Strange error with percolator after SAGE

[ypriverol]

Description of the bug

The exit status of the task that caused the workflow execution to fail was: 9

Error executing process > 'BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSMRESCORING:PERCOLATOR (200ngHela-MudPIT-v1-107)'

Caused by:
  Process `BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSMRESCORING:PERCOLATOR (200ngHela-MudPIT-v1-107)` terminated with an error exit status (9)


Command executed:

  OMP_NUM_THREADS=48 PercolatorAdapter \
      -in 200ngHela-MudPIT-v1-107_sage.idXML \
      -out 200ngHela-MudPIT-v1-107_sage_perc.idXML \
      -threads 48 \
      -subset_max_train 300000 \
      -decoy_pattern DECOY_ \
      -post_processing_tdc \
      -score_type pep \
      -debug 0 \
      2>&1 | tee 200ngHela-MudPIT-v1-107_sage_percolator.log
  
  cat <<-END_VERSIONS > versions.yml
  "BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSMRESCORING:PERCOLATOR":
      PercolatorAdapter: $(PercolatorAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
      percolator: $(percolator -h 2>&1 | grep -E '^Percolator version(.*)' | sed 's/Percolator version //g')
  END_VERSIONS

Command exit status:
  9

Command output:
  Loading input file: 200ngHela-MudPIT-v1-107_sage.idXML
  Merging peptide ids.
  Merging protein ids.
  Prepared percolator input.
  Standard output: Running: /opt/OpenMS/thirdparty/Percolator/percolator -U -m /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_target_pout_psms.tab -M /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_decoy_pout_psms.tab --num-threads 48 -N 300000 -Y /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_pin.tab
  
  Standard error: Percolator version 3.05.0, Build Date May 19 2020 06:55:29
  Copyright (c) 2006-9 University of Washington. All rights reserved.
  Written by Lukas Käll ([email protected]) in the
  Department of Genome Sciences at the University of Washington.
  Issued command:
  /opt/OpenMS/thirdparty/Percolator/percolator -U -m /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_target_pout_psms.tab -M /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_decoy_pout_psms.tab --num-threads 48 -N 300000 -Y /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_pin.tab
  Started Fri Dec 27 17:03:44 2024
  Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
  Reading tab-delimited input from datafile /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_pin.tab
  Features:
  mass peplen charge2 charge3 charge4 charge5 charge6 charge7 charge8 enzN enzC enzInt dm absdm score SAGE:ln(-poisson) SAGE:ln(delta_best) SAGE:ln(delta_next) SAGE:ln(matched_intensity_pct) SAGE:longest_b SAGE:longest_y SAGE:longest_y_pct SAGE:matched_peaks SAGE:scored_candidates 
  Exception caught: ERROR: Reached strange feature with val=inf col=15 for PSM with id controllerType=0controllerNumber=1scan=776
  Terminating.
  
  Process '/opt/OpenMS/thirdparty/Percolator/percolator' did not finish successfully (exit code: 1). Please check the log.
  
  PercolatorAdapter took 2.33 s (wall), 2.20 s (CPU), 0.14 s (system), 2.06 s (user); Peak Memory Usage: 167 MB.

Command wrapper:
  Loading input file: 200ngHela-MudPIT-v1-107_sage.idXML
  Merging peptide ids.
  Merging protein ids.
  Prepared percolator input.
  Standard output: Running: /opt/OpenMS/thirdparty/Percolator/percolator -U -m /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_target_pout_psms.tab -M /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_decoy_pout_psms.tab --num-threads 48 -N 300000 -Y /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_pin.tab
  
  Standard error: Percolator version 3.05.0, Build Date May 19 2020 06:55:29
  Copyright (c) 2006-9 University of Washington. All rights reserved.
  Written by Lukas Käll ([email protected]) in the
  Department of Genome Sciences at the University of Washington.
  Issued command:
  /opt/OpenMS/thirdparty/Percolator/percolator -U -m /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_target_pout_psms.tab -M /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_decoy_pout_psms.tab --num-threads 48 -N 300000 -Y /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_pin.tab
  Started Fri Dec 27 17:03:44 2024
  Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
  Reading tab-delimited input from datafile /tmp/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_1/20241227_170341_hl-codon-bm-15.ebi.ac.uk_42_2_pin.tab
  Features:
  mass peplen charge2 charge3 charge4 charge5 charge6 charge7 charge8 enzN enzC enzInt dm absdm score SAGE:ln(-poisson) SAGE:ln(delta_best) SAGE:ln(delta_next) SAGE:ln(matched_intensity_pct) SAGE:longest_b SAGE:longest_y SAGE:longest_y_pct SAGE:matched_peaks SAGE:scored_candidates 
  Exception caught: ERROR: Reached strange feature with val=inf col=15 for PSM with id controllerType=0controllerNumber=1scan=776
  Terminating.
  
  Process '/opt/OpenMS/thirdparty/Percolator/percolator' did not finish successfully (exit code: 1). Please check the log.
  
  PercolatorAdapter took 2.33 s (wall), 2.20 s (CPU), 0.14 s (system), 2.06 s (user); Peak Memory Usage: 167 MB.

Work dir:
  /hps/nobackup/juan/pride/reanalysis/absolute-expression/cell-lines/PXD009875/work/55/055fb7993e504b8275ede3ee48d146

Container:
  /hps/nobackup/juan/pride/reanalysis/singularity/ghcr.io-openms-openms-tools-thirdparty-sif-latest.img

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

[jpfeuffer]

Col 15 seems to be the first Sage column: SAGE:ln(-poisson)

If that is infinite, I can see it failing. We probably need to filter those psms or add a replacement threshold value.