Thu Oct 21 12:07:13 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 1037959168.
Total amount of memory in the Java virtual machine: 129761280.
Free memory: 102131528.
Java version: 1.8.0_231.
jshortcut.dll loaded via tmp generated pathname: C:\Users\Jai\AppData\Local\Temp\jshortcut-1383459766966532497.dll
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_231
os.name: Windows 10
memory: 27.7/129.9
processors available: 16
useCommandThread: false


Sat Oct 23 13:44:38 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 4219469824.
Total amount of memory in the Java virtual machine: 134217728.
Free memory: 121171368.
Java version: 17.0.1.


Sat Oct 23 14:55:29 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 4219469824.
Total amount of memory in the Java virtual machine: 134217728.
Free memory: 83126536.
Java version: 17.0.1.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 17.0.1
os.name: Windows 10
memory: 44.2/134.2
processors available: 16
useCommandThread: false


Sat Oct 23 14:58:30 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 4219469824.
Total amount of memory in the Java virtual machine: 134217728.
Free memory: 83215880.
Java version: 17.0.1.


Sat Oct 23 14:58:31 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 4219469824.
Total amount of memory in the Java virtual machine: 134217728.
Free memory: 83175912.
Java version: 17.0.1.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 17.0.1
os.name: Windows 10
memory: 45.9/134.2
processors available: 16
useCommandThread: false
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 17.0.1
os.name: Windows 10
memory: 46.5/134.2
processors available: 16
useCommandThread: false
Exception in thread "main" java.lang.ExceptionInInitializerError
	at java.base/javax.crypto.Cipher.getInstance(Cipher.java:546)
	at java.base/sun.security.ssl.SSLCipher.isTransformationAvailable(SSLCipher.java:511)
	at java.base/sun.security.ssl.SSLCipher.<init>(SSLCipher.java:500)
	at java.base/sun.security.ssl.SSLCipher.<clinit>(SSLCipher.java:82)
	at java.base/sun.security.ssl.CipherSuite.<clinit>(CipherSuite.java:69)
	at java.base/sun.security.ssl.SSLContextImpl.getApplicableSupportedCipherSuites(SSLContextImpl.java:343)
	at java.base/sun.security.ssl.SSLContextImpl$AbstractTLSContext.<clinit>(SSLContextImpl.java:556)
	at java.base/java.lang.Class.forName0(Native Method)
	at java.base/java.lang.Class.forName(Class.java:375)
	at java.base/java.security.Provider$Service.getImplClass(Provider.java:1933)
	at java.base/java.security.Provider$Service.getDefaultConstructor(Provider.java:1964)
	at java.base/java.security.Provider$Service.newInstanceOf(Provider.java:1878)
	at java.base/java.security.Provider$Service.newInstanceUtil(Provider.java:1886)
	at java.base/java.security.Provider$Service.newInstance(Provider.java:1861)
	at java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:236)
	at java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:164)
	at java.base/javax.net.ssl.SSLContext.getInstance(SSLContext.java:185)
	at java.base/javax.net.ssl.SSLContext.getDefault(SSLContext.java:110)
	at java.base/javax.net.ssl.SSLSocketFactory.getDefault(SSLSocketFactory.java:83)
	at java.base/javax.net.ssl.HttpsURLConnection.getDefaultSSLSocketFactory(HttpsURLConnection.java:336)
	at java.base/javax.net.ssl.HttpsURLConnection.<init>(HttpsURLConnection.java:292)
	at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.<init>(HttpsURLConnectionImpl.java:81)
	at java.base/sun.net.www.protocol.https.Handler.openConnection(Handler.java:62)
	at java.base/sun.net.www.protocol.https.Handler.openConnection(Handler.java:57)
	at java.base/java.net.URL.openConnection(URL.java:1094)
	at com.compomics.util.Util.sendGAUpdate(Util.java:115)
	at eu.isas.peptideshaker.gui.WelcomeDialog.<init>(WelcomeDialog.java:83)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:761)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538)
Caused by: java.lang.SecurityException: Can not initialize cryptographic mechanism
	at java.base/javax.crypto.JceSecurity.<clinit>(JceSecurity.java:119)
	... 29 more
Caused by: java.lang.SecurityException: Can't read cryptographic policy directory: unlimited
	at java.base/javax.crypto.JceSecurity.setupJurisdictionPolicies(JceSecurity.java:333)
	at java.base/javax.crypto.JceSecurity$1.run(JceSecurity.java:110)
	at java.base/javax.crypto.JceSecurity$1.run(JceSecurity.java:107)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
	at java.base/javax.crypto.JceSecurity.<clinit>(JceSecurity.java:106)
	... 29 more
Exception in thread "main" java.lang.ExceptionInInitializerError
	at java.base/javax.crypto.Cipher.getInstance(Cipher.java:546)
	at java.base/sun.security.ssl.SSLCipher.isTransformationAvailable(SSLCipher.java:511)
	at java.base/sun.security.ssl.SSLCipher.<init>(SSLCipher.java:500)
	at java.base/sun.security.ssl.SSLCipher.<clinit>(SSLCipher.java:82)
	at java.base/sun.security.ssl.CipherSuite.<clinit>(CipherSuite.java:69)
	at java.base/sun.security.ssl.SSLContextImpl.getApplicableSupportedCipherSuites(SSLContextImpl.java:343)
	at java.base/sun.security.ssl.SSLContextImpl$AbstractTLSContext.<clinit>(SSLContextImpl.java:556)
	at java.base/java.lang.Class.forName0(Native Method)
	at java.base/java.lang.Class.forName(Class.java:375)
	at java.base/java.security.Provider$Service.getImplClass(Provider.java:1933)
	at java.base/java.security.Provider$Service.getDefaultConstructor(Provider.java:1964)
	at java.base/java.security.Provider$Service.newInstanceOf(Provider.java:1878)
	at java.base/java.security.Provider$Service.newInstanceUtil(Provider.java:1886)
	at java.base/java.security.Provider$Service.newInstance(Provider.java:1861)
	at java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:236)
	at java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:164)
	at java.base/javax.net.ssl.SSLContext.getInstance(SSLContext.java:185)
	at java.base/javax.net.ssl.SSLContext.getDefault(SSLContext.java:110)
	at java.base/javax.net.ssl.SSLSocketFactory.getDefault(SSLSocketFactory.java:83)
	at java.base/javax.net.ssl.HttpsURLConnection.getDefaultSSLSocketFactory(HttpsURLConnection.java:336)
	at java.base/javax.net.ssl.HttpsURLConnection.<init>(HttpsURLConnection.java:292)
	at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.<init>(HttpsURLConnectionImpl.java:81)
	at java.base/sun.net.www.protocol.https.Handler.openConnection(Handler.java:62)
	at java.base/sun.net.www.protocol.https.Handler.openConnection(Handler.java:57)
	at java.base/java.net.URL.openConnection(URL.java:1094)
	at com.compomics.util.Util.sendGAUpdate(Util.java:115)
	at eu.isas.peptideshaker.gui.WelcomeDialog.<init>(WelcomeDialog.java:83)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:761)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538)
Caused by: java.lang.SecurityException: Can not initialize cryptographic mechanism
	at java.base/javax.crypto.JceSecurity.<clinit>(JceSecurity.java:119)
	... 29 more
Caused by: java.lang.SecurityException: Can't read cryptographic policy directory: unlimited
	at java.base/javax.crypto.JceSecurity.setupJurisdictionPolicies(JceSecurity.java:333)
	at java.base/javax.crypto.JceSecurity$1.run(JceSecurity.java:110)
	at java.base/javax.crypto.JceSecurity$1.run(JceSecurity.java:107)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
	at java.base/javax.crypto.JceSecurity.<clinit>(JceSecurity.java:106)
	... 29 more


