Bug with ConsensusID

[ypriverol]

Description of the bug

nf-core/quantms execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 8.

The full error message was:

Error executing process > 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:PROTEININFERENCER'

Caused by:
  Process `NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:PROTEININFERENCER` terminated with an error exit status (8)

Command executed:

  ProteinInference \
      -in ID_mapper_merge.consensusXML \
      -threads 15 \
      -picked_fdr true \
      -picked_decoy_string DECOY_ \
      -protein_fdr true \
      -Algorithm:use_shared_peptides true \
      -Algorithm:annotate_indistinguishable_groups true \
       \
      -Algorithm:score_aggregation_method best \
      -Algorithm:min_peptides_per_protein 1 \
      -out ID_mapper_merge_epi.consensusXML \
      -debug 0 \
      2>&1 | tee ID_mapper_merge_inference.log
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:PROTEININFERENCER":
      ProteinInference: $(ProteinInference 2>&1 | grep -E '^Version(.*) ' | sed 's/Version: //g' | cut -d ' ' -f 1)
  END_VERSIONS

Command exit status:
  8

Command output:
  Loading input...
  Loading input took 01:46 m (wall), 01:46 m (CPU), 3.29 s (system), 01:42 m (user)
   occurred 2 times
  Merging IDs across runs...
  Error: Unexpected internal error (Search settings are not matching across IdentificationRuns. See warnings. Aborting..)
  Searchengine settings or modifications from IDRun OpenMS/ConsensusID_best_2024-01-16T11:45:25_10081377358759304553 do not match with the others. You probably do not want to merge the results with this tool. For merging searches with different engines/settings please use ConsensusID or PercolatorAdapter to create a comparable score.

Command wrapper:
  Loading input...
  Loading input took 01:46 m (wall), 01:46 m (CPU), 3.29 s (system), 01:42 m (user)
   occurred 2 times
  Merging IDs across runs...
  Error: Unexpected internal error (Search settings are not matching across IdentificationRuns. See warnings. Aborting..)
  Searchengine settings or modifications from IDRun OpenMS/ConsensusID_best_2024-01-16T11:45:25_10081377358759304553 do not match with the others. You probably do not want to merge the results with this tool. For merging searches with different engines/settings please use ConsensusID or PercolatorAdapter to create a comparable score.

Work dir:
  /hps/nobackup/juan/pride/reanalysis/absolute-expression/platelet/PXD008467/work/0c/24e9a09f33ece60b674ef8bffb630b

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

Command used and terminal output

No response

Relevant files

No response

System information

No response

Here the folder for testing: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-errors/24e9a09f33ece60b674ef8bffb630b/

[jpfeuffer]

Which searchengines were used and where can I see the idXML file? Potentially the consensusXML would work too, for debugging.

[ypriverol]

SAGE and COMET.

[ypriverol]

With COMET only it works.

[jpfeuffer]

That is a bit big. idXML after ConsensusID would be better

[ypriverol]

Which is file that we need?

[jpfeuffer]

I dont know actually where the error starts. Is this not reproducible with a smaller dataset? Like two files of this whole thing?

[ypriverol]

Looks more like a dataset issue, because I have done others without problem.

[jpfeuffer]

Hmm I would guess it's the parameters for this dataset. E.g. tolerances, enzymes, modifications. Maybe some are not supported by all engines and then the settings stored in the idxml files look different. It would be really nice if you could try with just two files of this one.