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PRIDE-Toolsuite / pride-converter-2

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Unable to convert X!Tandem results to pride-xml. "reportfile not found" #9

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi,

I am trying to convert X!Tandem results to PRIDE-XML results.

Here is the command I am using:

java -cp ".:/home/dfermin/proteomeXchange/pride-converter/lib" -Xms2g -Xmx24g 
-jar 
/home/dfermin/proteomeXchange/pride-converter/pride-converter-2.0-SNAPSHOT.jar 
-converter -engine XTandem -fastafile /tpp.data/fasta/refseq47.Hs_plusREV.fa 
-fastaformat FULL -mode CONVERT -reportOnlyIdentifiedSpectra   -sourcefile 
/tpp.data/oabalbin/proteomeXchange.upload/xtandem_res/FT_A460_A01.tandem.xml 
-spectrafile /tpp.data/akyocum/NSCLC_ftA460.2011_07_30.215418/FT_A460_A01.mzXML 
-reportfile /tmp/FT_A460_A01-report.xml -outputfile ./FT_A460_A01.PRIDE.XML

This is the error message I get:

Exception in thread "main" 
uk.ac.ebi.pride.tools.converter.utils.ConverterException: Xml file to be 
indexed does not exist: /tmp/FT_A460_A01-report.xml
        at uk.ac.ebi.pride.tools.converter.report.io.ReportReader.<init>(ReportReader.java:55)
        at uk.ac.ebi.pride.tools.converter.conversion.PrideConverter.main(PrideConverter.java:224)
        at uk.ac.ebi.pride.tools.converter.gui.ConverterApplicationSelector.main(ConverterApplicationSelector.java:121)

I am using the latest download of pride-converter-2
I am Using Oracle JAVA 1.7.0_02 on RHEL 5.5 (64-bit).
I get a thread concurrency error from the GUI interface for the same file.

Any and all help would be greatly appreciated.

Thanks,
Damian

Original issue reported on code.google.com by dfer...@umich.edu on 28 Aug 2013 at 2:10

GoogleCodeExporter commented 9 years ago 
Dear Damian,

The 'reportfile' option is optional for the command line conversion. Could you 
try to conversion without the '-reportfile' option? 

Best wishes,
Rui

Original comment by harry.r....@gmail.com on 28 Aug 2013 at 9:35

GoogleCodeExporter commented 9 years ago 
Hi

I did try to run it without the
 -reportfile flag. I get the same error. This is why I used the option
in the command I sent in the email, hoping it would fix the problem.

Original comment by dfer...@umich.edu on 28 Aug 2013 at 11:59

GoogleCodeExporter commented 9 years ago 
Dear Damian,

I think you need to run the tool in "PRESCAN" mode first in order to generate a 
Report XML file, which is then needed for "CONVERT" mode.

Please could you try running a command along the lines of:

java -cp ".:/home/dfermin/proteomeXchange/pride-converter/lib" -Xms2g -Xmx24g 
-jar 
/home/dfermin/proteomeXchange/pride-converter/pride-converter-2.0-SNAPSHOT.jar 
-converter -mode PRESCAN -engine XTandem -fastafile 
/tpp.data/fasta/refseq47.Hs_plusREV.fa -fastaformat FULL 
-reportOnlyIdentifiedSpectra -sourcefile 
/tpp.data/oabalbin/proteomeXchange.upload/xtandem_res/FT_A460_A01.tandem.xml 
-spectrafile /tpp.data/akyocum/NSCLC_ftA460.2011_07_30.215418/FT_A460_A01.mzXML

And see how that goes? It should save a <sourcefile>-report.xml file in the 
sourcefile's directory.

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 19 Nov 2013 at 11:41