SEARCHENGINECOMET error

[inemesb]

Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (140521_MO_H710_Tn8_1_140523083511)'

Caused by:
Process NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (140521_MO_H710_Tn8_1_140523083511) terminated with an error exit status (9)

Command executed:

CometAdapter
-in 140521_MO_H710_Tn8_1_140523083511.mzML
-out 140521_MO_H710_Tn8_1_140523083511_comet.idXML
-threads 4
-database "UP000005640_9606_decoy.fasta"
-instrument low_res
-missed_cleavages 2
-min_peptide_length 6
-max_peptide_length 40
-num_hits 1
-num_enzyme_termini fully
-enzyme "Trypsin"
-isotope_error 0/1
-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 10.0
-precursor_error_units ppm
-fragment_mass_tolerance 0.2
-fragment_bin_offset 0.4
-minimum_peaks 10
-PeptideIndexing:IL_equivalent
-PeptideIndexing:unmatched_action warn
-debug 0
-force

2>&1 | tee 140521_MO_H710_Tn8_1_140523083511_comet.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET":
CometAdapter: $(CometAdapter 2>&1 | grep -E '^Version(.)' | sed 's/Version: //g' | cut -d ' ' -f 1)
Comet: $(comet 2>&1 | grep -E "Comet version." | sed 's/Comet version //g' | sed 's/"//g')
END_VERSIONS

Command exit status:
9

Command output:
Fragment bin size (== 2x 'fragment_mass_tolerance') or offset is quite low for low-res instruments (Comet recommends 1.005 Da bin size & 0.4 Da offset). Current value: fragment bin size = 0.4(=2x0.2) and offset = 0.4. Use the '-force' flag to continue anyway.
You used the '-force'!
Standard output: Running: /usr/local/bin/comet.exe -P/tmp/20240903_073255_366ae723c94f_267_1/param.txt -N/tmp/20240903_073255_366ae723c94f_267_1/result 140521_MO_H710_Tn8_1_140523083511.mzML
Warning - invalid parameter found: export_additional_pepxml_scores. Parameter will be ignored.
Comet version "2023.01 rev. 0"

Standard error: Process '/usr/local/bin/comet.exe' crashed hard (segfault-like). Please check the log.

CometAdapter took 0.30 s (wall), 0.30 s (CPU), 0.02 s (system), 0.28 s (user); Peak Memory Usage: 59 MB.

Command error:
Fragment bin size (== 2x 'fragment_mass_tolerance') or offset is quite low for low-res instruments (Comet recommends 1.005 Da bin size & 0.4 Da offset). Current value: fragment bin size = 0.4(=2x0.2) and offset = 0.4. Use the '-force' flag to continue anyway.
You used the '-force'!
Standard output: Running: /usr/local/bin/comet.exe -P/tmp/20240903_073255_366ae723c94f_267_1/param.txt -N/tmp/20240903_073255_366ae723c94f_267_1/result 140521_MO_H710_Tn8_1_140523083511.mzML
Warning - invalid parameter found: export_additional_pepxml_scores. Parameter will be ignored.
Comet version "2023.01 rev. 0"

Standard error: Process '/usr/local/bin/comet.exe' crashed hard (segfault-like). Please check the log.

CometAdapter took 0.30 s (wall), 0.30 s (CPU), 0.02 s (system), 0.28 s (user); Peak Memory Usage: 59 MB.

Work dir:
/home/inemesb/MTLS/Proteomics/CB2110/lab1/work/72/e81f74cea0b92c0c1a5bdd16e4acc4

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out