search

Immortalin / peptide-shaker

Automatically exported from code.google.com/p/peptide-shaker
1 stars 0 forks source link

Importing Data Cancelled #48

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?
Loading the identification file - a fasta file containing UniProt protein 
sequence and a MS spectrum of appropriate format and clicking load data

> What is the expected output? What do you see instead?
Information on crosslinked peptides

> What version of the product are you using? On what operating system?
0.27.4

> Please provide any additional information below.
Please see the errors as taken from error log:
Mon Apr 07 11:28:50 BST 2014: PeptideShaker version 0.27.4.
Memory given to the Java virtual machine: 1037959168.
Total amount of memory in the Java virtual machine: 129761280.
Free memory: 114646056.
Java version: 1.7.0_51.
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:509)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:6539)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:424)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:400)
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_51
os.name: Windows 8
memory: 31.4/129.8
processors available: 4
useCommandThread: false
Reindexing: 140331_101.mgf. (Reason: 
com.compomics.util.experiment.io.massspectrometry.MgfIndex; local class 
incompatible: stream classdesc serialVersionUID = 4769401753928606746, local 
class serialVersionUID = 1490481272256514169)
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for 
details.</CompomicsError>
java.lang.NullPointerException
    at com.compomics.util.experiment.biology.Peptide.getPotentialModificationSites(Peptide.java:724)
    at com.compomics.util.experiment.biology.PTMFactory.getExpectedPTMs(PTMFactory.java:876)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:881)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:489)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:457)
    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: 348023024

Mon Apr 07 11:44:44 BST 2014: PeptideShaker version 0.27.4.
Memory given to the Java virtual machine: 1037959168.
Total amount of memory in the Java virtual machine: 129761280.
Free memory: 114554896.
Java version: 1.7.0_51.
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:509)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:6539)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:424)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:400)
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_51
os.name: Windows 8
memory: 32.1/129.8
processors available: 4
useCommandThread: false

> 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 Tanya0...@gmail.com on 8 Apr 2014 at 9:02

GoogleCodeExporter commented 9 years ago 
Hi and thanks for reporting this issue.

It seems that an error occurred when mapping your modification (the linker?) 
onto the sequence of a peptide. Can you make your files available to me so that 
I can debug it?

my email is mvaudel@gmail.com

thank you, I will look at it right away.

Marc

Original comment by mvau...@gmail.com on 27 Apr 2014 at 8:25

GoogleCodeExporter commented 9 years ago 
We have now improved the PTM mapping, the error you reported should not occur 
anymore. If you encounter it again, please set a new issue.

Original comment by mvau...@gmail.com on 29 Jun 2014 at 3:39