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bpipe-0.9.9.2 internal error with local parallel pipeline #198

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gdevenyi opened this issue Feb 20, 2017 · 2 comments
Closed

bpipe-0.9.9.2 internal error with local parallel pipeline #198

gdevenyi opened this issue Feb 20, 2017 · 2 comments

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@gdevenyi
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bpipe.PipelineCategory	[36]	SEVERE	|4:44:39 Pipeline segment in thread Thread-12 failed with internal error: For input string: "" 
Exception:
java.lang.NumberFormatException: For input string: ""
	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
	at java.lang.Integer.parseInt(Integer.java:592)
	at java.lang.Integer.valueOf(Integer.java:766)
	at org.codehaus.groovy.runtime.StringGroovyMethods.toInteger(StringGroovyMethods.java:3333)
	at org.codehaus.groovy.runtime.dgm$1159.doMethodInvoke(Unknown Source)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:47)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.executor.LocalCommandExecutor.statusImpl(LocalCommandExecutor.groovy:133)
	at sun.reflect.GeneratedMethodAccessor429.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:158)
	at bpipe.executor.LocalCommandExecutor.status(LocalCommandExecutor.groovy:123)
	at sun.reflect.GeneratedMethodAccessor428.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:158)
	at bpipe.executor.LocalCommandExecutor.waitFor(LocalCommandExecutor.groovy:167)
	at sun.reflect.GeneratedMethodAccessor425.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.executor.ThrottledDelegatingCommandExecutor.waitFor(ThrottledDelegatingCommandExecutor.groovy:128)
	at sun.reflect.GeneratedMethodAccessor425.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.PipelineContext.exec(PipelineContext.groovy:1356)
	at bpipe.PipelineContext.exec(PipelineContext.groovy)
	at sun.reflect.GeneratedMethodAccessor532.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
	at bpipe.PipelineContext.exec(PipelineContext.groovy:1309)
	at sun.reflect.GeneratedMethodAccessor531.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
	at bpipe.PipelineContext.invokeMethod(PipelineContext.groovy)
	at sun.reflect.GeneratedMethodAccessor473.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
	at bpipe.PipelineDelegate.methodMissing(PipelineDelegate.groovy:156)
	at sun.reflect.GeneratedMethodAccessor471.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaClassImpl.invokeMissingMethod(MetaClassImpl.java:938)
	at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1261)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1214)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
	at bpipe.PipelineDelegate.invokeMethod(PipelineDelegate.groovy)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:446)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at minc-library$_run_closure11.doCall(minc-library.bpipe:191)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1251)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1214)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
	at groovy.lang.GroovyObjectSupport.invokeMethod(GroovyObjectSupport.java:46)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at bpipe.PipelineStage$_runBody_closure3$_closure9.doCall(PipelineStage.groovy:388)
	at bpipe.PipelineStage$_runBody_closure3$_closure9.doCall(PipelineStage.groovy)
	at sun.reflect.GeneratedMethodAccessor341.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.ParamsBinding.withLocalVariables(Runner.groovy:1001)
	at sun.reflect.GeneratedMethodAccessor338.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
	at bpipe.PipelineStage$_runBody_closure3.doCall(PipelineStage.groovy:387)
	at bpipe.PipelineStage$_runBody_closure3.doCall(PipelineStage.groovy)
	at sun.reflect.GeneratedMethodAccessor335.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.Closure.call(Closure.java:426)
	at groovy.lang.Closure.call(Closure.java:420)
	at org.codehaus.groovy.runtime.GroovyCategorySupport$ThreadCategoryInfo.use(GroovyCategorySupport.java:110)
	at org.codehaus.groovy.runtime.GroovyCategorySupport$ThreadCategoryInfo.access$400(GroovyCategorySupport.java:68)
	at org.codehaus.groovy.runtime.GroovyCategorySupport.use(GroovyCategorySupport.java:250)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.use(DefaultGroovyMethods.java:407)
	at org.codehaus.groovy.runtime.dgm$755.doMethodInvoke(Unknown Source)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:375)
	at sun.reflect.GeneratedMethodAccessor327.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:158)
	at bpipe.PipelineStage.run(PipelineStage.groovy:248)
	at sun.reflect.GeneratedMethodAccessor154.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.PipelineCategory$_plus_closure3.doCall(PipelineCategory.groovy:171)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1251)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1214)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
	at groovy.lang.GroovyObjectSupport.invokeMethod(GroovyObjectSupport.java:46)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at bpipe.PipelineStage$_runBody_closure3$_closure9.doCall(PipelineStage.groovy:388)
	at bpipe.PipelineStage$_runBody_closure3$_closure9.doCall(PipelineStage.groovy)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.ParamsBinding.withLocalVariables(Runner.groovy:1001)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
	at bpipe.PipelineStage$_runBody_closure3.doCall(PipelineStage.groovy:387)
	at bpipe.PipelineStage$_runBody_closure3.doCall(PipelineStage.groovy)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.Closure.call(Closure.java:426)
	at groovy.lang.Closure.call(Closure.java:420)
	at org.codehaus.groovy.runtime.GroovyCategorySupport$ThreadCategoryInfo.use(GroovyCategorySupport.java:110)
	at org.codehaus.groovy.runtime.GroovyCategorySupport$ThreadCategoryInfo.access$400(GroovyCategorySupport.java:68)
	at org.codehaus.groovy.runtime.GroovyCategorySupport.use(GroovyCategorySupport.java:250)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.use(DefaultGroovyMethods.java:407)
	at org.codehaus.groovy.runtime.dgm$755.doMethodInvoke(Unknown Source)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:375)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:158)
	at bpipe.PipelineStage.run(PipelineStage.groovy:248)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.PipelineCategory$_plus_closure3.doCall(PipelineCategory.groovy:151)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1251)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1214)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
	at groovy.lang.GroovyObjectSupport.invokeMethod(GroovyObjectSupport.java:46)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at bpipe.PipelineStage$_runBody_closure3$_closure9.doCall(PipelineStage.groovy:388)
	at bpipe.PipelineStage$_runBody_closure3$_closure9.doCall(PipelineStage.groovy)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.ParamsBinding.withLocalVariables(Runner.groovy:1001)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
	at bpipe.PipelineStage$_runBody_closure3.doCall(PipelineStage.groovy:387)
	at bpipe.PipelineStage$_runBody_closure3.doCall(PipelineStage.groovy)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.Closure.call(Closure.java:426)
	at groovy.lang.Closure.call(Closure.java:420)
	at org.codehaus.groovy.runtime.GroovyCategorySupport$ThreadCategoryInfo.use(GroovyCategorySupport.java:110)
	at org.codehaus.groovy.runtime.GroovyCategorySupport$ThreadCategoryInfo.access$400(GroovyCategorySupport.java:68)
	at org.codehaus.groovy.runtime.GroovyCategorySupport.use(GroovyCategorySupport.java:250)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.use(DefaultGroovyMethods.java:407)
	at org.codehaus.groovy.runtime.dgm$755.doMethodInvoke(Unknown Source)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:375)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:158)
	at bpipe.PipelineStage.run(PipelineStage.groovy:248)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at bpipe.Pipeline.runSegment(Pipeline.groovy:538)
	at bpipe.Pipeline$runSegment$14.call(Unknown Source)
	at bpipe.PipelineCategory$_splitOnMap_closure11$_closure38.doCall(PipelineCategory.groovy:527)
	at bpipe.PipelineCategory$_splitOnMap_closure11$_closure38.doCall(PipelineCategory.groovy)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
	at groovy.lang.Closure.call(Closure.java:426)
	at groovy.lang.Closure.call(Closure.java:420)
	at groovy.lang.Closure.run(Closure.java:507)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
@gdevenyi
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Run command was:

