Dear all,
I’m trying to wrap a number of knime workflows and launch them in parallel in a cluster. I got the following errors:
java.lang.IllegalStateException: Could not create metadata repository for: file:/users/bi/lcozzuto/.eclipse/611213136_linux_gtk_x86_64/configuration/org.eclipse.osgi/251/data/listener_1925729951/
at org.eclipse.equinox.internal.provisional.p2.directorywatcher.RepositoryListener.initializeMetadataRepository(RepositoryListener.java:112)
at org.eclipse.equinox.internal.provisional.p2.directorywatcher.RepositoryListener.(RepositoryListener.java:59)
at org.eclipse.equinox.internal.p2.reconciler.dropins.DropinsRepositoryListener.(DropinsRepositoryListener.java:82)
at org.eclipse.equinox.internal.p2.reconciler.dropins.Activator.watchDropins(Activator.java:540)
at org.eclipse.equinox.internal.p2.reconciler.dropins.Activator.start(Activator.java:173)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:774)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:767)
… 12 more
Root exception:
java.lang.IllegalStateException: Could not create metadata repository for: file:/users/bi/lcozzuto/.eclipse/611213136_linux_gtk_x86_64/configuration/org.eclipse.osgi/251/data/listener_1925729951/
at org.eclipse.equinox.internal.provisional.p2.directorywatcher.RepositoryListener.initializeMetadataRepository(RepositoryListener.java:112)
at org.eclipse.equinox.internal.provisional.p2.directorywatcher.RepositoryListener.(RepositoryListener.java:59)
at org.eclipse.equinox.internal.p2.reconciler.dropins.DropinsRepositoryListener.(DropinsRepositoryListener.java:82)
at org.eclipse.equinox.internal.p2.reconciler.dropins.Activator.watchDropins(Activator.java:540)
at org.eclipse.equinox.internal.p2.reconciler.dropins.Activator.start(Activator.java:173)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:774)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:767)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:724)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:932)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:309)
at org.eclipse.osgi.container.Module.doStart(Module.java:581)
at org.eclipse.osgi.container.Module.start(Module.java:449)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1620)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1600)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1571)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1514)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:340)
INFO main BatchExecutor ===== Executing workflow module_workflow_shotgun.knwf =====
WARN main WorkflowManager Unable to insert connection “[12(1) -> 9( 1)]”
WARN main WorkflowManager Unable to insert connection “[12(1) -> 10( 2)]”
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
WARN main Node Node can’t be executed - Node “Input File” not available (provided by “Freie Universitaet Berlin, Universitaet Tuebingen, and the GenericWorkflowNodes Team”; plugin “com.genericworkflownodes.knime” is installed)
INFO main BatchExecutor Workflow execution done Finished in 1 sec (1784ms)
INFO main BatchExecutor ========= Workflow did not execute sucessfully ============
Knime:
GTK+ Version Check
Command error:
Unable to init server: Could not connect: Connection refused
Knime: Cannot open display:
Knime:
JVM terminated. Exit code=4
/usr/local/knime_3.5.3//plugins/org.knime.binary.jre.linux.x86_64_1.8.0.152-01/jre/bin/java
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UnsyncloadClass
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Xmx2048m
-Dorg.eclipse.swt.internal.gtk.disablePrinting
-jar /usr/local/knime_3.5.3//plugins/org.eclipse.equinox.launcher_1.3.200.v20160318-1642.jar
-os linux
-ws gtk
-arch x86_64
-launcher /usr/local/knime_3.5.3/knime
-name Knime
–launcher.library /usr/local/knime_3.5.3//plugins/org.eclipse.equinox.launcher.gtk.linux.x86_64_1.1.400.v20160518-1444/eclipse_1617.so
-startup /usr/local/knime_3.5.3//plugins/org.eclipse.equinox.launcher_1.3.200.v20160318-1642.jar
–launcher.overrideVmargs
-exitdata 408027
-data /nfs/software/bi/biocore_tools/git/nextflow/Qcloud/work/1c/a4f416ae9666488e41d5ce1a532a91
-clean
-consoleLog
-application org.knime.product.KNIME_BATCH_APPLICATION
-reset
-nosave
-workflowFile=module_workflow_shotgun.knwf
-workflow.variable=input_mzml_file,QC01_180308_Q_QC1X_01_03.mzML,String
-workflow.variable=output_qcml_file,QC01_180308_Q_QC1X_01_03.qcml,String
-workflow.variable=output_featurexml_file,QC01_180308_Q_QC1X_01_03.featureXML,String
-workflow.variable=output_idxml_file,QC01_180308_Q_QC1X_01_03.idXML,String
-workflow.variable=input_fasta_file,shotgun_bsa.fasta,String
-workflow.variable=input_fasta_psq_file,shotgun_bsa.fasta.psq,String
-vm /usr/local/knime_3.5.3//plugins/org.knime.binary.jre.linux.x86_64_1.8.0.152-01/jre/bin/java
-vmargs
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UnsyncloadClass
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Xmx2048m
-Dorg.eclipse.swt.internal.gtk.disablePrinting
-jar /usr/local/knime_3.5.3//plugins/org.eclipse.equinox.launcher_1.3.200.v20160318-1642.jar
can you help me on this?
Thanks
Luca