-01A-01_29-1769-01A-01_W_JHUZ_201 │
  │                                                                              │
  ╰──────────────────────────────────────────────────────────────────────────────╯
  DEBUG:multiqc:Oops! The 'quantms' MultiQC module broke...
  ================================================================================
  Traceback (most recent call last):
    File "/usr/local/lib/python3.10/site-packages/multiqc/multiqc.py", line 654, in run
      output = mod()
    File "/usr/local/lib/python3.10/site-packages/pmultiqc/modules/quantms/quantms.py", line 172, in __init__
      self.parse_idxml(mt)
    File "/usr/local/lib/python3.10/site-packages/pmultiqc/modules/quantms/quantms.py", line 1237, in parse_idxml
      mzml_table[mzML_name]['Comet'] = identified_num
  KeyError: 'TCGA_114C_13-1409-01A-01_24-1416-01A-01_29-1769-01A-01_W_JHUZ_20130522_pool.mzML'
  ================================================================================
  |    custom_content | nf-core-quantms-methods-description: Found 1 sample (html)
  INFO:multiqc.modules.custom_content.custom_content:nf-core-quantms-methods-description: Found 1 sample (html)
  |    custom_content | software_versions: Found 1 sample (html)
  INFO:multiqc.modules.custom_content.custom_content:software_versions: Found 1 sample (html)
  |    custom_content | nf-core-quantms-summary: Found 1 sample (html)
  INFO:multiqc.modules.custom_content.custom_content:nf-core-quantms-summary: Found 1 sample (html)
  DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' not found.
  DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' not found for module 'nf-core/quantms Methods Description'.
  DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-methods-description' not found for module 'nf-core/quantms Methods Description'.
  DEBUG:multiqc:Reordering sections: anchor 'software_versions' not found for module 'nf-core/quantms Methods Description'.
  DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-summary' not found for module 'nf-core/quantms Methods Description'.
  DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' not found for module 'nf-core/quantms Software Versions'.
  DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-methods-description' not found for module 'nf-core/quantms Software Versions'.
  DEBUG:multiqc:Reordering sections: anchor 'software_versions' not found for module 'nf-core/quantms Software Versions'.
  DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-summary' not found for module 'nf-core/quantms Software Versions'.
  DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' not found for module 'nf-core/quantms Workflow Summary'.
  DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-methods-description' not found for module 'nf-core/quantms Workflow Summary'.
  DEBUG:multiqc:Reordering sections: anchor 'software_versions' not found for module 'nf-core/quantms Workflow Summary'.
  DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-summary' not found for module 'nf-core/quantms Workflow Summary'.
  |           multiqc | Compressing plot data
  INFO:multiqc:Compressing plot data
  |           multiqc | Report      : multiqc_report.html
  INFO:multiqc:Report      : multiqc_report.html
  |           multiqc | Data        : multiqc_data
  INFO:multiqc:Data        : multiqc_data
  DEBUG:multiqc:Moving data file from '/tmp/tmp7xyqp8h5/multiqc_data' to './multiqc_data'
  |           multiqc | Plots       : multiqc_plots
  INFO:multiqc:Plots       : multiqc_plots
  DEBUG:multiqc:Moving plots directory from '/tmp/tmp7xyqp8h5/multiqc_plots' to './multiqc_plots'
  |           multiqc | MultiQC complete
  INFO:multiqc:MultiQC complete

Work dir:
  /hps/nobackup/juan/pride/reanalysis/differential-expression/tmt/PDC000113/work/c7/59a83da997bde5052d937bdf1d9a69

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Folder here: http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/59a83da997bde5052d937bdf1d9a69/

WangHong007 commented 12 months ago

@ypriverol Yes, this issue was coused by the same bug in #82 .