Jun-06 14:14:11.808 [main] INFO nextflow.Nextflow - ---------------------------------------------------- Jun-06 14:14:11.984 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:multiqc|get_software_versions` matches process get_software_versions Jun-06 14:14:11.988 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Jun-06 14:14:11.989 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Jun-06 14:14:12.006 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Jun-06 14:14:12.010 [main] INFO nextflow.executor.Executor - [warm up] executor > slurm Jun-06 14:14:12.019 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Jun-06 14:14:12.026 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor Jun-06 14:14:12.027 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Jun-06 14:14:12.033 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: slurm Jun-06 14:14:12.034 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Jun-06 14:14:12.104 [main] DEBUG nextflow.Session - >>> barrier register (process: get_software_versions) Jun-06 14:14:12.112 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 4 Jun-06 14:14:12.212 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown variable 'gtf_makeSTARindex' Jun-06 14:14:12.283 [main] DEBUG nextflow.Session - The following nodes are still active: [process] get_software_versions status=ACTIVE port 0: (cntrl) - ; channel: $ Jun-06 14:14:12.293 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) Jun-06 14:14:12.316 [main] ERROR nextflow.cli.Launcher - @unknown groovy.lang.MissingPropertyException: Unknown variable 'gtf_makeSTARindex' at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:265) at nextflow.processor.ProcessConfig.getProperty(ProcessConfig.groovy:268) at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:190) at groovy.lang.Closure.getPropertyTryThese(Closure.java:319) at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:309) at groovy.lang.Closure.getProperty(Closure.java:294) at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:49) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:309) at _nf_script_902d0cea$_run_closure23.doCall(_nf_script_902d0cea:341) at _nf_script_902d0cea$_run_closure23.doCall(_nf_script_902d0cea) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:41) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:56) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:119) at nextflow.processor.ProcessFactory.createProcessor(ProcessFactory.groovy:218) at nextflow.processor.ProcessFactory.createProcessor(ProcessFactory.groovy) at nextflow.processor.ProcessFactory$createProcessor.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at nextflow.processor.ProcessFactory$createProcessor.call(Unknown Source) at nextflow.script.BaseScript.process(BaseScript.groovy:146) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176) at _nf_script_902d0cea.run(_nf_script_902d0cea:333) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:382) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:170) at nextflow.cli.CmdRun.run(CmdRun.groovy:240) at nextflow.cli.Launcher.run(Launcher.groovy:445) at nextflow.cli.Launcher.main(Launcher.groovy:622)