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PRIDE-Toolsuite / pride-converter-2

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AN ERROR OCCURRED WHILE GENERATING THE pride xml FILE #17

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.THE LAST STEP OF GENERATING THE PRIDE XML FILES
2.
3.

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

The XML file is not generated, instead a error message appeared.  
What version of the product are you using? On what operating system?
Pride-converter 2

Please provide any additional information below.

ERROR REPORT
Error while generating PRIDE XML file: While converting spectrum 21.raw 
java.lang.RuntimeException: While converting spectrum 21.raw at 
uk.ac.ebi.pride.tools.converter.dao.impl.msf.MsfDao$1.next(MsfDao.java:419) at 
uk.ac.ebi.pride.tools.converter.dao.impl.msf.MsfDao$1.next(MsfDao.java:406) at 
uk.ac.ebi.pride.tools.converter.conversion.io.PrideXmlWriter.writeXml(PrideXmlWr
iter.java:202) at 
uk.ac.ebi.pride.tools.converter.gui.forms.FileExportForm.finish(FileExportForm.j
ava:182) 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) Caused by: 
java.lang.StringIndexOutOfBoundsException: String index out of range: -1 at 
java.lang.String.substring(Unknown Source) at 
com.compomics.thermo_msf_parser_API.lowmeminstance.controllers.SpectrumLowMemCon
troller.getMSMSPeaks(SpectrumLowMemController.java:89) at 
uk.ac.ebi.pride.tools.converter.dao.impl.msf.converters.SpectrumConverter.conver
t(SpectrumConverter.java:47) at 
uk.ac.ebi.pride.tools.converter.dao.impl.msf.MsfDao$1.next(MsfDao.java:417) ... 
10 more MODULE: WRAPPER-EXPORT

Original issue reported on code.google.com by hongta...@gmail.com on 21 Jan 2015 at 9:41

Attachments:

GoogleCodeExporter commented 9 years ago 
Dear Hongtao,

The PRIDE Converter 2 tool still may have problems dealing with input .msf 
files, despite previous updates to improve support for that format. It is 
unlikely that this is going to be changed further in the future.

As an alternative to PRIDE XML, the ProeomeXchange and PRIDE support the 
mzIdentML format: http://www.ebi.ac.uk/pride/help/archive/submission/mzidentml
So in your case with your files, the best thing(*) would be to convert your msf 
files into mzIdentML (and peak files) with the ProCon tool: 
http://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en
(*)The problem at the moment is that ProCon cannot generate valid mzIdentML 
files. Work is currently underway to update ProCon, so hopefully in the near 
future everything will be working well.

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 22 Jan 2015 at 8:57