Sat Oct 23 15:22:13 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 4219469824.
Total amount of memory in the Java virtual machine: 134217728.
Free memory: 83531144.
Java version: 17.0.1.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 17.0.1
os.name: Windows 10
memory: 45.9/134.2
processors available: 16
useCommandThread: false
Exception in thread "main" java.lang.ExceptionInInitializerError
	at java.base/javax.crypto.Cipher.getInstance(Cipher.java:546)
	at java.base/sun.security.ssl.SSLCipher.isTransformationAvailable(SSLCipher.java:511)
	at java.base/sun.security.ssl.SSLCipher.<init>(SSLCipher.java:500)
	at java.base/sun.security.ssl.SSLCipher.<clinit>(SSLCipher.java:82)
	at java.base/sun.security.ssl.CipherSuite.<clinit>(CipherSuite.java:69)
	at java.base/sun.security.ssl.SSLContextImpl.getApplicableSupportedCipherSuites(SSLContextImpl.java:343)
	at java.base/sun.security.ssl.SSLContextImpl$AbstractTLSContext.<clinit>(SSLContextImpl.java:556)
	at java.base/java.lang.Class.forName0(Native Method)
	at java.base/java.lang.Class.forName(Class.java:375)
	at java.base/java.security.Provider$Service.getImplClass(Provider.java:1933)
	at java.base/java.security.Provider$Service.getDefaultConstructor(Provider.java:1964)
	at java.base/java.security.Provider$Service.newInstanceOf(Provider.java:1878)
	at java.base/java.security.Provider$Service.newInstanceUtil(Provider.java:1886)
	at java.base/java.security.Provider$Service.newInstance(Provider.java:1861)
	at java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:236)
	at java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:164)
	at java.base/javax.net.ssl.SSLContext.getInstance(SSLContext.java:185)
	at java.base/javax.net.ssl.SSLContext.getDefault(SSLContext.java:110)
	at java.base/javax.net.ssl.SSLSocketFactory.getDefault(SSLSocketFactory.java:83)
	at java.base/javax.net.ssl.HttpsURLConnection.getDefaultSSLSocketFactory(HttpsURLConnection.java:336)
	at java.base/javax.net.ssl.HttpsURLConnection.<init>(HttpsURLConnection.java:292)
	at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.<init>(HttpsURLConnectionImpl.java:81)
	at java.base/sun.net.www.protocol.https.Handler.openConnection(Handler.java:62)
	at java.base/sun.net.www.protocol.https.Handler.openConnection(Handler.java:57)
	at java.base/java.net.URL.openConnection(URL.java:1094)
	at com.compomics.util.Util.sendGAUpdate(Util.java:115)
	at eu.isas.peptideshaker.gui.WelcomeDialog.<init>(WelcomeDialog.java:83)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:761)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538)
Caused by: java.lang.SecurityException: Can not initialize cryptographic mechanism
	at java.base/javax.crypto.JceSecurity.<clinit>(JceSecurity.java:119)
	... 29 more
Caused by: java.lang.SecurityException: Can't read cryptographic policy directory: unlimited
	at java.base/javax.crypto.JceSecurity.setupJurisdictionPolicies(JceSecurity.java:333)
	at java.base/javax.crypto.JceSecurity$1.run(JceSecurity.java:110)
	at java.base/javax.crypto.JceSecurity$1.run(JceSecurity.java:107)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
	at java.base/javax.crypto.JceSecurity.<clinit>(JceSecurity.java:106)
	... 29 more


