Closed ypriverol closed 5 months ago
When Lys-C/P to OpenMS enzyme, We transform to sentence style (Lys-c/p), However, OpenMS uses Sentence and Camel combined. This definition https://github.com/bigbio/sdrf-pipelines/blob/07c1dea93569ef9ca789739f93a96115b46fe2a0/sdrf_pipelines/openms/openms.py#L126 must be extended.
export SAGE_LOG=trace SageAdapter \ -in 170830_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top10.mzML 170830_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top5.mzML 170911_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top10.mzML 170911_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top5.mzML 170929_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top10.mzML 170929_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top5.mzML \ -out out_0_sage.idXML \ -threads 15 \ -database "uniprotkb_Saccharomyces_cerevisiae_AND_51_UPS_2024_04_05_decoy.fasta" \ -decoy_prefix DECOY_ \ -min_len 6 \ -max_len 40 \ -min_matched_peaks 1 \ -min_peaks 1 \ -max_peaks 500 \ -missed_cleavages 2 \ -report_psms 1 \ -enzyme "Lys-c/p" \ -precursor_tol_left -20.0 \ -precursor_tol_right 20.0 \ -precursor_tol_unit ppm \ -fragment_tol_left -20.0 \ -fragment_tol_right 20.0 \ -fragment_tol_unit ppm \ -fixed_modifications 'Carbamidomethyl (C)' \ -variable_modifications 'Acetyl (Protein N-term)' 'Deamidated (N)' 'Deamidated (Q)' 'Oxidation (M)' \ -max_variable_mods 3 \ -isotope_error_range 0,1 \ -PeptideIndexing:IL_equivalent \ -PeptideIndexing:unmatched_action warn \ -debug 0 \ \ 2>&1 | tee out_0_sage.log if [[ 6 -ge 2 ]]; then IDRipper -in out_0_sage.idXML -out . -split_ident_runs rm out_0_sage.idXML for f in *.idXML do mv "$f" "${f%.*}_sage.idXML" done fi cat <<-END_VERSIONS > versions.yml "NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINESAGE": SageAdapter: $(SageAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1) sage: $(sage 2>&1 | grep -E 'Version [0-9]+\.[0-9]+\.[0-9]+') END_VERSIONS Command exit status: 6 Command output: Invalid string parameter value 'Lys-c/p' for parameter 'enzyme' given! Valid values are: 'Arg-C/P,Asp-N,Asp-N/B,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate'. Updating failed! Parameters passed to 'SageAdapter' are invalid. To prevent usage of wrong defaults, please update/fix the parameters!
When Lys-C/P to OpenMS enzyme, We transform to sentence style (Lys-c/p), However, OpenMS uses Sentence and Camel combined. This definition https://github.com/bigbio/sdrf-pipelines/blob/07c1dea93569ef9ca789739f93a96115b46fe2a0/sdrf_pipelines/openms/openms.py#L126 must be extended.