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bigbio / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
https://quantms.org
MIT License
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TMT ProteinInference bug with SAGE #299

Open ypriverol opened 11 months ago

ypriverol commented 11 months ago

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 6 \
      -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 10:41 m (wall), 10:35 m (CPU), 23.92 s (system), 10:12 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_2023-10-03T15:33:01_4096749395125007416 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 10:41 m (wall), 10:35 m (CPU), 23.92 s (system), 10:12 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_2023-10-03T15:33:01_4096749395125007416 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/differential-expression/tmt/PDC000113/work/0a/6482206953dcb4781af6f4294fad69

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

The workflow was completed at 2023-10-03T16:38:19.029433+01:00 (duration: 1h 26m 13s)

The command used to launch the workflow was as follows:

nextflow run /hps/nobackup/juan/pride/reanalysis/quantms/main.nf -c /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config -profile ebislurm --input PDC000113.sdrf.tsv --search_engines comet,sage --root_folder /hps/nobackup/juan/pride/reanalysis/differential-expression/tmt/PDC000113/ --local_input_type raw --outdir PDC000113 --database /hps/nobackup/juan/pride/reanalysis/multiomics-configs/databases/Homo-sapiens-uniprot-reviewed-contaminants-decoy-202210.fasta --protein_level_fdr_cutoff 0.01 --posterior_probabilities percolator --psm_level_fdr_cutoff 0.05 --quantify_decoys true --reference_channel 114 --sage_processes 10 -resume

Command used and terminal output

nextflow run /hps/nobackup/juan/pride/reanalysis/quantms/main.nf -c /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config -profile ebislurm --input PDC000113.sdrf.tsv --search_engines comet,sage --root_folder /hps/nobackup/juan/pride/reanalysis/differential-expression/tmt/PDC000113/ --local_input_type raw --outdir PDC000113 --database /hps/nobackup/juan/pride/reanalysis/multiomics-configs/databases/Homo-sapiens-uniprot-reviewed-contaminants-decoy-202210.fasta --protein_level_fdr_cutoff 0.01 --posterior_probabilities percolator --psm_level_fdr_cutoff 0.05 --quantify_decoys true --reference_channel 114 --sage_processes 10 -resume

Relevant files

No response

System information

No response

jpfeuffer commented 11 months ago

Do you have the idxmls of the different search engines for one file? I assume it's a consensusid, otherwise it's weird ;)