Restart with peakpicking openms

[ypriverol]

@jpfeuffer sometimes the pipeline fails in the id part because of the peak-peaking step by the ThermoRawFileParser. Would be great to "restart" the pipeline, same parameters but with the openms peak peaking enable.

[jpfeuffer]

Makes sense. Can you post how such an error would look like? Maybe we can also check in an independent step, if everything is correctly picked first.

[ypriverol]

Error executing process > 'search_engine_comet (14)'

Caused by:
  Process `search_engine_comet (14)` terminated with an error exit status (4)

Command executed:

  CometAdapter  -in Fetal_Heart_bRP_Elite_19_f22.mzML \
                -out Fetal_Heart_bRP_Elite_19_f22_comet.idXML \
                -threads 8 \
                -database "uniprot-swissprot-isoforms-contaminants_decoy.fasta" \
                -instrument high_res \
                -missed_cleavages 2 \
                -num_hits 1 \
                -num_enzyme_termini fully \
                -enzyme "Trypsin/P" \
                -precursor_charge 2:4 \
                -fixed_modifications 'Carbamidomethyl (C)' \
                -variable_modifications 'Acetyl (Protein N-term)' 'Oxidation (M)' \
                -max_variable_mods_in_peptide 3 \
                -precursor_mass_tolerance 10 \
                -precursor_error_units ppm \
                -fragment_mass_tolerance 0.05 \
                -fragment_bin_offset 0.0 \
                -debug 10 \
  -force \
                > Fetal_Heart_bRP_Elite_19_f22_comet.log

Command exit status:
  4

Command output:
  (empty)

Command wrapper:

      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

      declare -a sum=(0 0 0 0 0 0 0 0)

  (... more ...)
  ------------------------------------------------------------

  Exited with exit code 4.

  Resource usage summary:

      CPU time :                                   9.16 sec.
      Max Memory :                                 -
      Average Memory :                             -
      Total Requested Memory :                     16384.00 MB
      Delta Memory :                               -
      Max Swap :                                   -
      Max Processes :                              -
      Max Threads :                                -
      Run time :                                   37 sec.
      Turnaround time :                            37 sec.

  The output (if any) is above this job summary.

Work dir:
  /hps/nobackup2/proteomics/yperez_temp/reanalysis-datasets/tissue-projects/PXD000561/sdrf-PXD000561-Sample-19/75/a18b4b9d8b90e45f9ab40aba2aeb59

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

[jpfeuffer]

Was this because of empty spectra where there is no peakpicking/centroided annotation performed by TRFP?