Sat Oct 23 15:22:57 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 4219469824.
Total amount of memory in the Java virtual machine: 134217728.
Free memory: 81744592.
Java version: 17.0.1.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 17.0.1
os.name: Windows 10
memory: 46.7/134.2
processors available: 16
useCommandThread: false
Exception in thread "main" java.lang.ExceptionInInitializerError
	at java.base/javax.crypto.Cipher.getInstance(Cipher.java:546)
	at java.base/sun.security.ssl.SSLCipher.isTransformationAvailable(SSLCipher.java:511)
	at java.base/sun.security.ssl.SSLCipher.<init>(SSLCipher.java:500)
	at java.base/sun.security.ssl.SSLCipher.<clinit>(SSLCipher.java:82)
	at java.base/sun.security.ssl.CipherSuite.<clinit>(CipherSuite.java:69)
	at java.base/sun.security.ssl.SSLContextImpl.getApplicableSupportedCipherSuites(SSLContextImpl.java:343)
	at java.base/sun.security.ssl.SSLContextImpl$AbstractTLSContext.<clinit>(SSLContextImpl.java:556)
	at java.base/java.lang.Class.forName0(Native Method)
	at java.base/java.lang.Class.forName(Class.java:375)
	at java.base/java.security.Provider$Service.getImplClass(Provider.java:1933)
	at java.base/java.security.Provider$Service.getDefaultConstructor(Provider.java:1964)
	at java.base/java.security.Provider$Service.newInstanceOf(Provider.java:1878)
	at java.base/java.security.Provider$Service.newInstanceUtil(Provider.java:1886)
	at java.base/java.security.Provider$Service.newInstance(Provider.java:1861)
	at java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:236)
	at java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:164)
	at java.base/javax.net.ssl.SSLContext.getInstance(SSLContext.java:185)
	at java.base/javax.net.ssl.SSLContext.getDefault(SSLContext.java:110)
	at java.base/javax.net.ssl.SSLSocketFactory.getDefault(SSLSocketFactory.java:83)
	at java.base/javax.net.ssl.HttpsURLConnection.getDefaultSSLSocketFactory(HttpsURLConnection.java:336)
	at java.base/javax.net.ssl.HttpsURLConnection.<init>(HttpsURLConnection.java:292)
	at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.<init>(HttpsURLConnectionImpl.java:81)
	at java.base/sun.net.www.protocol.https.Handler.openConnection(Handler.java:62)
	at java.base/sun.net.www.protocol.https.Handler.openConnection(Handler.java:57)
	at java.base/java.net.URL.openConnection(URL.java:1094)
	at com.compomics.util.Util.sendGAUpdate(Util.java:115)
	at eu.isas.peptideshaker.gui.WelcomeDialog.<init>(WelcomeDialog.java:83)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:761)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538)
Caused by: java.lang.SecurityException: Can not initialize cryptographic mechanism
	at java.base/javax.crypto.JceSecurity.<clinit>(JceSecurity.java:119)
	... 29 more
Caused by: java.lang.SecurityException: Can't read cryptographic policy directory: unlimited
	at java.base/javax.crypto.JceSecurity.setupJurisdictionPolicies(JceSecurity.java:333)
	at java.base/javax.crypto.JceSecurity$1.run(JceSecurity.java:110)
	at java.base/javax.crypto.JceSecurity$1.run(JceSecurity.java:107)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
	at java.base/javax.crypto.JceSecurity.<clinit>(JceSecurity.java:106)
	... 29 more


