kdommaraju
commented
10 months ago Added google-lifesciences in the executor list fixed the following error
Error: File not found (the file 'MSGFPlus.jar' could not be found)
if ((workflow.containerEngine || (task.executor == "awsbatch") || (task.executor == google-lifesciences’))
Description of the bug
Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA2_F2)'
Caused by: Process
NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA2_F2)terminated with an error exit status (1)Command executed:
MSGFPlusAdapter \ -protocol automatic \ -in BSA2_F2.mzML \ -out BSA2_F2_msgf.idXML \ \ -threads 2 \ -java_memory 6144 \ -database "18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta" \ -instrument high_res \ -matches_per_spec 1 \ -min_precursor_charge 2 \ -max_precursor_charge 4 \ -min_peptide_length 6 \ -max_peptide_length 40 \ -max_missed_cleavages 2 \ -isotope_error_range 0,1 \ -enzyme "Trypsin/P" \ -tryptic fully \ -precursor_mass_tolerance 5 \ -precursor_error_units ppm \ -fixed_modifications 'Carbamidomethyl (C)' \ -variable_modifications 'Oxidation (M)' \ -max_mods 3 \ -PeptideIndexing:IL_equivalent \ -PeptideIndexing:unmatched_action warn \ -debug 0 \ \ 2>&1 | tee BSA2_F2_msgf.log
cat <<-END_VERSIONS > versions.yml "NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF": MSGFPlusAdapter: $(MSGFPlusAdapter 2>&1 | grep -E '^Version(.)' | sed 's/Version: //g' | cut -d ' ' -f 1) msgf_plus: $(msgf_plus 2>&1 | grep -E '^MS-GF+ Release.') END_VERSIONS
Command exit status: 1
Command output: Input file 'MSGFPlus.jar' could not be found (by searching on PATH). Either provide a full filepath or fix your PATH environment! Error: File not found (the file 'MSGFPlus.jar' could not be found)
Command used and terminal output
No response
Relevant files
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System information
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