PPMErrorCharter error when fewer than 500 PSMs passed the filters

[biodavidjm]

call-ppm_errorcharter fails when "No PSMs passed the filters". For example:

                    "message": "Task proteomics_msgfplus.ppm_errorcharter:41:2 failed. Job exit code 255. Check gs://proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-ppm_errorcharter/shard-41/attempt-2/stderr for more information. PAPI error code 9. Please check the log file for more details: gs://proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-ppm_errorcharter/shard-41/attempt-2/ppm_errorcharter-41.log.",
                    "causedBy": []


PPMErrorCharter, version 1.2.7632.25833 (November 23, 2020)

Using options:
 PSM results file:       /cromwell_root/proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-msgf_tryptic/shard-41/output_msgf_tryptic/04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06.mzid
 Fixed .mzML file        /cromwell_root/proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-msconvert_mzrefiner/shard-41/output_msconvert_mzrefiner/04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06_FIXED.mzML
 Histogram plot:         output_ppm_errorcharter/04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06-histograms.png
 Mass Errors plot:       output_ppm_errorcharter/04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06-masserrors.png
 Spec EValue threshold:  1.0E-10
 Histogram bin size:     0.5
 Generating plots with:  Python


Creating plots for "04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06.mzid"

Loading data from the .mzid file
  Fewer than 500 PSMs passed the filters (0)

  No PSMs passed the filters

No PSM results were read from 04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06.mzid; nothing to plot

No PSM results were read from 04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06.mzid; nothing to plot
2023/06/05 19:49:50 Starting delocalization.
2023/06/05 19:49:50 Delocalization script execution started...
2023/06/05 19:49:50 Delocalizing output /cromwell_root/memory_retry_rc -> gs://proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-ppm_errorcharter/shard-41/attempt-2/memory_retry_rc
2023/06/05 19:49:52 Delocalizing output /cromwell_root/rc -> gs://proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-ppm_errorcharter/shard-41/attempt-2/rc
2023/06/05 19:49:54 Delocalizing output /cromwell_root/monitoring.log -> gs://proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-ppm_errorcharter/shard-41/attempt-2/monitoring.log
2023/06/05 19:49:55 Delocalizing output /cromwell_root/stdout -> gs://proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-ppm_errorcharter/shard-41/attempt-2/stdout
2023/06/05 19:49:57 Delocalizing output /cromwell_root/stderr -> gs://proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-ppm_errorcharter/shard-41/attempt-2/stderr
2023/06/05 19:49:58 Delocalizing output /cromwell_root/output_ppm_errorcharter/04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06-histograms.png -> gs://proteomics-pipeline/results/proteomics_msgfplus/809e1173-06ed-46c4-b7f6-0085abf0117f/call-ppm_errorcharter/shard-41/attempt-2/output_ppm_errorcharter/04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06-histograms.png
Required file output '/cromwell_root/output_ppm_errorcharter/04MOTRPAC_PASS1A-06_T55_PH_PN_20190419_f06-histograms.png' does not exist.

Matt proposed: "simply proceed with running MS-GF+ on the original .mzML file."