Error converting Mascot .dat files

[GoogleCodeExporter]

What steps will reproduce the problem?
1.1.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: "An error occurred while trying to parse Fxxxxxx...See 
error log for more details...PRIDE xml not created" 

What version of the product are you using? On what operating system?
Mac, Pride converter 2.1.0

Please provide any additional information below.

Thu Jun 26 20:00:23 BST 2014: Error when trying to read file: 
java.io.FileNotFoundException: /Users/snow/mgf eport from Progenesis to Mascot 
STD (No such file or directory)
    at java.io.FileInputStream.open(Native Method)
    at java.io.FileInputStream.<init>(FileInputStream.java:146)
    at java.io.FileReader.<init>(FileReader.java:72)
    at no.uib.prideconverter.gui.SpectraSelectionNoIdentifications$17.run(SpectraSelectionNoIdentifications.java:983)
    at java.lang.Thread.run(Thread.java:745)
Thu Jun 26 20:07:25 BST 2014: Warning: One or more of your preselected 
ontologies have not been found in OLS
Sat Jun 28 13:36:44 BST 2014: XML Parser: Ran out of memory!
java.lang.OutOfMemoryError: Java heap space
    at java.util.Arrays.copyOf(Arrays.java:2367)
    at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
    at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
    at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:535)
    at java.lang.StringBuffer.append(StringBuffer.java:322)
    at java.io.BufferedReader.readLine(BufferedReader.java:363)
    at java.io.BufferedReader.readLine(BufferedReader.java:382)
    at com.compomics.mascotdatfile.util.mascot.index.Controller.processSectionToHashMap(Controller.java:125)
    at com.compomics.mascotdatfile.util.mascot.index.Controller.readSectionAsHashMap(Controller.java:76)
    at com.compomics.mascotdatfile.util.mascot.MascotDatfile_Index.getQuery(MascotDatfile_Index.java:328)
    at com.compomics.mascotdatfile.util.mascot.iterator.QueryEnumerator.nextElement(QueryEnumerator.java:59)
    at no.uib.prideconverter.MascotDatConverter.transformSpectraFromMascotDatFile(MascotDatConverter.java:187)
    at no.uib.prideconverter.PRIDEConverter$3.run(PRIDEConverter.java:451)
Sat Jun 28 14:14:25 BST 2014: XML Parser: Ran out of memory!
java.lang.OutOfMemoryError: GC overhead limit exceeded
    at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1248)
    at java.lang.Double.parseDouble(Double.java:540)
    at com.compomics.mascotdatfile.util.mascot.Query.getPeakArray(Query.java:523)
    at com.compomics.mascotdatfile.util.mascot.Query.parseQueryHashMap(Query.java:170)
    at com.compomics.mascotdatfile.util.mascot.Query.<init>(Query.java:143)
    at com.compomics.mascotdatfile.util.mascot.MascotDatfile_Index.getQuery(MascotDatfile_Index.java:348)
    at com.compomics.mascotdatfile.util.mascot.iterator.QueryEnumerator.nextElement(QueryEnumerator.java:59)
    at no.uib.prideconverter.MascotDatConverter.transformSpectraFromMascotDatFile(MascotDatConverter.java:187)
    at no.uib.prideconverter.PRIDEConverter$3.run(PRIDEConverter.java:451)
Sat Jun 28 14:27:48 BST 2014: XML Parser: Ran out of memory!
java.lang.OutOfMemoryError: Java heap space
    at java.util.Arrays.copyOf(Arrays.java:2367)
    at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
    at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
    at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:535)
    at java.lang.StringBuffer.append(StringBuffer.java:322)
    at java.io.BufferedReader.readLine(BufferedReader.java:363)
    at java.io.BufferedReader.readLine(BufferedReader.java:382)
    at com.compomics.mascotdatfile.util.mascot.index.Controller.processSectionToHashMap(Controller.java:125)
    at com.compomics.mascotdatfile.util.mascot.index.Controller.readSectionAsHashMap(Controller.java:76)
    at com.compomics.mascotdatfile.util.mascot.MascotDatfile_Index.getQuery(MascotDatfile_Index.java:328)
    at com.compomics.mascotdatfile.util.mascot.iterator.QueryEnumerator.nextElement(QueryEnumerator.java:59)
    at no.uib.prideconverter.MascotDatConverter.transformSpectraFromMascotDatFile(MascotDatConverter.java:187)
    at no.uib.prideconverter.PRIDEConverter$3.run(PRIDEConverter.java:451)
Sat Jun 28 16:40:38 BST 2014: An error occured while trying to parse: HUVEC 
flow Phospho.dat

Original issue reported on code.google.com by amytaved...@googlemail.com on 30 Jun 2014 at 9:29

[GoogleCodeExporter]

Dear Amy,

Sorry you've been experiencing problems trying to convert your Mascot .dat 
files into PRIDE XML.

I see that you're using the "PRIDE Converter v 2.1.0" tool - I think you're on 
the old tool. Please could you use the newer "PRIDE Converter 2" tool? This is 
on v 2.0.21 now:
https://code.google.com/p/pride-converter-2/
ftp://ftp.pride.ebi.ac.uk/pride/resources/tools/converter-2/latest/pride-convert
er-2.zip
For more information about generating PRIDE XML in general, please see:
http://www.ebi.ac.uk/pride/help/archive/submission/pridexml

If you're interested in making a 'complete' submission to PX and still have 
access to the Mascot software, instead of using PRIDE XML you could 
alternatively export mzIdentML (and related peak files):
http://www.ebi.ac.uk/pride/help/archive/submission/mzidentml
http://www.ebi.ac.uk/pride/help/archive/faq#complete-PX

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 30 Jun 2014 at 9:40