Importing data - canceled

[GoogleCodeExporter]

> What steps will reproduce the problem?
I am using searchGUI and peptide-shaker for the first time, and have problems 
loading the search output file into peptide-shaker. The search in searchGUI 
went fine, and I have followed the tutorial for using both programs 
step-by-step.

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

I get the following output (the issue tracker does not allow me to upload any 
files, it says "issue attachment storage quota exceeded", so I just paste it 
here): 
Mon Nov 10 14:04:39 CET 2014        Import process for search 1 (Sample: spot 
1, Replicate: 0)

Mon Nov 10 14:04:39 CET 2014        Importing sequences from 
uniprot-human-reviewed-november2014_concatenated_target_decoy.fasta.
Mon Nov 10 14:04:42 CET 2014        Estimated import time: 5 minutes.
Mon Nov 10 14:04:42 CET 2014            See 
http://code.google.com/p/compomics-utilities/wiki/ProteinInference.
Mon Nov 10 14:07:24 CET 2014        FASTA file import completed.
Mon Nov 10 14:07:24 CET 2014        Establishing local database connection.
Mon Nov 10 14:07:25 CET 2014        Reading identification files.
Mon Nov 10 14:07:25 CET 2014        Parsing spot 1.omx.
Mon Nov 10 14:07:27 CET 2014        Loading spectra for spot 1.omx.
Mon Nov 10 14:07:27 CET 2014        Importing spot 1.mgf
Mon Nov 10 14:07:27 CET 2014        spot 1.mgf imported.
Mon Nov 10 14:07:27 CET 2014        Mapping peptides to proteins.
Mon Nov 10 14:07:33 CET 2014        null
Mon Nov 10 14:07:33 CET 2014        Please contact the developers 
(http://code.google.com/p/peptide-shaker/issues/list).
Mon Nov 10 14:07:52 CET 2014        Importing PSMs from spot 1.omx

Mon Nov 10 14:07:52 CET 2014        Importing Data Canceled!
Mon Nov 10 14:07:52 CET 2014        An error occured while loading the 
identification files.
Mon Nov 10 14:07:52 CET 2014        Please see the error log (Help Menu > Bug 
Report) for details.

The bug report is as follows:

Mon Nov 10 14:02:46 CET 2014: PeptideShaker version 0.35.1.
Memory given to the Java virtual machine: 954728448.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 113453888.
Java version: 1.7.0_71.

Mon Nov 10 14:03:15 CET 2014: PeptideShaker version 0.35.1.
Memory given to the Java virtual machine: 954728448.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 113365960.
Java version: 1.7.0_71.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.7.0_71
os.name: Windows 7
memory: 36.7/129.5
processors available: 8
useCommandThread: false
java.lang.NullPointerException
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.reduceNodeCacheSize(ProteinTree.java:1548)
    at com.compomics.util.experiment.identification.SequenceFactory.reduceNodeCacheSize(SequenceFactory.java:164)
    at eu.isas.peptideshaker.protein_inference.PeptideMapper.mapPeptide(PeptideMapper.java:212)
    at eu.isas.peptideshaker.protein_inference.PeptideMapper.access$200(PeptideMapper.java:27)
    at eu.isas.peptideshaker.protein_inference.PeptideMapper$PeptideMapperRunnable.run(PeptideMapper.java:262)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for 
details.</CompomicsError>
java.lang.NullPointerException
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.reduceNodeCacheSize(ProteinTree.java:1548)
    at com.compomics.util.experiment.identification.SequenceFactory.reduceNodeCacheSize(SequenceFactory.java:164)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:778)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:486)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:454)
    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)
Free memory: 301646712

> What version of the product are you using? On what operating system?
peptide-shaker v0.35.1 on windows 7

> Please provide any additional information below.

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\resources folder).

Original issue reported on code.google.com by Linda.Hj...@gmail.com on 10 Nov 2014 at 1:30

[GoogleCodeExporter]

Hi and thank you for contacting us on this.

It seems that your computer runs out of memory. We will soon release a new 
version which handles the problem more nicely.

Can you make sure that you have Java 64bits installed, and check how much 
memory is given to the tool? At start, please go under "Settings and Help" -> 
"Settings" -> "Java Settings", and verify that nothing is red. You will find 
more help here: https://code.google.com/p/peptide-shaker/#Troubleshooting

Best regards,

Marc

Original comment by mvau...@gmail.com on 10 Nov 2014 at 4:15

• Changed state: Accepted

[GoogleCodeExporter]

Thanks for the help. Only 1 GB memody was given to the tool, and after I 
increased it the program worked nicely.

Original comment by Linda.Hj...@gmail.com on 11 Nov 2014 at 10:15

[GoogleCodeExporter]

Great! If you get any other issues don't hesitate to let us know.

Original comment by harald.b...@gmail.com on 11 Nov 2014 at 2:08

• Changed state: Fixed