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PRIDE-Toolsuite / pride-converter-2

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Error parsing Proteome Discoverer v1.3 MSF file #6

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?

1. Click Launch Pride Converter
3. Choose Proteome Discoverer and click Next
4. Choose MSF file Testing Decoy-Dash.msf via Browse button
5. Click Next
6. Progress bar appears, but after some time message "Error executing 
background job" is shown.
7. If I click on Report Error button, more errors appear.

What is the expected output? What do you see instead?
The next step on PRIDE conversion process.

What version of the product are you using? On what operating system?
I'm using Pride Converter 2.0.14-bin on Windows XP SP3 (32bits) with JRE 1.6, 
but same error when running it on Windows 7 64bits with JRE 1.7.

Console output:

Reading properties file: D:\Oscar\Mis 
documentos\Baixades\ForMIAPEToolkit\pride-converter-
2.0.14-bin\.\converter.properties
Bootstrap command: "C:\Archivos de programa\Java\jre6\bin\java.exe"  -Xms64M 
-Xmx1024M -cp
 "./pride-converter-2.0-SNAPSHOT.jar" uk.ac.ebi.pride.tools.converter.gui.ConverterApplica
tionSelector$ConverterLauncher

Name of the OS: Windows XP
Version of the OS: 5.1
Architecture of The OS: x86
Java Home: C:\Archivos de programa\Java\jre6
Java Version: 1.6.0_37 (Sun Microsystems Inc.)
Number of processors: 2
Memory Usage: 61MB used, 53MB free, 989MB Max
Validator Loaded
DynMod_1:11#43
StatMod_1:2#8

Please provide any additional information below.
You can download the test MSF file from:
http://goo.gl/HGr8c

Stack trace from the error dialogue while processing MSF file:

An error occurred while processing the conversion 
java.lang.IllegalArgumentException: Please provide a valid, non-null, accession 
and database name to the accession resolver at 
uk.ac.ebi.pride.tools.utils.AccessionResolver. (AccessionResolver.java:61) at 
uk.ac.ebi.pride.tools.converter.report.io.ReportWriter.writeReport(ReportWriter.
java:149) at 
uk.ac.ebi.pride.tools.converter.report.io.ReportWriter.writeReport(ReportWriter.
java:78) at 
uk.ac.ebi.pride.tools.converter.gui.util.IOUtilities.generateReportFile(IOUtilit
ies.java:367) at 
uk.ac.ebi.pride.tools.converter.gui.util.IOUtilities.generateReportFiles(IOUtili
ties.java:244) 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$1.call(Unknown Source) at 
java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at 
java.util.concurrent.FutureTask.run(Unknown Source) at 
javax.swing.SwingWorker.run(Unknown Source) at 
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at 
java.lang.Thread.run(Unknown Source) MODULE: NAVIGATOR_PANEL

Stack trace from console output when Report Error button is pressed:

