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Fix command line output


How do I parse command line arguments in Bash?Is there an equivalent of 'which' on the Windows command line?How to pass command line arguments to a rake taskHow to count lines in a document?How do I set a variable to the output of a command in Bash?List all environment variables from command line?How to change the output color of echo in LinuxHow do I run two commands in one line in Windows CMD?Node.js version on the command line? (not the REPL)How to import an SQL file using the command line in MySQL?






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0















Command line showing problems I need help fixing



I currently completing a assignment for a placement application and I am trying to run the program from an input command line statement but it is not giving me any output as all these errors are printed. This command line program is written in the java environment.



C:UsersSpencer DuDocumentsMSc Computing with placement Cardiff UniEMBL-EBI Assignment taskpia-1.3.10>java -cp pia-1.3.10.jar de.mpc.pia.intermediate.compiler.PIACompiler -infile C:UsersSpencer DuDocumentsMSc Computing with placement Cardiff UniEMBL-EBI Assignment taskMSFragger-20190222MSFragger-201902221a-QExHF04026.pepxml -outfile de.mpc.pia.intermediate.compiler.PIACompiler
[23-Mar-2019 18:32:38 - INFO] "file: C:UsersSpencer
 name: Spencer
 type: null
 additional info file: null" (de.mpc.pia.intermediate.compiler.PIACompiler:1342)
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/logback-classic-1.1.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/log4j-slf4j-impl-2.5.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
18:32:38,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
18:32:38,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
18:32:38,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath.
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/px-submission-core-2.0.15.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-util-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-converters-3.0.8.jar!/logback.xml]
18:32:38,386 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@a4102b8 - URL [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml] is not of type file
18:32:38,438 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
18:32:38,441 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Setting ReconfigureOnChangeFilter scanning period to 30 seconds
18:32:38,441 |-INFO in ReconfigureOnChangeFilterinvocationCounter=0 - Will scan for changes in [[]] every 30 seconds.
18:32:38,441 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Adding ReconfigureOnChangeFilter as a turbo filter
18:32:38,445 |-INFO in ch.qos.logback.classic.joran.action.LoggerContextListenerAction - Adding LoggerContextListener of type [ch.qos.logback.classic.jul.LevelChangePropagator] to the object stack
18:32:38,463 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating DEBUG level on Logger[ROOT] onto the JUL framework
18:32:38,463 |-INFO in ch.qos.logback.classic.joran.action.LoggerContextListenerAction - Starting LoggerContextListener
18:32:38,463 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
18:32:38,465 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [console]
18:32:38,469 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [uk.ac.ebi.pride.jmztab] to ERROR
18:32:38,492 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating ERROR level on Logger[uk.ac.ebi.pride.jmztab] onto the JUL framework
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to ERROR
18:32:38,492 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating ERROR level on Logger[ROOT] onto the JUL framework
18:32:38,492 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [console] to Logger[ROOT]
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
18:32:38,493 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@69930714 - Registering current configuration as safe fallback point

SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
E|JDBCAccess |Cannot open the SQLite DB: C:UsersSpencer via JDBC
E|JDBCAccess |SQLite-Error - SQLState: 0 SQLMessage: opening db: 'C:UsersSpencer': Access is denied
E|JDBCAccess |JDBC-Error(JDBC): No connection to the database


Thanks
Spencer






command-line







share|improve this question
























  • Post the errors here as text.

    – Anurag Srivastava
    Mar 23 at 17:18











  • I have updated the post with the errors

    – Spencer Du
    Mar 23 at 18:34











  • @AnuragSrivastava

    – Spencer Du
    Mar 23 at 18:47






  • 1





    Search the web for the last error: JDBC-Error(JDBC): No connection to the database

    – Anurag Srivastava
    Mar 23 at 18:49











  • @AnuragSrivastava Is that all I need to fix everything. A connection to the database?

    – Spencer Du
    Mar 23 at 18:51


















0















Command line showing problems I need help fixing



I currently completing a assignment for a placement application and I am trying to run the program from an input command line statement but it is not giving me any output as all these errors are printed. This command line program is written in the java environment.



