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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 9 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 9 months ago

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