Error memory TMT dataset PXD012574

[ypriverol]

Description of the bug

URL of the working file: http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/proteogenomics/benchmakrs/15acadc82868c799e567dd1b219b44/

nf-core/quantms execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 130.

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 (130)

Command executed:

  ProteinInference \
      -in ID_mapper_merge.consensusXML \
      -threads 48 \
      -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 \
      |& 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:
  130

Command output:
  Loading input...
  Loading input took 41.49 s (wall), 41.40 s (CPU), 0.63 s (system), 40.77 s (user)
   occurred 2 times
  Merging IDs across runs...
  Merging IDs across runs took 0.00 s (wall), 0.00 s (CPU), 0.00 s (system), 0.00 s (user)
  Aggregating protein scores...
  Building graph on 738370 features, 18751 unassigned spectra (if chosen) and 22415 proteins.
  Progress of 'Building graph...':
  
  -- done [took 0.66 s (CPU), 0.66 s (Wall)] -- 
  Progress of 'Annotating indistinguishable proteins...':
  
  -- done [took 1.23 s (CPU), 0.07 s (Wall)] -- 
  Found 17785 connected components.
  Aggregating protein scores took 0.00 s (wall), 0.00 s (CPU), 0.00 s (system), 0.00 s (user)
  Calculating target-decoy q-values...
  Storing output...
  ConsensusXMLFile::store():  found 1 invalid unique ids

Command wrapper:
  Aggregating protein scores...
  Building graph on 738370 features, 18751 unassigned spectra (if chosen) and 22415 proteins.
  Progress of 'Building graph...':
  
  -- done [took 0.66 s (CPU), 0.66 s (Wall)] -- 
  Progress of 'Annotating indistinguishable proteins...':
  
  -- done [took 1.23 s (CPU), 0.07 s (Wall)] -- 
  Found 17785 connected components.
  Aggregating protein scores took 0.00 s (wall), 0.00 s (CPU), 0.00 s (system), 0.00 s (user)
  Calculating target-decoy q-values...
  Storing output...
  ConsensusXMLFile::store():  found 1 invalid unique ids
  
  ------------------------------------------------------------
  Sender: LSF System 
  Subject: Job 7751604:  in cluster  Exited
  
  Job  was submitted from host  by user  in cluster  at Thu Nov 24 18:00:09 2022
  Job was executed on host(s) <48*hl-codon-bm-07>, in queue , as user  in cluster  at Thu Nov 24 18:00:19 2022
   was used as the home directory.
   was used as the working directory.
  Started at Thu Nov 24 18:00:19 2022
  Terminated at Thu Nov 24 18:10:28 2022
  Results reported at Thu Nov 24 18:10:28 2022
  
  Your job looked like:
  
  ------------------------------------------------------------
  # LSBATCH: User input
  ------------------------------------------------------------
  
  TERM_MEMLIMIT: job killed after reaching LSF memory usage limit.
  Exited with exit code 130.
  
  Resource usage summary:
  
      CPU time :                                   612.00 sec.
      Max Memory :                                 318248 MB
      Average Memory :                             151518.11 MB
      Total Requested Memory :                     307200.00 MB
      Delta Memory :                               -11048.00 MB
      Max Swap :                                   -
      Max Processes :                              13
      Max Threads :                                68
      Run time :                                   608 sec.
      Turnaround time :                            619 sec.
  
  The output (if any) is above this job summary.

Work dir:
  /hps/nobackup/juan/pride/reanalysis/differential-expression/tmt/PXD012574/work/39/15acadc82868c799e567dd1b219b44

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Command used and terminal output

No response

Relevant files

No response

System information

No response