An error occurred while loading the spectrum file(s)

[esraaelmligy]

Urgent matter:

I am using the ReportsCLI and have a SearchGUI zipped file as an input but it gives me this error upon execution

code used: java -cp PeptideShaker-2.2.23.jar eu.isas.peptideshaker.cmd.ReportCLI -in "/home/user/path/to/search_gui_run/searchgui_out.zip" -out_reports "/home/user/path/to/pep_shaker_run" -reports "0, 3"

Log:

Memory given to the Java virtual machine: 995426304. Total amount of memory in the Java virtual machine: 62849024. Free memory: 50604880. Java version: 11.0.18. java.lang.NullPointerException at eu.isas.peptideshaker.utils.PsdbParent.loadSpectrumFiles(PsdbParent.java:435) at eu.isas.peptideshaker.utils.PsdbParent.loadSpectrumFiles(PsdbParent.java:411) at eu.isas.peptideshaker.cmd.ReportCLI.call(ReportCLI.java:152) at eu.isas.peptideshaker.cmd.ReportCLI.main(ReportCLI.java:508)

[hbarsnes]

The input to the ReportsCLI command line is a processed PeptideShaker project (-in PeptideShaker project (.psdb or zip file)), i.e. not the SearchGUI search results.

You can solve this in two ways. Either first use the PeptideShakerCLI command line to process the search results and then use the ReportsCLI command line with the PeptideShaker project as input. Or use the PeptideShakerCLI command line and add the ReportsCLI export options to the same command line. The latter means that you can get away with a single command line.

[esraaelmligy]

Thank you so much for the fast answer, can you please refer me to the exact code where i can process the SearchGUI results with peptideshaker to be ready for generating the reports?

[hbarsnes]

You can find all the details about the command lines here: https://github.com/compomics/peptide-shaker/wiki/PeptideShakerCLI

And here is the specific command line for processing SearchGUI results: https://github.com/compomics/peptide-shaker/wiki/PeptideShakerCLI#a---peptideshakercli