javax.mail.AuthenticationFailedException
        at javax.mail.Service.connect(Service.java:319)
        at javax.mail.Service.connect(Service.java:169)
        at uk.ac.ebi.pride.tools.converter.gui.util.error.EmailErrorReporter.sendEmailButt
onClicked(EmailErrorReporter.java:89)
        at uk.ac.ebi.pride.tools.converter.gui.util.error.EmailErrorReporter.reportError(E
mailErrorReporter.java:41)
        at org.jdesktop.swingx.plaf.basic.BasicErrorPaneUI$1.actionPerformed(BasicErrorPan
eUI.java:196)
        at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
        at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
        at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
        at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
        at com.jtattoo.plaf.BaseButtonListener.mouseReleased(Unknown Source)
        at java.awt.Component.processMouseEvent(Unknown Source)
        at javax.swing.JComponent.processMouseEvent(Unknown Source)
        at java.awt.Component.processEvent(Unknown Source)
        at java.awt.Container.processEvent(Unknown Source)
        at java.awt.Component.dispatchEventImpl(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Window.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$400(Unknown Source)
        at java.awt.EventQueue$2.run(Unknown Source)
        at java.awt.EventQueue$2.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.Dialog$1.run(Unknown Source)
        at java.awt.Dialog$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.awt.Dialog.show(Unknown Source)
        at java.awt.Component.show(Unknown Source)
        at java.awt.Component.setVisible(Unknown Source)
        at java.awt.Window.setVisible(Unknown Source)
        at java.awt.Dialog.setVisible(Unknown Source)
        at org.jdesktop.swingx.JXErrorPane$1.run(JXErrorPane.java:393)
        at org.jdesktop.swingx.JXErrorPane.showDialog(JXErrorPane.java:406)
        at uk.ac.ebi.pride.tools.converter.gui.util.error.ErrorDialogHandler.showErrorDial
og(ErrorDialogHandler.java:35)
        at uk.ac.ebi.pride.tools.converter.gui.NavigationPanel$5.propertyChange(Navigation
Panel.java:419)
        at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
        at javax.swing.SwingWorker$SwingWorkerPropertyChangeSupport.firePropertyChange(Unk
nown Source)
        at javax.swing.SwingWorker$SwingWorkerPropertyChangeSupport$1.run(Unknown Source)
        at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source)
        at sun.swing.AccumulativeRunnable.run(Unknown Source)
        at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown So
urce)
        at javax.swing.Timer.fireActionPerformed(Unknown Source)
        at javax.swing.Timer$DoPostEvent.run(Unknown Source)
        at java.awt.event.InvocationEvent.dispatch(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$400(Unknown Source)
        at java.awt.EventQueue$2.run(Unknown Source)
        at java.awt.EventQueue$2.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.Dialog$1.run(Unknown Source)
        at java.awt.Dialog$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.awt.Dialog.show(Unknown Source)
        at java.awt.Component.show(Unknown Source)
        at java.awt.Component.setVisible(Unknown Source)
        at java.awt.Window.setVisible(Unknown Source)
        at java.awt.Dialog.setVisible(Unknown Source)
        at uk.ac.ebi.pride.tools.converter.gui.NavigationPanel.next(NavigationPanel.java:4
35)
        at uk.ac.ebi.pride.tools.converter.gui.NavigationPanel.access$1400(NavigationPanel
.java:47)
        at uk.ac.ebi.pride.tools.converter.gui.NavigationPanel$7.actionPerformed(Navigatio
nPanel.java:754)
        at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
        at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
        at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
        at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
        at com.jtattoo.plaf.BaseButtonListener.mouseReleased(Unknown Source)
        at java.awt.Component.processMouseEvent(Unknown Source)
        at javax.swing.JComponent.processMouseEvent(Unknown Source)
        at java.awt.Component.processEvent(Unknown Source)
        at java.awt.Container.processEvent(Unknown Source)
        at java.awt.Component.dispatchEventImpl(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Window.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$400(Unknown Source)
        at java.awt.EventQueue$2.run(Unknown Source)
        at java.awt.EventQueue$2.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)

Original issue reported on code.google.com by ogallard on 29 Jan 2013 at 11:19

GoogleCodeExporter commented 9 years ago 
Hello again!

I found a XML file in the folder where the test MSF file was placed.
See attached file.

Thank you for your help. :)

Original comment by ogallard on 29 Jan 2013 at 11:23

Attachments:

GoogleCodeExporter commented 9 years ago 
Hello,

Pride-converter-2 doesn't support .msf format, for now.

Original comment by benoit.g...@live.fr on 30 Jan 2013 at 4:48

GoogleCodeExporter commented 9 years ago 
Hello Benoit

PRIDE Converter 2 does support MSF files, but only those of version 1.3.

Original comment by rglc...@gmail.com on 30 Jan 2013 at 4:53

GoogleCodeExporter commented 9 years ago 
Hello, 

I have a similar problem, 1 PD 1.3 file worked several other files did not 
work. I used versions 2.0.16 and 17 the same output with both verions. The 
converter produces an error at the generation of the XML file. Is there a 
solution how to convert those files?

However, I also have PD 1.2 files, is there a possibility to convert them also 
for Pride or proteome exchange. When I tried, the converter seeme to have 
trouble recognizing certain columns such as iTRAQ quantitation.

best regards
Andreas

Original comment by schmidta...@gmail.com on 20 Jun 2013 at 4:53