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Comet -- Error: No index found for enzyme Trypsin. #366
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There are two trypsin versions included as defaults: "Trypsin" and "Trypsin_(no_P_rule)". It seems like it's the last one that you want? It includes the setting you list above, i.e. no restrictions before and after the cleavage site, and seems to work fine as far as I can tell. In other words, I'm not able to reproduce the no index found error. Are you perhaps creating your own enzyme? Or editing the SearchGUI parameter file directly? |
Thanks for the immediate response. If I set the values to "Trypsin_(no_P_rule)" such that ... Then none of the other searches are able to complete. For example: I would prefer to set the enzyme, then also the "restrictionBefore": [], and "restrictionAfter": [], parameters independently. Any and all suggestions are welcome. |
Ahh! Typo. Missing the ")", Seems to work fine now for Tide and others ... Thanks for the feedback. Still looking for the SearchCLI documentation on enzyme nomenclature. |
I'm not sure if we ever documented this properly. I had a look at https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI, but the closest I could find was the listing of available enzymes via the However, we did also implement command line support for creating new enzymes: https://github.com/compomics/compomics-utilities/tree/master/src/main/java/com/compomics/cli/enzymes. Seems like this never made it into the wiki pages though. There currently also seems to be a bug resulting in null pointer when trying to run |
Interesting. Most the other algorithms accept Trypsin_(no_P_rule), except Comet, I noticed Tide also has a warning. java -cp SearchGUI-4.3.1.jar eu.isas.searchgui.cmd.SearchCLI -id_params trypNoP3ptm_0.1Da.par .. -comet 1 -tide 1 Thu Oct 19 15:59:50 UTC 2023 Indexing ...fasta for Tide. Thu Oct 19 16:00:11 UTC 2023 Importing spectrum files. |
The specificity is in using no underscore for "Trypsin (no P rule)". That seems to work with SearchCLI now for all algorithms. |
Ubuntu 20 LTS
SearchCLI 4.3.1
Leaving enzyme restriction null in the params file results in a error for comet execution.
Suggested error location: CometProcessBuilder.java L266
Suggested fault: CometProcessBuilder.java > getEnzymeListing L901
searchcli.par:
...
"restrictionBefore": [],
"restrictionAfter": [],
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