Closed GoogleCodeExporter closed 9 years ago
From the log it seems like you are running out of memory when trying to load
the file. There are a couple of points mentioned under the PeptideShaker
troubleshooting section
(http://code.google.com/p/peptide-shaker/#Troubleshooting). Did you have a look
at these?
Essentially the bigger the datasets the more memory is required. And in order
to give Java (and thus PeptideShaker) a significant amount of memory you will
need a 64 bit version of Java (the 32 bit Java version is limited to around 1.5
GB of memory), which of course requires a 64 bit operating system.
PeptideShaker tries to default to the 64 bit Java version if installed. So most
likely you either do not have Java 64 bit installed, or do not have a 64 bit
operating system.
To check how much memory you are currently giving PeptideShaker, re-open the
tool and in the Welcome dialog click the Settings & Help link in the lower left
corner, and then Settings > Java Memory Settings. (Or )
Let me know if this information helped you solve the problem.
Original comment by harald.b...@gmail.com
on 25 Mar 2013 at 10:04
Hi,
I finally got around to trying this on a 64-bit system. It still failed.
The log follows. I gave PeptideShaker 6 GB of RAM to work with and I
monitored it during the import. It did not run out of RAM, it didn't even
get close. Admittedly, it was using Java32, not the 64 bit version, I don't
know if that's significant.
I've loaded the "matching" OMSSA and Mascot files from the same MGF on a
32-bit stem with no problems.
Thanks
Log**
Tue Apr 02 09:06:36 EST 2013: PeptideShaker version 0.19.2.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43 2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.7.0_17
os.name: Windows XP
memory: 31.5/129.8
processors available: 8
useCommandThread: false
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown
Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at
com.compomics.util.experiment.io.identifications.IdfileReaderFactory.getFileRead
er(IdfileReaderFactory.java:142)
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(Fil
eImporter.java:627)
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(Fi
leImporter.java:507)
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground
(FileImporter.java:465)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Unknown Source)
at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(Unknown
Source)
at java.lang.AbstractStringBuilder.append(Unknown Source)
at java.lang.StringBuffer.append(Unknown Source)
at org.apache.xerces.dom.NodeImpl.getTextContent(Unknown Source)
at org.apache.xerces.dom.ParentNode.getTextContent(Unknown Source)
at org.apache.xerces.dom.ParentNode.getTextContent(Unknown Source)
at
de.proteinms.xtandemparser.parser.XTandemParser.parseXTandemFile(XTandemParser.j
ava:928)
at
de.proteinms.xtandemparser.parser.XTandemParser.<init>(XTandemParser.java:82)
at
de.proteinms.xtandemparser.xtandem.XTandemFile.<init>(XTandemFile.java:89)
at
de.proteinms.xtandemparser.parser.XTandemIdfileReader.<init>(XTandemIdfileReader
.java:67)
... 15 more
java.lang.NullPointerException
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(Fil
eImporter.java:633)
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(Fi
leImporter.java:507)
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground
(FileImporter.java:465)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
java.lang.NullPointerException
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(Fil
eImporter.java:641)
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(Fi
leImporter.java:507)
at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground
(FileImporter.java:465)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Original comment by snoor...@gmail.com
on 1 Apr 2013 at 10:18
If you look at the log you will see "Caused by: java.lang.OutOfMemoryError:
Java heap space". In other words you did run out of memory.
Running PeptideShaker on a 64-bit system is not enough to increase the memory
provided beyond around 1.5 GB, you also need to install Java 64-bit and make
sure that you use this Java version and not the 32-bit one.
To see the details of how PeptideShaker is started see the file called
"startup.log" in the resources/conf folder. Here you will see how much memory
it is given and which Java version that is used. If you don't understand the
content of this file, upload it here and I'll help you.
Original comment by harald.b...@gmail.com
on 2 Apr 2013 at 8:21
(Issue assumed fixed in later versions. Will be reopened if the user confirms
otherwise.)
Original comment by harald.b...@gmail.com
on 3 Mar 2014 at 11:01
Original issue reported on code.google.com by
snoor...@gmail.com
on 25 Mar 2013 at 9:29