bpipe run -n 8 -m 13930 ../minc-bpipe-library/pipeline.bpipe ../input/ADNI_027_S_0120_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20090316150744380_S63578_I139053.mnc ../input/ADNI_027_S_0179_MR_MPR-R__GradWarp__B1_Correction__N3__Scaled_2_Br_20081002152248907_S11781_I119071.mnc ../input/ADNI_027_S_0179_MR_MPR-R__GradWarp__B1_Correction__N3__Scaled_Br_20061222180304669_S11781_I34136.mnc ../input/ADNI_027_S_0179_MR_MPR-R__GradWarp__B1_Correction__N3__Scaled_Br_20070807080551065_S28889_I65293.mnc ../input/ADNI_027_S_0179_MR_MPR-R__GradWarp__B1_Correction__N3__Scaled_Br_20080320170137051_S46628_I99065.mnc ../input/ADNI_027_S_0179_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20061222181103848_S18956_I34141.mnc ../input/ADNI_027_S_0179_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20071027172607283_S39424_I78876.mnc ../input/ADNI_027_S_0179_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20090422153502117_S64193_I142362.mnc

@gdevenyi
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Okay, so some more info:
I am running multiple bpipe "local" runs, across a shared filesystem on multiple computers.

This looks like perhaps bpipe is clobbering other runs from other machines (or otherwise conflicting with them).

Is that possible? Should bpipe be encoding the hostID in the job control so this doesn't happen?

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