Failure loading X!Tandem

[GoogleCodeExporter]

> What steps will reproduce the problem?

Loading X!Tandem files fails. IT says it's going to skip that file, but it just 
cancels the entire importation process.

I'm using PeptideShaker 0.19.1 with SearchGUI 1.12.0. I was using 1.11.0, but I 
updated it and redid the X!tandem searches. No joy. These files are currently 
loading fine with Scaffold, but Scaffold is not as good as PeptideShaker.

> What version of the product are you using? On what operating system?
Versions noted above. They are running on Windows Server 2007, SP2 applied, 
32-bit. I can try Win7, 32-bit if required, but I've never seen a difference 
when run on the different OS.

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

Tue Mar 26 07:37:09 EST 2013: PeptideShaker version 0.19.1.

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_15
os.name: Windows Server 2008
memory: 29.8/129.8
processors available: 4
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.getFileReader(IdfileReaderFactory.java:142)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:627)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.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$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.OutOfMemoryError: Java heap space
    at java.util.Arrays.copyOfRange(Unknown Source)
    at java.lang.String.<init>(Unknown Source)
    at java.lang.StringBuffer.toString(Unknown Source)
    at org.apache.xerces.dom.ParentNode.getTextContent(Unknown Source)
    at de.proteinms.xtandemparser.parser.XTandemParser.parseXTandemFile(XTandemParser.java:928)
    at de.proteinms.xtandemparser.parser.XTandemParser.<init>(XTandemParser.java:82)
    at de.proteinms.xtandemparser.xtandem.XTandemFile.<init>(XTandemFile.java:89)
    at de.proteinms.xtandemparser.parser.XTandemIdfileReader.<init>(XTandemIdfileReader.java:67)
    ... 15 more
java.lang.NullPointerException
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:633)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:507)
    at eu.isas.peptideshaker.fileimport.FileImporter$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(FileImporter.java:641)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:507)
    at eu.isas.peptideshaker.fileimport.FileImporter$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 issue reported on code.google.com by snoor...@gmail.com on 25 Mar 2013 at 9:29

[GoogleCodeExporter]

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

• Changed state: Started

[GoogleCodeExporter]

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

[GoogleCodeExporter]

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

[GoogleCodeExporter]

(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

• Changed state: Done