Another CPTAC error of pmultiqc, memory


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:
    File "/usr/local/lib/python3.10/site-packages/pmultiqc/modules/quantms/quantms.py", line 1284, in parse_out_mzTab
      mztab_data = mztab.MzTab(self.out_mzTab_path)
    File "/usr/local/lib/python3.10/site-packages/pyteomics/mztab.py", line 650, in __init__
      self._transform_tables()
    File "/usr/local/lib/python3.10/site-packages/pyteomics/mztab.py", line 695, in _transform_tables
      self.peptide_table = self.peptide_table.as_df()
    File "/usr/local/lib/python3.10/site-packages/pyteomics/mztab.py", line 480, in as_df
      table = pd.DataFrame(data=self.rows, columns=self.header)
    File "/usr/local/lib/python3.10/site-packages/pandas/core/frame.py", line 745, in __init__
      arrays, columns, index = nested_data_to_arrays(
    File "/usr/local/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 510, in nested_data_to_arrays
      arrays, columns = to_arrays(data, columns, dtype=dtype)
    File "/usr/local/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 865, in to_arrays
      arr = _list_to_arrays(data)
    File "/usr/local/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 886, in _list_to_arrays
      content = lib.to_object_array(data)
    File "pandas/_libs/lib.pyx", line 2967, in pandas._libs.lib.to_object_array
  numpy.core._exceptions._ArrayMemoryError: Unable to allocate 254. GiB for an array with shape (4152066, 8203) and data type object
  ================================================================================
  |    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/tmpl9ecldw0/multiqc_data' to './multiqc_data'
  |           multiqc | Plots       : multiqc_plots
  INFO:multiqc:Plots       : multiqc_plots
  DEBUG:multiqc:Moving plots directory from '/tmp/tmpl9ecldw0/multiqc_plots' to './multiqc_plots'
  |           multiqc | MultiQC complete
  INFO:multiqc:MultiQC complete

Work dir:
  /hps/nobackup/juan/pride/reanalysis/differential-expression/tmt/PDC000116/work/40/9a81ffca2f533130c8afa812c6fa13

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
bigbio / pmultiqc

Another CPTAC error of pmultiqc, memory #85
