hbarsnes
commented
1 year ago The first thing you can try is increasing the amount of memory given to PeptideShaker. This is done via the PeptideShaker Welcome dialog > Settings & Help > Settings > Java Settings > Memory. It is recommended to set this as high as possible, but of course not higher than the amount of memory you have available on the machine running the analysis.
If run via the command line you can add the -Xmx option to your PeptideShaker command line, e.g. java -Xmx8000M -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI [parameters] would allow PeptideShaker to use around 8GB of memory.
carolinelennartsson
I am running 78 files though a ms-gf+ search and are encountering issues when writing the search output to PeptideShaker format.
The error from SearchGUI PeptideShaker log file. ... Wed Oct 05 19:47:59 CEST 2022 Checking spectra for 20190709_QE6_nLC4_JE_SUMOvcp_wt_r4_f5.msgf.mzid.gz. Wed Oct 05 19:47:59 CEST 2022 Importing PSMs from 20190709_QE6_nLC4_JE_SUMOvcp_wt_r4_f5.msgf.mzid.gz Wed Oct 05 19:48:00 CEST 2022 Parsing 20190709_QE6_nLC4_JE_SUMOvcp_wt_r4_f6.msgf.mzid.gz. Wed Oct 05 19:48:00 CEST 2022 Checking spectra for 20190709_QE6_nLC4_JE_SUMOvcp_wt_r4_f6.msgf.mzid.gz. Wed Oct 05 19:48:00 CEST 2022 Importing PSMs from 20190709_QE6_nLC4_JE_SUMOvcp_wt_r4_f6.msgf.mzid.gz Wed Oct 05 19:48:01 CEST 2022 [351298 first hits passed the initial filtering] Wed Oct 05 19:48:01 CEST 2022 Computing assumptions probabilities. Wed Oct 05 19:48:01 CEST 2022 Saving assumptions probabilities, selecting best match, scoring modification localization.
Wed Oct 05 19:48:03 CEST 2022 Importing Data Canceled!
The error from importing to PeptideShaker:
Importing one processed identity-file + mzML file works fine. So there doesn't seem to be an issue with the search in itself. Just in opening all files at the same time and from SearchGUI.
Thank you for the help. :)