Sat Oct 23 17:02:53 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 3750756352.
Total amount of memory in the Java virtual machine: 163053568.
Free memory: 114474824.
Java version: 1.8.0_311.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_311
os.name: Windows 10
memory: 59.8/163.1
processors available: 16
useCommandThread: false
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for details.</CompomicsError>
java.io.FileNotFoundException: C:\Users\Jai\Desktop\uniprot-bovine.fmi\uniprot-bovine_concatenated_target_decoy.fmi (The system cannot find the path specified)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(Unknown Source)
	at java.io.FileOutputStream.<init>(Unknown Source)
	at java.io.FileOutputStream.<init>(Unknown Source)
	at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1346)
	at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.<init>(FMIndex.java:581)
	at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:957)
	at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219)
	at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219)
	at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736)
	at java.lang.Thread.run(Unknown Source)
Free memory: 1575106520


Sat Oct 23 18:35:32 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 3750756352.
Total amount of memory in the Java virtual machine: 128974848.
Free memory: 115808464.
Java version: 1.8.0_311.


Sat Oct 23 21:14:39 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 3750756352.
Total amount of memory in the Java virtual machine: 128974848.
Free memory: 113593784.
Java version: 1.8.0_311.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_311
os.name: Windows 10
memory: 61.6/163.1
processors available: 16
useCommandThread: false
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for details.</CompomicsError>
java.io.FileNotFoundException: C:\Users\Jai\Desktop\uniprot-bovine.fmi\uniprot-bovine_concatenated_target_decoy.fmi (The system cannot find the path specified)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(Unknown Source)
	at java.io.FileOutputStream.<init>(Unknown Source)
	at java.io.FileOutputStream.<init>(Unknown Source)
	at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1346)
	at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.<init>(FMIndex.java:581)
	at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:957)
	at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219)
	at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219)
	at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736)
	at java.lang.Thread.run(Unknown Source)
Free memory: 1117629680
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for details.</CompomicsError>
java.io.FileNotFoundException: C:\Users\Jai\Desktop\uniprot-bovine.fmi\uniprot-bovine_concatenated_target_decoy.fmi (The system cannot find the path specified)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(Unknown Source)
	at java.io.FileOutputStream.<init>(Unknown Source)
	at java.io.FileOutputStream.<init>(Unknown Source)
	at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1346)
	at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.<init>(FMIndex.java:581)
	at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:957)
	at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219)
	at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219)
	at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736)
	at java.lang.Thread.run(Unknown Source)
Free memory: 1383302080


Sun Oct 24 00:19:45 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 3750756352.
Total amount of memory in the Java virtual machine: 128974848.
Free memory: 115800672.
Java version: 1.8.0_311.


Sun Oct 24 12:03:56 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 3750756352.
Total amount of memory in the Java virtual machine: 128974848.
Free memory: 112545928.
Java version: 1.8.0_311.
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
	at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
	at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
	at com.compomics.software.autoupdater.MetaDataXMLParser.<init>(MetaDataXMLParser.java:31)
	at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
	at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
	at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8479)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:627)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538)
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_311
os.name: Windows 10
memory: 59.5/163.1
processors available: 16
useCommandThread: false


Sun Oct 24 12:07:56 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 3750756352.
Total amount of memory in the Java virtual machine: 163053568.
Free memory: 144754760.
Java version: 1.8.0_311.
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
	at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
	at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
	at com.compomics.software.autoupdater.MetaDataXMLParser.<init>(MetaDataXMLParser.java:31)
	at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
	at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
	at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8479)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:627)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538)
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_311
os.name: Windows 10
memory: 64.5/163.1
processors available: 16
useCommandThread: false


Sun Oct 24 12:08:30 IST 2021: PeptideShaker version 2.2.0.
Memory given to the Java virtual machine: 3750756352.
Total amount of memory in the Java virtual machine: 163053568.
Free memory: 144445464.
Java version: 1.8.0_311.
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
	at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
	at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
	at com.compomics.software.autoupdater.MetaDataXMLParser.<init>(MetaDataXMLParser.java:31)
	at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
	at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
	at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8479)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:627)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538)
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_311
os.name: Windows 10
memory: 63.2/163.1
processors available: 16
useCommandThread: false