Importing data cancelled

[GoogleCodeExporter]

Import of data is cancelled after importing PSMs from several search files. 
Happens on a regular basis sometimes already after the import of the 2nd file 
sometimes it aborts later, but sadly all files are never finished.

Peptide Shaker version 0.40.3

Windows 7 64-bit, Java 64 bit 1.7.0_21, 4gb memory

Here is the report from the log file:

Wed Jun 24 08:43:43 CEST 2015: PeptideShaker version 0.40.3.
Memory given to the Java virtual machine: 3817799680.
Total amount of memory in the Java virtual machine: 128647168.
Free memory: 115430240.
Java version: 1.7.0_21.
java.net.UnknownHostException: genesis.ugent.be
    at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
    at java.net.PlainSocketImpl.connect(Unknown Source)
    at java.net.SocksSocketImpl.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at sun.net.NetworkClient.doConnect(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.<init>(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
    at java.net.URL.openStream(Unknown Source)
    at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:34)
    at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
    at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:518)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:6874)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:506)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:448)
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_21
os.name: Windows 7
memory: 36.6/128.6
processors available: 4
useCommandThread: false
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for 
details.</CompomicsError>
java.lang.InterruptedException: PSM import timed out. Please contact the 
developers.
    at eu.isas.peptideshaker.fileimport.PsmImporter.importPsmsMultipleThreads(PsmImporter.java:282)
    at eu.isas.peptideshaker.fileimport.PsmImporter.importPsms(PsmImporter.java:244)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:735)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:451)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:419)
    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.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Free memory: 756202312

Original issue reported on code.google.com by frieder....@gmail.com on 25 Jun 2015 at 6:21

[GoogleCodeExporter]

Hi and thank you for reporting this issue. It seems that the tool is having 
issues importing your files. Is there anything special with this dataset, in 
terms of size, complexity, or database?

Would it be possible for you to share them with us?

Best regards and sorry for the inconvenience,

Marc

Original comment by mvau...@gmail.com on 25 Jun 2015 at 3:29

• Changed state: Accepted

[GoogleCodeExporter]

Thanks for the answer. 

Sadly i am not able to share the data with you as it is falling under the 
category of sensitive information :-(

However i might try to describe if there is something special with the dataset. 

The runs are done on an Orbitrap Velos with 180 min gradient, with some dynamic 
exclusion settings to not measure highly abundant proteins. Approximately 40000 
spectra are contained in each file. Only a low amount of different proteins ~10 
to 50 are found besides a highly abundant protein. These proteins are very low 
concentrated. Only a very minor part of all 40000 spectra is expected to lead 
to successful identification of a protein, besides the highly abundant one.

Files are converted to mgf using msconvert with vendor peak picking. mgfs have 
a size of ~700 MB. Proteome Discoverer 1.4 is used as well with Sequest and it 
runs with the same Fasta.

Any further information, relevant for you?

Regards & thanks

Original comment by frieder....@gmail.com on 26 Jun 2015 at 8:55

[GoogleCodeExporter]

Hi and thank you for these details,
40k spectra should definitely not be an issue for the tool. If you share the 
data with us it will obviously be treated as confidential and used only for the 
purpose of debugging.
Is thee anything special to know concerning the database? The search settings? 
Feel free to answer via my work email: marc.vaudel at uib.no
Best regards,
Marc

Original comment by mvau...@gmail.com on 29 Jun 2015 at 7:51

[GoogleCodeExporter]

Original comment by harald.b...@gmail.com on 29 Jun 2015 at 12:03

[GoogleCodeExporter]

Just a short question? Did you receive the Mail i sent, as it sometimes get 
stuck in the filter due to company policy.

Original comment by frieder....@gmail.com on 2 Jul 2015 at 9:47

[GoogleCodeExporter]

Thanks for the notification, it was indeed in my spam list :) Will answer right 
away!

Original comment by mvau...@gmail.com on 2 Jul 2015 at 10:03

[GoogleCodeExporter]

Original comment by mvau...@gmail.com on 17 Jul 2015 at 11:22

• Changed state: Fixed