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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
edited Mar 23 at 18:49
Anurag Srivastava
2,52921220
asked Mar 23 at 17:17
Spencer DuSpencer Du
11
|
show 2 more comments
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
edited Mar 23 at 18:49
Anurag Srivastava
2,52921220
asked Mar 23 at 17:17
Spencer DuSpencer Du
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
|
show 2 more comments
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
edited Mar 23 at 18:49
Anurag Srivastava
2,52921220
asked Mar 23 at 17:17
Spencer DuSpencer Du
11
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
edited Mar 23 at 18:49
Anurag Srivastava
2,52921220
asked Mar 23 at 17:17
Spencer DuSpencer Du
11
edited Mar 23 at 18:49
Anurag Srivastava
2,52921220
asked Mar 23 at 17:17
Spencer DuSpencer Du
11
edited Mar 23 at 18:49
Anurag Srivastava
2,52921220
edited Mar 23 at 18:49
Anurag Srivastava
2,52921220
edited Mar 23 at 18:49
Anurag Srivastava
2,52921220
2,52921220
asked Mar 23 at 17:17
Spencer DuSpencer Du
11
asked Mar 23 at 17:17
Spencer DuSpencer Du
11
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
|
show 2 more comments
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
|
show 2 more comments
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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