Re: [TASSEL-Group] Error with includeSitesInFile plugin

[Terry Casstevens]

Please send your command and all output.

Terry

On Wed, Sep 30, 2015 at 10:21 AM, Abby L. <ladejo...@gmail.com> wrote:
> Hello,
>
> I am trying to use the includeSitesInFile plugin to filter out specific SNP
> sites but I get the error below. I have followed the instruction in the
> manual for producing my snp sites file - Individual site names are separated
> by white space.
>
> Thank you.
>
>
> [Thread-4] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version:
> 5.2.14 Date: August 27, 2015
> [Thread-4] INFO net.maizegenetics.tassel.TasselLogging - Max Available
> Memory Reported by JVM: 1365 MB
> [Thread-4] INFO net.maizegenetics.tassel.TasselLogging - Java Version:
> 1.8.0_60
> [Thread-4] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
> [Thread-4] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished
> net.maizegenetics.tassel.TasselLogging: time: Sep 30, 2015 14:50:13
> [Thread-5] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting
> net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin: time: Sep 30,
> 2015 14:50:20
> [AWT-EventQueue-0] DEBUG net.maizegenetics.dna.snp.io.JSONUtils - Unexpected
> char 83 at (line no=1, column no=1, offset=0)
> javax.json.stream.JsonParsingException: Unexpected char 83 at (line no=1,
> column no=1, offset=0)
> at org.glassfish.json.JsonTokenizer.unexpectedChar(JsonTokenizer.java:532)
> at org.glassfish.json.JsonTokenizer.nextToken(JsonTokenizer.java:415)
> at
> org.glassfish.json.JsonParserImpl$NoneContext.getNextEvent(JsonParserImpl.java:222)
> at
> org.glassfish.json.JsonParserImpl$StateIterator.next(JsonParserImpl.java:172)
> at org.glassfish.json.JsonParserImpl.next(JsonParserImpl.java:149)
> at org.glassfish.json.JsonReaderImpl.readObject(JsonReaderImpl.java:101)
> at
> net.maizegenetics.dna.snp.io.JSONUtils.importPositionListFromJSON(JSONUtils.java:262)
> at
> net.maizegenetics.plugindef.AbstractPlugin.convert(AbstractPlugin.java:226)
> at
> net.maizegenetics.plugindef.AbstractPlugin.setParameter(AbstractPlugin.java:548)
> at
> net.maizegenetics.plugindef.AbstractPlugin$2.actionPerformed(AbstractPlugin.java:614)
> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
> at
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
> at java.awt.Component.processMouseEvent(Component.java:6535)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
> at java.awt.Component.processEvent(Component.java:6300)
> at java.awt.Container.processEvent(Container.java:2236)
> at java.awt.Component.dispatchEventImpl(Component.java:4891)
> at java.awt.Container.dispatchEventImpl(Container.java:2294)
> at java.awt.Component.dispatchEvent(Component.java:4713)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
> at java.awt.Container.dispatchEventImpl(Container.java:2280)
> at java.awt.Window.dispatchEventImpl(Window.java:2750)
> at java.awt.Component.dispatchEvent(Component.java:4713)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
> at java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.awt.EventQueue$3.run(EventQueue.java:709)
> at java.awt.EventQueue$3.run(EventQueue.java:703)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
> at java.awt.EventQueue$4.run(EventQueue.java:731)
> at java.awt.EventQueue$4.run(EventQueue.java:729)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
> at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
> at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
> at java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.awt.EventQueue$3.run(EventQueue.java:709)
> at java.awt.EventQueue$3.run(EventQueue.java:703)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
> [AWT-EventQueue-0] DEBUG net.maizegenetics.plugindef.AbstractPlugin -
> JSONUtils: importPositionListFromJSON: problem reading file:
> /home/ool21/Documents/DataFiles/Book3.txt
> Unexpected char 83 at (line no=1, column no=1, offset=0)
> java.lang.IllegalStateException: JSONUtils: importPositionListFromJSON:
> problem reading file: /home/ool21/Documents/DataFiles/Book3.txt
> Unexpected char 83 at (line no=1, column no=1, offset=0)
> at
> net.maizegenetics.dna.snp.io.JSONUtils.importPositionListFromJSON(JSONUtils.java:271)
