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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Peptide Shaker Processing Cancelled. See peptide Shaker Log for deatils. How to get rid of this problem #522

Closed Annesha-1312 closed 11 months ago

Annesha-1312 commented 1 year ago

Fri Aug 11 18:42:32 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 87262664. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/peptideshaker/PeptideShaker/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) jshortcut.dll loaded via tmp generated pathname: C:\Users\Lenovo\AppData\Local\Temp\jshortcut-488412101770414799.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: 20.0.2 os.name: Windows 10 memory: 56.0/134.2 processors available: 8 useCommandThread: false java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/searchgui/SearchGUI/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:34) at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105) at eu.isas.peptideshaker.gui.WelcomeDialog.checkForNewSearchGUIVersion(WelcomeDialog.java:1034) at eu.isas.peptideshaker.gui.WelcomeDialog$25.run(WelcomeDialog.java:762) at java.base/java.lang.Thread.run(Thread.java:1623)

Fri Aug 11 19:15:17 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 118006704. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=AKV murine leukemia virus&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Actinidia chinensis var. chinensis&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Actinidia deliciosa&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Anaplasma phagocytophilum (strain HZ)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704)

Thu Aug 17 11:02:55 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 87498064. Java version: 20.0.2. java.net.UnknownHostException: genesis.ugent.be at java.base/sun.nio.ch.NioSocketImpl.connect(NioSocketImpl.java:565) at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:327) at java.base/java.net.Socket.connect(Socket.java:666) at java.base/sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:304) at java.base/sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:181) at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:183) at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:532) at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:637) at java.base/sun.net.www.protocol.https.HttpsClient.(HttpsClient.java:264) at java.base/sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:378) at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:193) at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1241) at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1127) at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:179) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1657) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 20.0.2 os.name: Windows 10 memory: 51.9/134.2 processors available: 8 useCommandThread: false

PeptideShaker processing failed. See the PeptideShaker log for details.

java.io.FileNotFoundException: C:\Users\Lenovo\Downloads\uniprotkb_Human_AND_reviewed_true_2023_08_11.fmi\uniprotkb_Human_AND_reviewed_true_2023_08_11_concatenated_target_decoy.fmi (The system cannot find the path specified) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:295) at java.base/java.io.FileOutputStream.(FileOutputStream.java:236) at java.base/java.io.FileOutputStream.(FileOutputStream.java:124) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1353) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.(FMIndex.java:590) at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:984) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:224) at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736) at java.base/java.lang.Thread.run(Thread.java:1623) Free memory: 1287233344

Thu Aug 17 12:24:04 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 118006704. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=AKV murine leukemia virus&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Actinidia chinensis var. chinensis&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Actinidia deliciosa&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Anaplasma phagocytophilum (strain HZ)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704)

Thu Aug 17 15:06:55 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 87879808. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/peptideshaker/PeptideShaker/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 20.0.2 os.name: Windows 10 memory: 53.0/134.2 processors available: 8 useCommandThread: false

Thu Aug 17 15:07:10 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 87318488. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/peptideshaker/PeptideShaker/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 20.0.2 os.name: Windows 10 memory: 52.7/134.2 processors available: 8 useCommandThread: false java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/searchgui/SearchGUI/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:34) at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105) at eu.isas.peptideshaker.gui.WelcomeDialog.checkForNewSearchGUIVersion(WelcomeDialog.java:1034) at eu.isas.peptideshaker.gui.WelcomeDialog$25.run(WelcomeDialog.java:762) at java.base/java.lang.Thread.run(Thread.java:1623) Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.util.ArrayList.toArray()" because "species" is null at eu.isas.peptideshaker.gui.pride.ProjectsFilterDialog.(ProjectsFilterDialog.java:72) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI.findMenuItemActionPerformed(PrideReshakeGUI.java:1583) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI.access$4100(PrideReshakeGUI.java:102) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI$27.actionPerformed(PrideReshakeGUI.java:1238) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6620) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6385) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4995) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4827) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4827) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Thu Aug 17 15:07:34 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 87867480. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/peptideshaker/PeptideShaker/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 20.0.2 os.name: Windows 10 memory: 53.6/134.2 processors available: 8 useCommandThread: false

Thu Aug 17 15:09:25 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 86873528. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/peptideshaker/PeptideShaker/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 20.0.2 os.name: Windows 10 memory: 53.5/134.2 processors available: 8 useCommandThread: false

PeptideShaker processing failed. See the PeptideShaker log for details.

