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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Go Analysis #487

Closed bargarge closed 1 year ago

bargarge commented 1 year ago

Hello I can't display GO Analysis. I thought it might be a problem with the proxy settings, but I have it configured in JavaOptions.txt according to the instructions on the PeptideShaker website.

Thanks for your help in advance

hbarsnes commented 1 year ago

Thanks for letting us know. Can you have a look at the PeptideShaker log file and maybe share the file here? You will find it via the PeptideShaker Welcome dialog > Settings & Help > Help > Bug Report.

bargarge commented 1 year ago

I send you the PeptideShaker log file. Thanks

El 20/09/2022 a las 12:14, Harald Barsnes escribió:

Thanks for letting us know. Can you have a look at the PeptideShaker log file and maybe share the file here? You will find it via the PeptideShaker Welcome dialog > Settings & Help > Help > Bug Report.

— Reply to this email directly, view it on GitHub https://github.com/compomics/peptide-shaker/issues/487#issuecomment-1252138107, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3FQXK6D66RLRSCTQ5CWGXDV7GFA7ANCNFSM6AAAAAAQQYCJYU. You are receiving this because you authored the thread.Message ID: @.***>

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Thu Jul 21 09:23:39 CEST 2022: PeptideShaker version 2.2.9. Memory given to the Java virtual machine: 9544663040. Total amount of memory in the Java virtual machine: 163053568. Free memory: 87879312. Java version: 1.8.0_291. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.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:522) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8480) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:627) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538) jshortcut.dll loaded via tmp generated pathname: C:\Users\Gemma\AppData\Local\Temp\jshortcut-9177257967409138189.dll 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_291 os.name: Windows 10 memory: 79.3/231.2 processors available: 32 useCommandThread: false

Thu Jul 21 12:12:48 CEST 2022: PeptideShaker version 2.2.9. Memory given to the Java virtual machine: 9544663040. Total amount of memory in the Java virtual machine: 128974848. Free memory: 110569208. Java version: 1.8.0_291. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.queryEnsembl(ProteinGeneDetailsProvider.java:503) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadGoMappings(ProteinGeneDetailsProvider.java:419) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.downloadMappings(ProteinGeneDetailsProvider.java:1062) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.getGeneMaps(ProteinGeneDetailsProvider.java:162) at eu.isas.peptideshaker.fileimport.FileImporter.importGenes(FileImporter.java:995) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:244) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1249) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465)

Fri Jul 22 11:03:15 CEST 2022: PeptideShaker version 2.2.9. Memory given to the Java virtual machine: 9544663040. Total amount of memory in the Java virtual machine: 128974848. Free memory: 105678480. Java version: 1.8.0_291. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1209) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:245) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1465) java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.read(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.readHeader(Unknown Source) at sun.security.ssl.SSLSocketInputRecord.decode(Unknown Source) at sun.security.ssl.SSLTransport.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.decode(Unknown Source) at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source) at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHt

hbarsnes commented 1 year ago

It seems like the data could not be downloaded when the PeptideShaker project was created. Can you try reprocessing the data in PeptideShaker to see of that solves the problem? (As the download of the gene annotations seems to be working fine on my end.)

hbarsnes commented 1 year ago

Issue assumed resolved. If this is not the case, please let us know and we'll reopen the issue.