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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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data import cancelled #86

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?
when I try to integrate search result from more than one DB

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

> What version of the product are you using? On what operating system?
ver 0.40.3 ,xeon  processor, 13 Gb RAM allotted, windows 7.0 SP1 os, java 1.8.45

> Please provide any additional information below.
peptide shaker seems to require larger RAM compared to other java based 
GUI,even when I am using MZID from msgf+ (27mb size) for peptide shaker 
analysis it is taking more than 4hrs. methods/ tricks to decrease analysis time 
are welcome.
I have converted thermo .raw (380mb) file to .mgf(211mb) using ms convert, with 
peak picking option and analysed the data with search GUI (MSGF+).
> 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 bhanu.ra...@gmail.com on 29 Jun 2015 at 10:22

GoogleCodeExporter commented 9 years ago 
Mon Jun 29 13:10:28 IST 2015: PeptideShaker version 0.40.3.
Memory given to the Java virtual machine: 12407799808.
Total amount of memory in the Java virtual machine: 128974848.
Free memory: 110591632.
Java version: 1.8.0_45.
java.net.ConnectException: Connection refused: connect
    at java.net.DualStackPlainSocketImpl.connect0(Native Method)
    at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
    at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
    at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
    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.plainConnect0(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.getInputStream0(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: 1.8.0_45
os.name: Windows 7
memory: 30.8/129.0
processors available: 8
useCommandThread: false
Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead 
limit exceeded
java.sql.SQLException: Java exception: 'GC overhead limit exceeded: 
java.lang.OutOfMemoryError'.
    at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.javaException(Unknown Source)
    at org.apache.derby.impl.jdbc.TransactionResourceImpl.wrapInSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.TransactionResourceImpl.handleException(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.handleException(Unknown Source)
    at org.apache.derby.impl.jdbc.ConnectionChild.handleException(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedStatement.execute(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedStatement.executeQuery(Unknown Source)
    at com.compomics.util.db.ObjectsDB.retrieveObjectSynchronized(ObjectsDB.java:811)
    at com.compomics.util.db.ObjectsDB.retrieveObject(ObjectsDB.java:760)
    at com.compomics.util.db.ObjectsDB.retrieveObject(ObjectsDB.java:722)
    at com.compomics.util.experiment.identification.IdentificationDB.getRawAssumptions(IdentificationDB.java:498)
    at com.compomics.util.experiment.identification.Identification.getRawAssumptions(Identification.java:1256)
    at com.compomics.util.experiment.identification.Identification.getRawAssumptions(Identification.java:1276)
    at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:354)
    at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:62)
    at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1303)
    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)
Caused by: java.sql.SQLException: Java exception: 'GC overhead limit exceeded: 
java.lang.OutOfMemoryError'.
    at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
    ... 23 more
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
java.sql.SQLNonTransientConnectionException: No current connection.
    at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.noCurrentConnection(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.checkIfClosed(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.createStatement(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.createStatement(Unknown Source)
    at com.compomics.util.db.ObjectsDB.savedInDB(ObjectsDB.java:936)
    at com.compomics.util.db.ObjectsDB.inDB(ObjectsDB.java:909)
    at com.compomics.util.db.ObjectsCache.saveObject(ObjectsCache.java:472)
    at com.compomics.util.db.ObjectsCache.saveObject(ObjectsCache.java:442)
    at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:514)
    at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:289)
    at com.compomics.util.db.ObjectsDB.insertObject(ObjectsDB.java:298)
    at com.compomics.util.experiment.identification.IdentificationDB.addAssumptions(IdentificationDB.java:473)
    at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1585)
    at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1609)
    at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:646)
    at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:399)
    at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:62)
    at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1303)
    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)
Caused by: java.sql.SQLException: No current connection.
    at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
    ... 26 more
java.sql.SQLNonTransientConnectionException: No current connection.
    at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.noCurrentConnection(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.checkIfClosed(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.getMetaData(Unknown Source)
    at com.compomics.util.db.ObjectsDB.getTables(ObjectsDB.java:260)
    at com.compomics.util.db.ObjectsDB.hasTable(ObjectsDB.java:239)
    at com.compomics.util.db.ObjectsDB.saveLongKeys(ObjectsDB.java:1197)
    at com.compomics.util.db.ObjectsDB.close(ObjectsDB.java:1236)
    at com.compomics.util.experiment.identification.IdentificationDB.close(IdentificationDB.java:1530)
    at com.compomics.util.experiment.identification.Identification.close(Identification.java:1940)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:455)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:419)
    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)
Caused by: java.sql.SQLException: No current connection.
    at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
    ... 20 more
this is the error for the file mentioned above.
Regards
Bhanu

Original comment by bhanu.ra...@gmail.com on 29 Jun 2015 at 10:56

GoogleCodeExporter commented 9 years ago 
Hi Bhanu and thank you for reporting this issue.

What fasta database are you using?

Can you try to load the example file available in the resources of the chapter 
1.4 of our tutorials 
(http://compomics.com/bioinformatics-for-proteomics/identification/) so that we 
can compare to what we have on our side? This should not take more than a 
couple of minutes.

In order to improve the speed it is important that you don't locate files 
(installation folder, fasta, mgf) on a remote server/disc, but keep everything 
locally in order to minimize the time spent in IO. Also, make sure that java 64 
bits is installed on your computer and that the maximal amount of memory 
available on the machine is given to the tool.

Hope that helps,

Marc

Original comment by mvau...@gmail.com on 29 Jun 2015 at 2:04

GoogleCodeExporter commented 9 years ago

Original comment by harald.b...@gmail.com on 29 Jun 2015 at 2:09

GoogleCodeExporter commented 9 years ago 
I am using uniprot human database as suggested. there are about 140000 protein 
entires. you can suggest any alternate database.

Original comment by bhanu.ra...@gmail.com on 30 Jun 2015 at 5:21

GoogleCodeExporter commented 9 years ago 
Hi again,

Working with this database should not be a problem, can you try with the files 
(mgf, fasta, and search results) of the tutorial indicated above, and tell us 
whether you have speed/memory issues there as well?

Best regards,

Marc

Original comment by mvau...@gmail.com on 30 Jun 2015 at 6:47

mvaudel commented 9 years ago

Hi again,

The new version of PeptideShaker should be less memory hungry. If you encounter issues again please open a new issue.

Best regards,

Marc