Outofmemory error in peptideshaker

[GoogleCodeExporter]

> What steps will reproduce the problem?
An error always occurred at importing PSMs from .mzid file.

> What is the expected output? What do you see instead?
Thu Apr 23 13:30:07 KST 2015        Import process for test (Sample: tesd, 
Replicate: 0)

Thu Apr 23 13:30:07 KST 2015        Importing sequences from 
uniprot-human_11-14-2014_concatenated_target_decoy.fasta.
Thu Apr 23 13:30:16 KST 2015        FASTA file import completed.
Thu Apr 23 13:30:16 KST 2015        Establishing local database connection.
Thu Apr 23 13:30:17 KST 2015        Reading identification files.
Thu Apr 23 13:30:17 KST 2015        Parsing 20111216_CON_PE_01.msgf.mzid.
Thu Apr 23 13:33:32 KST 2015        Loading spectra for 
20111216_CON_PE_01.msgf.mzid.
Thu Apr 23 13:33:32 KST 2015        Importing 20111216_CON_PE_01.mgf
Thu Apr 23 13:33:32 KST 2015        20111216_CON_PE_01.mgf imported.
Thu Apr 23 13:33:32 KST 2015        Mapping peptides to proteins.
Thu Apr 23 13:34:53 KST 2015        Importing PSMs from 
20111216_CON_PE_01.msgf.mzid
Thu Apr 23 22:22:37 KST 2015        An error occurred: Java exception: 'Java 
heap space: java.lang.OutOfMemoryError'.
Thu Apr 23 22:22:37 KST 2015        Please contact the developers 
(http://code.google.com/p/peptide-shaker/issues/list).

Thu Apr 23 22:22:37 KST 2015        Importing Data Canceled!
Thu Apr 23 22:22:37 KST 2015        An error occurred: No current connection.
Thu Apr 23 22:22:37 KST 2015        Please contact the developers 
(http://code.google.com/p/peptide-shaker/issues/list).
Thu Apr 23 22:22:38 KST 2015        6 PSMs (0.0%) excluded by the import 
filters:
Thu Apr 23 22:22:38 KST 2015            - 100.0% peptide mapping to both target 
and decoy.

> What version of the product are you using? On what operating system?
PeptideShaker 0.38.0

> Please provide any additional information below.
My computer has 64.0GB RAM and 2 of 2.40 GHz Intel Xeon processor.

Eventhough i tried it at other computers, the error was always occured in the 
same step.

I just want to see the matched spectra.

The input file was searched with MSGF+ in the SEARCH GUI.

MSCONVERT was used for file convert RAW to mzXML and mzXML to MGF.

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\resources folder).

Original issue reported on code.google.com by tilldaw...@gmail.com on 23 Apr 2015 at 6:25

[GoogleCodeExporter]

Thanks for telling us about this. How much memory did you give to 
PeptideShaker? You can set this via the Welcome Dialog: Settings & Help > 
Settings > Java Settings > Memory. If you have 64 GB of RAM I'd recommend 
setting this value to 60000 (MB).

If this does not help, please let us know and we'll reopen the issue.

Original comment by harald.b...@gmail.com on 23 Apr 2015 at 9:59

• Changed state: Fixed