API tools faq
paste
Advertisement
Guest User

publishDir

a guest
Dec 14th, 2016
118
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 9.36 KB | None | 0 0
raw download clone embed print report
  1. Dec-14 16:33:36.662 [main] DEBUG nextflow.cli.CmdRun -
  2. Version: 0.22.6 build 4116
  3. Modified: 04-12-2016 21:50 UTC (13:50 PDT)
  4. System: Linux 3.19.0-61-generic
  5. Runtime: Groovy 2.4.7 on OpenJDK 64-Bit Server VM 1.7.0_101-b00
  6. Encoding: UTF-8 (UTF-8)
  7. Process: 42866@sierra [127.0.1.1]
  8. CPUs: 56 - Mem: 503.8 GB (107.3 GB) - Swap: 511.9 GB (511.9 GB)
  9.  
  10. Dec-14 16:33:37.915 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > onlyfoo -- maxForks: 56
  11. Dec-14 16:33:37.922 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
  12. Dec-14 16:33:37.922 [main] DEBUG nextflow.Session - Session await
  13. Dec-14 16:33:37.935 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <memory> Poison pill arrived
  14. Dec-14 16:33:37.935 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - <onlyfoo> Poison pill arrived
  15. Dec-14 16:33:37.950 [Actor Thread 1] DEBUG nextflow.processor.StateObj - <memory> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
  16. Dec-14 16:33:37.951 [Actor Thread 4] DEBUG nextflow.processor.StateObj - <onlyfoo> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
  17. Dec-14 16:33:37.983 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > onlyfoo (1)
  18. Dec-14 16:33:38.008 [Actor Thread 6] ERROR nextflow.processor.TaskProcessor - Error executing process > 'onlyfoo (1)'
  19.  
  20. Caused by:
  21. java.lang.NullPointerException
  22.  
  23. java.lang.NullPointerException: null
  24. at nextflow.processor.PublishDir.apply(PublishDir.groovy:191)
  25. at nextflow.processor.TaskProcessor.publishOutputs(TaskProcessor.groovy:1205)
  26. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  27. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  28. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  29. at java.lang.reflect.Method.invoke(Method.java:606)
  30. at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
  31. at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
  32. at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
  33. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
  34. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
  35. at nextflow.processor.TaskProcessor.finalizeTask0(TaskProcessor.groovy:1973)
  36. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  37. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  38. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  39. at java.lang.reflect.Method.invoke(Method.java:606)
  40. at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
  41.  
  42. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  43. at java.lang.reflect.Method.invoke(Method.java:606)
  44. at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
  45. at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
  46. at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
  47. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
  48. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
  49. at nextflow.processor.TaskProcessor.finalizeTask0(TaskProcessor.groovy:1973)
  50. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  51. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  52. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  53. at java.lang.reflect.Method.invoke(Method.java:606)
  54. at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
  55. at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
  56. at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
  57. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
  58. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
  59. at nextflow.processor.TaskProcessor.checkStoredOutput(TaskProcessor.groovy:785)
  60. at nextflow.processor.TaskProcessor$checkStoredOutput$3.callCurrent(Unknown Source)
  61. at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
  62. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
  63. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
  64. at nextflow.processor.TaskProcessor.invokeTask(TaskProcessor.groovy:554)
  65. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  66. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  67. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  68. at java.lang.reflect.Method.invoke(Method.java:606)
  69. at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
  70. at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
  71. at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
  72. at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1082)
  73. at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
  74. at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1261)
  75. at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1217)
  76. at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
  77. at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
  78. at groovy.lang.GroovyObjectSupport.invokeMethod(GroovyObjectSupport.java:46)
  79. at groovy.lang.Script.invokeMethod(Script.java:80)
  80. at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
  81. at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
  82. at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
  83. at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
  84. at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
  85. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
  86. at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
  87. at Script268F736790F82E694C1041E30D0FE6DF$_run_closure1.doCall(Script268F736790F82E694C1041E30D0FE6DF:1)
  88. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  89. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  90. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  91. at java.lang.reflect.Method.invoke(Method.java:606)
  92. at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
  93. at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
  94. at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
  95. at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
  96. at groovy.lang.Closure.call(Closure.java:414)
  97. at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
  98. at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.access$001(ForkingDataflowOperatorActor.java:35)
  99. at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor$1.run(ForkingDataflowOperatorActor.java:58)
  100. at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
  101. at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
  102. at java.lang.Thread.run(Thread.java:745)
  103. Dec-14 16:33:38.021 [Actor Thread 6] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.NullPointerException
  104. Dec-14 16:33:38.029 [Thread-1] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm)
  105. Dec-14 16:33:38.029 [main] DEBUG nextflow.Session - Session await > all process finished
  106. Dec-14 16:33:38.030 [main] DEBUG nextflow.Session - Session await > all barriers passed
  107. Dec-14 16:33:38.033 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <memory> After stop
  108. Dec-14 16:33:38.033 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - <onlyfoo> After stop
  109. Dec-14 16:33:38.041 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
  110. Dec-14 16:33:38.052 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
  111. Dec-14 16:33:38.469 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!