Error converting Mascot file (.dat)

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What steps will reproduce the problem?
1.format selection-> MascotDAT
2.upload .dat file 
3.proceed to the next step using default parameter

What is the expected output? What do you see instead?

Moving further in the conversion procedure.
It returns an error: "Error executing background job" 

What version of the product are you using? On what operating system?
 Pride-converter 2.0 on Windows 7

Please provide any additional information below.

Details of error message:

An error occurred while processing the conversion java.lang.Exception: Out of 
memory at 
matrix_science.msparser.msparserJNI.ms_inputquery_getNumberOfPeaks(Native 
Method) at 
matrix_science.msparser.ms_inputquery.getNumberOfPeaks(ms_inputquery.java:109) 
at 
uk.ac.ebi.pride.tools.converter.dao.impl.MascotDAO.prescanSpectra(MascotDAO.java
:444) at uk.ac.ebi.pride.tools.converter.dao.impl.MascotDAO. 
(MascotDAO.java:409) at 
uk.ac.ebi.pride.tools.converter.dao.DAOFactory.getDAO(DAOFactory.java:136) at 
uk.ac.ebi.pride.tools.converter.dao.DAOFactory.getDAO(DAOFactory.java:128) at 
uk.ac.ebi.pride.tools.converter.gui.util.IOUtilities.generateReportFile(IOUtilit
ies.java:363) at 
uk.ac.ebi.pride.tools.converter.gui.util.IOUtilities.generateReportFiles(IOUtili
ties.java:264) at 
uk.ac.ebi.pride.tools.converter.gui.forms.FileSelectionForm.finish(FileSelection
Form.java:1338) at 
uk.ac.ebi.pride.tools.converter.gui.NavigationPanel$4.doInBackground(NavigationP
anel.java:334) at javax.swing.SwingWorker$1.call(Unknown Source) at 
java.util.concurrent.FutureTask.run(Unknown Source) at 
javax.swing.SwingWorker.run(Unknown Source) at 
java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at 
java.lang.Thread.run(Unknown Source) MODULE: NAVIGATOR_PANEL

Original issue reported on code.google.com by stfn.rom...@gmail.com on 24 Apr 2014 at 9:11

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the version of the pride-convertor is 2.0.20

thank you for your help!

Original comment by stfn.rom...@gmail.com on 24 Apr 2014 at 9:13

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Dear stfn.romano,

It seems that you've ran into an "out of memory" problem whne using the PRIDE 
Converter 2 tool. Please could you edit the 'converter.properties' file 
contained within the tool's directory and edit the line:
jvm.args=-Xms64M -Xmx1024M
so it can use a higher amount of RAM, e.g.:
jvm.args=-Xms64M -Xmx2048M
or
jvm.args=-Xms64M -Xmx3G

https://code.google.com/p/pride-converter-2/wiki/HowToConfigureApplication

This should hopefully resolve your problem.

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 24 Apr 2014 at 9:20

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Original comment by tob...@ebi.ac.uk on 30 Jun 2014 at 9:42

• Changed state: Done