Bug with LFQ data

[ypriverol]

Description of the bug

We have a big error with LFQ data:

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:LFQ:PROTEOMICSLFQ (PDC000111.sdrf_openms_design)'

Caused by:
  Process `NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ (PDC000111.sdrf_openms_design)` terminated with an error exit status (8)

Command executed:

  ProteomicsLFQ \
      -threads 12 \
      -in TCGA-AA-3525-01A-12_W_VU_20121210_A0218_7F_R_FR04.mzML TCGA-A6-3810-01A-
      -design PDC000111.sdrf_openms_design.tsv \
      -fasta Homo-sapiens-uniprot-reviewed-contaminants-decoy-202210.fasta \
      -protein_inference aggregation \
      -quantification_method feature_intensity \
      -targeted_only false \
      -mass_recalibration false \
      -transfer_ids mean \
      -protein_quantification unique_peptides \
      -alignment_order star \
      -PeptideQuantification:quantify_decoys \
      -psmFDR 0.05 \
      -proteinFDR 0.01 \
      -picked_proteinFDR true \
      -out_cxml PDC000111.sdrf_openms_design_openms.consensusXML \
      -out PDC000111.sdrf_openms_design_openms.mzTab \
      -out_msstats PDC000111.sdrf_openms_design_msstats_in.csv \
       \
      -debug 0 \
      |& tee proteomicslfq.log
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ":
      ProteomicsLFQ: $(ProteomicsLFQ 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -c 1-50)
  END_VERSIONS

Command exit status:
  8

Command output:
  Peptide identification engine: MS-GF+
  Enzyme: Trypsin/P
  Info: using 'full' as enzyme specificity (obtained from idXML) for digestion.
  Building trie ... done (0s)
  Compressing trie to BFS format ...
   done (0s)
  Mapping 2301 peptides to 41372 proteins.
  Searching with up to 3 ambiguous amino acid(s) and 0 mismatch(es)!
  Merge took: 0.00 s (wall), 0.00 s (CPU), 0.00 s (system), 0.00 s (user)
  Memory usage (Aho-Corasick): 0 MB (working set delta), 0 MB (peak working set delta)
  
  
  Aho-Corasick done:
    found 3704 hits for 2301 of 2301 peptides.
  Peptide hits passing enzyme filter: 3704
       ... rejected by enzyme filter: 154
  -----------------------------------
  Peptide statistics
  
    unmatched                : 0 (0 %)
    target/decoy:
      match to target DB only: 2109 (91 %)
      match to decoy DB only : 190 (8 %)
      match to both          : 2 (0 %)
  
    mapping to proteins:
      no match (to 0 protein)         : 0
      unique match (to 1 protein)     : 1835
      non-unique match (to >1 protein): 466
  -----------------------------------
  Protein statistics
  
    total proteins searched: 41372
    matched proteins       : 1405 (1405 new)
    matched target proteins: 1232 (87 %)
    matched decoy proteins : 173 (12 %)
    orphaned proteins      : 31 (all removed)
  -----------------------------------
  Progress of 'mass trace detection':
  
    1.90 %               
  -- done [took 0.13 s (CPU), 0.13 s (Wall)] -- 
  Median chromatographic FWHM: 12.8086
  Using 1844 seeds from untargeted feature extraction.
  RT window size calculated as 256.172 seconds.
  Preparing mapping of peptide data...
  #Seeds without RT and m/z overlap with identified peptides added: 999
  Progress of 'Creating assay library and extracting chromatograms':
  Error: Unexpected internal error (Chromatogram must be sorted by position)
   occurred 2 times

Command wrapper:
      done < <(ps -e -o pid= -o ppid=)
  
      pstat() {
          local x_pid=$1
          local STATUS=$(2> /dev/null < /proc/$1/status egrep 'Vm|ctxt')
  
          if [ $? = 0 ]; then
          local  x_vsz=$(echo "$STATUS" | grep VmSize | awk '{print $2}' || echo -n '0')
          local  x_rss=$(echo "$STATUS" | grep VmRSS | awk '{print $2}' || echo -n '0')
          local x_peak=$(echo "$STATUS" | egrep 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
          local x_pmem=$(awk -v rss=$x_rss -v mem_tot=$mem_tot 'BEGIN {printf "%.0f", rss/mem_tot*100*10}' || echo -n '0')
          local vol_ctxt=$(echo "$STATUS" | grep '\bvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
          local inv_ctxt=$(echo "$STATUS" | grep '\bnonvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
          cpu_stat[x_pid]="$x_pid $x_pmem $x_vsz $x_rss $x_peak $vol_ctxt $inv_ctxt"
          fi
      }
  
      pwalk() {
          pstat $1
          for i in ${ALL_CHILDREN[$1]:=}; do pwalk $i; done
      }
  
      pwalk $1
  }
  
  nxf_stat() {
      cpu_stat=()
      nxf_tree $1
  
  
  (... more ...)
  ------------------------------------------------------------
  
  Exited with exit code 8.
  
  Resource usage summary:
  
      CPU time :                                   112508.00 sec.
      Max Memory :                                 6203 MB
      Average Memory :                             3972.73 MB
      Total Requested Memory :                     81920.00 MB
      Delta Memory :                               75717.00 MB
      Max Swap :                                   -
      Max Processes :                              17
      Max Threads :                                36
      Run time :                                   17862 sec.
      Turnaround time :                            17863 sec.
  
  The output (if any) is above this job summary.

Work dir:
  /hps/nobackup/juan/pride/reanalysis/differential-expression/lfq/PDC000111/work/4a/da465f0711161814f64179319671bc

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Command used and terminal output

No response

Relevant files

No response

System information

No response