MIDAS files upload

[MartinH]

Hi,

I tried to download few files as a result of MIDAS experiment. Out of
8 files I succeded only in one of them, the rest gave me this message:
java.lang.OutOfMemoryError: Java heap space
at org.apache.commons.codec.binary.Base64.discardNonBase64
(Base64.java:474)
at org.apache.commons.codec.binary.Base64.decodeBase64(Base64.java:
374)
at org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor
$Scan.getDecodedPeaks(MzXmlFileProcessor.java:126)
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.handleMS2Scan
(MzXmlFileProcessor.java:480)
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.parse
(MzXmlFileProcessor.java:318)
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.access
$2(MzXmlFileProcessor.java:234)
at org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor
$1.run(MzXmlFileProcessor.java:211)
at
org.systemsbiology.aebersoldlab.core.db.HibernateUtil.runInTransaction
(HibernateUtil.java:461)
at
org.systemsbiology.aebersoldlab.tiqam.importdata.MzXmlFileProcessor.process
(MzXmlFileProcessor.java:207)
at org.systemsbiology.aebersoldlab.tiqam.importdata.ImportTask.run
(ImportTask.java:75)
at org.eclipse.jface.operation.ModalContext$ModalContextThread.run
(ModalContext.java:113)


Any idea what I should do differently? Could be the size of the file
an issue? It ranges from 120-160 MB. Or could java be corrupted or so?

thanks.

Martin

[Mi-Youn Brusniak]

Dear Martin,

In order to make hardware requirement lower for TIQAM in many different
platform, we use JVM size (512M).
We are planning to make next TIQAM release with at 1GByte JVM size. It will
solve memory issues similar to yours.
Meanwhile, please load small number of mzXML at a time. All parsed
protein/peptides/transitions are in your database.
Therefore, you can still view them all 8 mzXML experiments. The issue here
is not enough JVM memory for parsing itself.

Cheers,

Mi-Youn

Mi-Youn Brusniak, Ph.D.
Computational Biology
Seattle Proteome Center
mbru...@systemsbiology.org
Tel: (206) 732-1327

[Martin Hubalek]

thanks Mi-Youn for the response,

but I do not attempt to load all files together, I only try one at a time. Only once I succeded, the rest 7 files did not work even as single files. Is there anything that will solve this? The only idea I have is to run shorted gradient to make the file smaller, will this help.

Martin


> ------------ Původní zpráva ------------
> Od: Mi-Youn Brusniak <mbru...@systemsbiology.org>
> Předmět: RE: MIDAS files upload
> Datum: 27.5.2009 18:28:43
> ----------------------------------------