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bigbio / pmultiqc

A library for QC report based on MultiQC framework
GNU General Public License v3.0
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Error in plasama dataset #93

Closed ypriverol closed 7 months ago

ypriverol commented 7 months ago 

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:

  set -x
  set -e

  # leaving here to ease debugging
  ls -lcth *

  echo ">>>>>>>>> Experimental Design <<<<<<<<<"
  cat results/*openms_design.tsv

  echo ">>>>>>>>> Running Multiqc <<<<<<<<<"
  multiqc \
      -f \
      --config ./results/multiqc_config.yml \
       \
       \
       \
      --ignored_idxml \
      --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:
  664   blood plasma    664 67
  665   blood plasma    665 67
  666   blood plasma    666 67
  667   blood plasma    667 67
  668   blood plasma    668 67
  669   blood plasma    669 67
  670   blood plasma    670 67
  671   blood plasma    671 68
  672   blood plasma    672 68
  673   blood plasma    673 68
  674   blood plasma    674 68
  675   blood plasma    675 68
  676   blood plasma    676 68
  677   blood plasma    677 68
  678   blood plasma    678 68
  679   blood plasma    679 68
  680   blood plasma    680 68
  681   blood plasma    681 69
  682   blood plasma    682 69
  683   blood plasma    683 69
  684   blood plasma    684 69
  685   blood plasma    685 69
  686   blood plasma    686 69
  687   blood plasma    687 69
  688   blood plasma    688 69
  689   blood plasma    689 69
  690   blood plasma    690 69
  691   blood plasma    691 70
  692   blood plasma    692 70
  693   blood plasma    693 70
  694   blood plasma    694 70
  695   blood plasma    695 70
  696   blood plasma    696 70
  697   blood plasma    697 70
  698   blood plasma    698 70
  699   blood plasma    699 70
  700   blood plasma    700 70
  701   blood plasma    701 71
  702   blood plasma    702 71
  703   blood plasma    703 71
  704   blood plasma    704 71
  705   blood plasma    705 71
  706   blood plasma    706 71
  707   blood plasma    707 71
  708   blood plasma    708 71
  709   blood plasma    709 71
  710   blood plasma    710 71
  >>>>>>>>> Running Multiqc <<<<<<<<<
  Warning: OPENMS_DATA_PATH environment variable not found and no share directory was installed. Some functionality might not work as expected.
  No decoy peptides found -> only showing target peptides

Command error:
      output = mod()
               ^^^^^
    File "/usr/local/lib/python3.11/site-packages/pmultiqc/modules/quantms/quantms.py", line 189, in __init__
      self.CalHeatMapScore()
    File "/usr/local/lib/python3.11/site-packages/pmultiqc/modules/quantms/quantms.py", line 1025, in CalHeatMapScore
      pep_median = np.median([j for j in T if not math.isnan(j) is True])
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/pmultiqc/modules/quantms/quantms.py", line 1025, in 
      pep_median = np.median([j for j in T if not math.isnan(j) is True])
                                                  ^^^^^^^^^^^^^
  TypeError: must be real number, not NoneType
  ================================================================================
  DEBUG:multiqc.modules.custom_content.custom_content:No samples found: custom content (total_ion_chromatograms)
  DEBUG:multiqc.modules.custom_content.custom_content:No samples found: custom content (base_peak_chromatograms)
  DEBUG:multiqc.modules.custom_content.custom_content:No samples found: custom content (number_of_peaks)
  DEBUG:multiqc.modules.custom_content.custom_content:No samples found: custom content (general_stats)
  |    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.utils.software_versions:Reading software versions from config.software_versions
  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'.
  DEBUG: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/tmpqqlnzaby/multiqc_data' to './multiqc_data'
  DEBUG:multiqc:Full report path: multiqc_report.html
  |           multiqc | Plots       : multiqc_plots
  INFO:multiqc:Plots       : multiqc_plots
  DEBUG:multiqc:Moving plots directory from '/tmp/tmpqqlnzaby/multiqc_plots' to './multiqc_plots'
  |           multiqc | Flat-image plots used. Disable with '--interactive'. See 
  docs.
  |           multiqc | MultiQC complete
  INFO:multiqc:MultiQC complete

Work dir:
  /hps/nobackup/juan/pride/reanalysis/absolute-expression/platelet/PXD008468/work/de/66f71ea3a7c499e6cec2a2355dda46

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