> at
> net.maizegenetics.plugindef.AbstractPlugin.convert(AbstractPlugin.java:226)
> at
> net.maizegenetics.plugindef.AbstractPlugin.setParameter(AbstractPlugin.java:548)
> at
> net.maizegenetics.plugindef.AbstractPlugin$2.actionPerformed(AbstractPlugin.java:614)
> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
> at
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
> at java.awt.Component.processMouseEvent(Component.java:6535)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
> at java.awt.Component.processEvent(Component.java:6300)
> at java.awt.Container.processEvent(Container.java:2236)
> at java.awt.Component.dispatchEventImpl(Component.java:4891)
> at java.awt.Container.dispatchEventImpl(Container.java:2294)
> at java.awt.Component.dispatchEvent(Component.java:4713)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
> at java.awt.Container.dispatchEventImpl(Container.java:2280)
> at java.awt.Window.dispatchEventImpl(Window.java:2750)
> at java.awt.Component.dispatchEvent(Component.java:4713)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
> at java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.awt.EventQueue$3.run(EventQueue.java:709)
> at java.awt.EventQueue$3.run(EventQueue.java:703)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
> at java.awt.EventQueue$4.run(EventQueue.java:731)
> at java.awt.EventQueue$4.run(EventQueue.java:729)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
> at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
> at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
> at java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.awt.EventQueue$3.run(EventQueue.java:709)
> at java.awt.EventQueue$3.run(EventQueue.java:703)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
> [AWT-EventQueue-0] DEBUG net.maizegenetics.plugindef.AbstractPlugin -
> Position List: JSONUtils: importPositionListFromJSON: problem reading file:
> /home/ool21/Documents/DataFiles/Book3.txt
> Unexpected char 83 at (line no=1, column no=1, offset=0) Problem converting:
> /home/ool21/Documents/DataFiles/Book3.txt to PositionList
> java.lang.IllegalArgumentException: Position List: JSONUtils:
> importPositionListFromJSON: problem reading file:
> /home/ool21/Documents/DataFiles/Book3.txt
> Unexpected char 83 at (line no=1, column no=1, offset=0) Problem converting:
> /home/ool21/Documents/DataFiles/Book3.txt to PositionList
> at
> net.maizegenetics.plugindef.AbstractPlugin.setParameter(AbstractPlugin.java:551)
> at
> net.maizegenetics.plugindef.AbstractPlugin$2.actionPerformed(AbstractPlugin.java:614)
> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
> at
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
> at java.awt.Component.processMouseEvent(Component.java:6535)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
> at java.awt.Component.processEvent(Component.java:6300)
> at java.awt.Container.processEvent(Container.java:2236)
> at java.awt.Component.dispatchEventImpl(Component.java:4891)
> at java.awt.Container.dispatchEventImpl(Container.java:2294)
> at java.awt.Component.dispatchEvent(Component.java:4713)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
> at java.awt.Container.dispatchEventImpl(Container.java:2280)
> at java.awt.Window.dispatchEventImpl(Window.java:2750)
> at java.awt.Component.dispatchEvent(Component.java:4713)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
> at java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.awt.EventQueue$3.run(EventQueue.java:709)
> at java.awt.EventQueue$3.run(EventQueue.java:703)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
> at java.awt.EventQueue$4.run(EventQueue.java:731)
> at java.awt.EventQueue$4.run(EventQueue.java:729)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
> at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
> at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
> at java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.awt.EventQueue$3.run(EventQueue.java:709)
> at java.awt.EventQueue$3.run(EventQueue.java:703)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
>
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