C:UsersSpencer DuDocumentsMSc Computing with placement Cardiff UniEMBL-EBI Assignment taskpia-1.3.10>java -cp pia-1.3.10.jar de.mpc.pia.intermediate.compiler.PIACompiler -infile C:UsersSpencer DuDocumentsMSc Computing with placement Cardiff UniEMBL-EBI Assignment taskMSFragger-20190222MSFragger-201902221a-QExHF04026.pepxml -outfile de.mpc.pia.intermediate.compiler.PIACompiler
[23-Mar-2019 18:32:38 - INFO] "file: C:UsersSpencer
 name: Spencer
 type: null
 additional info file: null" (de.mpc.pia.intermediate.compiler.PIACompiler:1342)
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/logback-classic-1.1.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/log4j-slf4j-impl-2.5.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
18:32:38,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
18:32:38,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
18:32:38,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath.
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/px-submission-core-2.0.15.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-util-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-converters-3.0.8.jar!/logback.xml]
18:32:38,386 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@a4102b8 - URL [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml] is not of type file
18:32:38,438 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
18:32:38,441 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Setting ReconfigureOnChangeFilter scanning period to 30 seconds
18:32:38,441 |-INFO in ReconfigureOnChangeFilterinvocationCounter=0 - Will scan for changes in [[]] every 30 seconds.
18:32:38,441 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Adding ReconfigureOnChangeFilter as a turbo filter
18:32:38,445 |-INFO in ch.qos.logback.classic.joran.action.LoggerContextListenerAction - Adding LoggerContextListener of type [ch.qos.logback.classic.jul.LevelChangePropagator] to the object stack
18:32:38,463 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating DEBUG level on Logger[ROOT] onto the JUL framework
18:32:38,463 |-INFO in ch.qos.logback.classic.joran.action.LoggerContextListenerAction - Starting LoggerContextListener
18:32:38,463 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
18:32:38,465 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [console]
18:32:38,469 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [uk.ac.ebi.pride.jmztab] to ERROR
18:32:38,492 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating ERROR level on Logger[uk.ac.ebi.pride.jmztab] onto the JUL framework
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to ERROR
18:32:38,492 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating ERROR level on Logger[ROOT] onto the JUL framework
18:32:38,492 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [console] to Logger[ROOT]
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
18:32:38,493 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@69930714 - Registering current configuration as safe fallback point

SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
E|JDBCAccess |Cannot open the SQLite DB: C:UsersSpencer via JDBC
E|JDBCAccess |SQLite-Error - SQLState: 0 SQLMessage: opening db: 'C:UsersSpencer': Access is denied
E|JDBCAccess |JDBC-Error(JDBC): No connection to the database


Thanks
Spencer






command-line







share|improve this question
























  • Post the errors here as text.

    – Anurag Srivastava
    Mar 23 at 17:18











  • I have updated the post with the errors

    – Spencer Du
    Mar 23 at 18:34











  • @AnuragSrivastava

    – Spencer Du
    Mar 23 at 18:47






  • 1





    Search the web for the last error: JDBC-Error(JDBC): No connection to the database

    – Anurag Srivastava
    Mar 23 at 18:49











  • @AnuragSrivastava Is that all I need to fix everything. A connection to the database?

    – Spencer Du
    Mar 23 at 18:51














0












0








0








Command line showing problems I need help fixing



I currently completing a assignment for a placement application and I am trying to run the program from an input command line statement but it is not giving me any output as all these errors are printed. This command line program is written in the java environment.