java.io.FileNotFoundException: C:\Users\Lenovo\Downloads\uniprotkb_Human_AND_reviewed_true_2023_08_11.fmi\uniprotkb_Human_AND_reviewed_true_2023_08_11_concatenated_target_decoy.fmi (The system cannot find the path specified) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:295) at java.base/java.io.FileOutputStream.(FileOutputStream.java:236) at java.base/java.io.FileOutputStream.(FileOutputStream.java:124) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1353) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.(FMIndex.java:590) at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:984) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:224) at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736) at java.base/java.lang.Thread.run(Thread.java:1623) Free memory: 1098003680 Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters.getIonTypes()" because "specificAnnotationParameters" is null at eu.isas.peptideshaker.gui.PeptideShakerGUI.updateAnnotationMenus(PeptideShakerGUI.java:5884) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel.updateBubblePlot(OverviewPanel.java:4244) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel$94.run(OverviewPanel.java:3986) at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:318) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Thu Aug 17 15:35:59 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 118006704. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=AKV murine leukemia virus&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Actinidia chinensis var. chinensis&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Actinidia deliciosa&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Anaplasma phagocytophilum (strain HZ)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) java.io.IOException: Server returned HTTP response code: 400 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)&format=tab&columns=id at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) 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:1419) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:259) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1704) Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters.getIonTypes()" because "specificAnnotationParameters" is null at eu.isas.peptideshaker.gui.PeptideShakerGUI.updateAnnotationMenus(PeptideShakerGUI.java:5884) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel.updateBubblePlot(OverviewPanel.java:4244) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel$94.run(OverviewPanel.java:3986) at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:318) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Thu Aug 17 15:49:05 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 87890832. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/peptideshaker/PeptideShaker/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 20.0.2 os.name: Windows 10 memory: 54.1/134.2 processors available: 8 useCommandThread: false java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/searchgui/SearchGUI/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:34) at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105) at eu.isas.peptideshaker.gui.WelcomeDialog.checkForNewSearchGUIVersion(WelcomeDialog.java:1034) at eu.isas.peptideshaker.gui.WelcomeDialog$25.run(WelcomeDialog.java:762) at java.base/java.lang.Thread.run(Thread.java:1623) https://www.ebi.ac.uk/pride/ws/archive/project/count org.springframework.web.client.HttpClientErrorException$NotFound: 404 : "{ "timestamp" : 1692267576359, "status" : 404, "error" : "Not Found", "message" : "No message available", "path" : "/pride/ws/archive/v2/project/count"}" at org.springframework.web.client.HttpClientErrorException.create(HttpClientErrorException.java:113) at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:168) at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:122) at org.springframework.web.client.ResponseErrorHandler.handleError(ResponseErrorHandler.java:63) at org.springframework.web.client.RestTemplate.handleResponse(RestTemplate.java:819) at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:777) at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:711) at org.springframework.web.client.RestTemplate.getForEntity(RestTemplate.java:361) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI$33.run(PrideReshakeGUI.java:2523)

Thu Aug 17 15:49:46 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 86869096. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/peptideshaker/PeptideShaker/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 20.0.2 os.name: Windows 10 memory: 52.8/134.2 processors available: 8 useCommandThread: false

PeptideShaker processing failed. See the PeptideShaker log for details.

java.io.FileNotFoundException: C:\Users\Lenovo\Downloads\uniprotkb_Human_AND_reviewed_true_2023_08_11.fmi\uniprotkb_Human_AND_reviewed_true_2023_08_11_concatenated_target_decoy.fmi (The system cannot find the path specified) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:295) at java.base/java.io.FileOutputStream.(FileOutputStream.java:236) at java.base/java.io.FileOutputStream.(FileOutputStream.java:124) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1353) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.(FMIndex.java:590) at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:984) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:224) at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736) at java.base/java.lang.Thread.run(Thread.java:1623) Free memory: 624106408

Thu Aug 17 16:40:53 IST 2023: PeptideShaker version 2.2.25. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 87413352. Java version: 20.0.2. java.io.IOException: Server returned HTTP response code: 502 for URL: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/peptideshaker/PeptideShaker/maven-metadata.xml at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1980) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1581) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at java.base/java.net.URL.openStream(URL.java:1317) 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:731) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8646) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:628) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:539) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 20.0.2 os.name: Windows 10 memory: 53.2/134.2 processors available: 8 useCommandThread: false

hbarsnes commented 1 year ago

It is a bit difficult to see from the log file which particular issue you are referring to. Can you provide some more details about the issue you are experiencing?

hbarsnes commented 11 months ago

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