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compomics / compomics-utilities

Open source Java library for computational proteomics
http://compomics.github.io/projects/compomics-utilities.html
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Peptide Shaker CLI #17

Closed CarlaCristinaUranga closed 7 years ago

CarlaCristinaUranga commented 7 years ago

Hi, the Peptide Shaker CLI instruction website is down, for some reason. Is Peptide Shaker OK for 3-4GB Orbitrap data files?

hbarsnes commented 7 years ago

The PeptideShaker command line pages should be back online soon. In the meantime you can access them here: https://github.com/compomics/peptide-shaker/wiki/PeptideShakerCLI.

Is Peptide Shaker OK for 3-4GB Orbitrap data files?

Yes, should be ok as long as you give is enough memory.

hbarsnes commented 7 years ago

The standard PeptideShaker CLI web page is now back online: http://compomics.github.io/peptide-shaker/wiki/peptideshakercli.html.

CarlaCristinaUranga commented 7 years ago

I am giving it an Xmx of 500G, and even with the new version (Peptideshaker-1.15.0) I am getting this error message:

java.lang.NullPointerException at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:567) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:931)

These are my command line arguments: java -Djava.awt.headless=true -Xmx500G -cp PeptideShaker-1.15.0.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment "L1pep" -sample "MXL28" -replicate 1 -spectrum_files "L1.mgf" -id_params "HCD.par" -identification_files "L1_out.zip" -out "/LUSTRE/curanga/proteomica/Orb/L1.cpsx"

Thank you!

hbarsnes commented 7 years ago

You have to provide the complete path to the input files, i.e. the mgf, par and identification files. If you change this it should work.