C:UsersSpencer DuDocumentsMSc Computing with placement Cardiff UniEMBL-EBI Assignment taskpia-1.3.10>java -cp pia-1.3.10.jar de.mpc.pia.intermediate.compiler.PIACompiler -infile C:UsersSpencer DuDocumentsMSc Computing with placement Cardiff UniEMBL-EBI Assignment taskMSFragger-20190222MSFragger-201902221a-QExHF04026.pepxml -outfile de.mpc.pia.intermediate.compiler.PIACompiler
[23-Mar-2019 18:32:38 - INFO] "file: C:UsersSpencer
 name: Spencer
 type: null
 additional info file: null" (de.mpc.pia.intermediate.compiler.PIACompiler:1342)
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/logback-classic-1.1.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/log4j-slf4j-impl-2.5.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
18:32:38,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
18:32:38,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
18:32:38,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath.
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/px-submission-core-2.0.15.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-util-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-converters-3.0.8.jar!/logback.xml]
18:32:38,386 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@a4102b8 - URL [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml] is not of type file
18:32:38,438 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
18:32:38,441 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Setting ReconfigureOnChangeFilter scanning period to 30 seconds
18:32:38,441 |-INFO in ReconfigureOnChangeFilterinvocationCounter=0 - Will scan for changes in [[]] every 30 seconds.
18:32:38,441 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Adding ReconfigureOnChangeFilter as a turbo filter
18:32:38,445 |-INFO in ch.qos.logback.classic.joran.action.LoggerContextListenerAction - Adding LoggerContextListener of type [ch.qos.logback.classic.jul.LevelChangePropagator] to the object stack
18:32:38,463 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating DEBUG level on Logger[ROOT] onto the JUL framework
18:32:38,463 |-INFO in ch.qos.logback.classic.joran.action.LoggerContextListenerAction - Starting LoggerContextListener
18:32:38,463 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
18:32:38,465 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [console]
18:32:38,469 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [uk.ac.ebi.pride.jmztab] to ERROR
18:32:38,492 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating ERROR level on Logger[uk.ac.ebi.pride.jmztab] onto the JUL framework
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to ERROR
18:32:38,492 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating ERROR level on Logger[ROOT] onto the JUL framework
18:32:38,492 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [console] to Logger[ROOT]
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
18:32:38,493 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@69930714 - Registering current configuration as safe fallback point

SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
E|JDBCAccess |Cannot open the SQLite DB: C:UsersSpencer via JDBC
E|JDBCAccess |SQLite-Error - SQLState: 0 SQLMessage: opening db: 'C:UsersSpencer': Access is denied
E|JDBCAccess |JDBC-Error(JDBC): No connection to the database


Thanks
Spencer






command-line







share|improve this question
















Command line showing problems I need help fixing



I currently completing a assignment for a placement application and I am trying to run the program from an input command line statement but it is not giving me any output as all these errors are printed. This command line program is written in the java environment.



C:UsersSpencer DuDocumentsMSc Computing with placement Cardiff UniEMBL-EBI Assignment taskpia-1.3.10>java -cp pia-1.3.10.jar de.mpc.pia.intermediate.compiler.PIACompiler -infile C:UsersSpencer DuDocumentsMSc Computing with placement Cardiff UniEMBL-EBI Assignment taskMSFragger-20190222MSFragger-201902221a-QExHF04026.pepxml -outfile de.mpc.pia.intermediate.compiler.PIACompiler
[23-Mar-2019 18:32:38 - INFO] "file: C:UsersSpencer
 name: Spencer
 type: null
 additional info file: null" (de.mpc.pia.intermediate.compiler.PIACompiler:1342)
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/logback-classic-1.1.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/log4j-slf4j-impl-2.5.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
18:32:38,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
18:32:38,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
18:32:38,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath.
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/px-submission-core-2.0.15.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-util-3.0.8.jar!/logback.xml]
18:32:38,378 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-converters-3.0.8.jar!/logback.xml]
18:32:38,386 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@a4102b8 - URL [jar:file:/C:/Users/Spencer%20Du/Documents/MSc%20Computing%20with%20placement%20Cardiff%20Uni/EMBL-EBI%20Assignment%20task/pia-1.3.10/lib/jmztab-modular-model-3.0.8.jar!/logback.xml] is not of type file
18:32:38,438 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
18:32:38,441 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Setting ReconfigureOnChangeFilter scanning period to 30 seconds
18:32:38,441 |-INFO in ReconfigureOnChangeFilterinvocationCounter=0 - Will scan for changes in [[]] every 30 seconds.
18:32:38,441 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Adding ReconfigureOnChangeFilter as a turbo filter
18:32:38,445 |-INFO in ch.qos.logback.classic.joran.action.LoggerContextListenerAction - Adding LoggerContextListener of type [ch.qos.logback.classic.jul.LevelChangePropagator] to the object stack
18:32:38,463 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating DEBUG level on Logger[ROOT] onto the JUL framework
18:32:38,463 |-INFO in ch.qos.logback.classic.joran.action.LoggerContextListenerAction - Starting LoggerContextListener
18:32:38,463 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
18:32:38,465 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [console]
18:32:38,469 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [uk.ac.ebi.pride.jmztab] to ERROR
18:32:38,492 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating ERROR level on Logger[uk.ac.ebi.pride.jmztab] onto the JUL framework
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to ERROR
18:32:38,492 |-INFO in ch.qos.logback.classic.jul.LevelChangePropagator@11dc3715 - Propagating ERROR level on Logger[ROOT] onto the JUL framework
18:32:38,492 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [console] to Logger[ROOT]
18:32:38,492 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
18:32:38,493 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@69930714 - Registering current configuration as safe fallback point

SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
E|JDBCAccess |Cannot open the SQLite DB: C:UsersSpencer via JDBC
E|JDBCAccess |SQLite-Error - SQLState: 0 SQLMessage: opening db: 'C:UsersSpencer': Access is denied
E|JDBCAccess |JDBC-Error(JDBC): No connection to the database


Thanks
Spencer






command-line




command-line






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited Mar 23 at 18:49









Anurag Srivastava

2,52921220




2,52921220










asked Mar 23 at 17:17









Spencer DuSpencer Du

11




11












  • Post the errors here as text.

    – Anurag Srivastava
    Mar 23 at 17:18











  • I have updated the post with the errors

    – Spencer Du
    Mar 23 at 18:34











  • @AnuragSrivastava

    – Spencer Du
    Mar 23 at 18:47






  • 1





    Search the web for the last error: JDBC-Error(JDBC): No connection to the database

    – Anurag Srivastava
    Mar 23 at 18:49











  • @AnuragSrivastava Is that all I need to fix everything. A connection to the database?

    – Spencer Du
    Mar 23 at 18:51


















  • Post the errors here as text.

    – Anurag Srivastava
    Mar 23 at 17:18











  • I have updated the post with the errors

    – Spencer Du
    Mar 23 at 18:34











  • @AnuragSrivastava

    – Spencer Du
    Mar 23 at 18:47






  • 1





    Search the web for the last error: JDBC-Error(JDBC): No connection to the database

    – Anurag Srivastava
    Mar 23 at 18:49











  • @AnuragSrivastava Is that all I need to fix everything. A connection to the database?

    – Spencer Du
    Mar 23 at 18:51

















Post the errors here as text.

– Anurag Srivastava
Mar 23 at 17:18





Post the errors here as text.

– Anurag Srivastava
Mar 23 at 17:18













I have updated the post with the errors

– Spencer Du
Mar 23 at 18:34





I have updated the post with the errors

– Spencer Du
Mar 23 at 18:34













@AnuragSrivastava

– Spencer Du
Mar 23 at 18:47





@AnuragSrivastava

– Spencer Du
Mar 23 at 18:47




1




1





Search the web for the last error: JDBC-Error(JDBC): No connection to the database

– Anurag Srivastava
Mar 23 at 18:49





Search the web for the last error: JDBC-Error(JDBC): No connection to the database

– Anurag Srivastava
Mar 23 at 18:49













@AnuragSrivastava Is that all I need to fix everything. A connection to the database?

– Spencer Du
Mar 23 at 18:51






@AnuragSrivastava Is that all I need to fix everything. A connection to the database?

– Spencer Du
Mar 23 at 18:51













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