Mar-09 13:54:12.776 [main] DEBUG nextflow.cli.Launcher - $> /home/kaisa/bin/nextflow run /home/kaisa/tools/BACTpipe/bactpipe.nf -profile rackham -params-file params_brachy.yaml --reads *R{1,2}.fastq.gz Mar-09 13:54:13.679 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.27.6 Mar-09 13:54:13.868 [main] INFO nextflow.cli.CmdRun - Launching `/home/kaisa/tools/BACTpipe/bactpipe.nf` [stoic_watson] - revision: 5c10176841 Mar-09 13:54:14.064 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/kaisa/tools/BACTpipe/nextflow.config Mar-09 13:54:14.066 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/kaisa/tools/BACTpipe/nextflow.config Mar-09 13:54:16.068 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'rackham' Mar-09 13:54:17.779 [main] DEBUG nextflow.Session - Session uuid: e86e4819-75d4-4994-9a3a-27330aaa3be7 Mar-09 13:54:17.780 [main] DEBUG nextflow.Session - Run name: stoic_watson Mar-09 13:54:17.780 [main] DEBUG nextflow.Session - Executor pool size: 40 Mar-09 13:54:17.875 [main] DEBUG nextflow.cli.CmdRun - Version: 0.27.6 build 4775 Modified: 19-02-2018 08:45 UTC (09:45 CEST) System: Linux 3.10.0-693.17.1.el7.x86_64 Runtime: Groovy 2.4.13 on OpenJDK 64-Bit Server VM 1.8.0_161-b14 Encoding: UTF-8 (UTF-8) Process: 10928@rackham4.uppmax.uu.se [89.44.250.85] CPUs: 40 - Mem: 251.4 GB (91.8 GB) - Swap: 7.9 GB (7.9 GB) Mar-09 13:54:17.975 [main] DEBUG nextflow.Session - Work-dir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work [lustre] Mar-09 13:54:19.809 [main] DEBUG nextflow.Session - Session start invoked Mar-09 13:54:19.813 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start Mar-09 13:54:19.814 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing Mar-09 13:54:21.375 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Mar-09 13:54:21.379 [main] INFO nextflow.Nextflow - ============================================================ Mar-09 13:54:21.379 [main] INFO nextflow.Nextflow - BACTpipe Mar-09 13:54:21.379 [main] INFO nextflow.Nextflow - Version 2.4b-dev Mar-09 13:54:21.379 [main] INFO nextflow.Nextflow - Bacterial whole genome analysis pipeline Mar-09 13:54:21.379 [main] INFO nextflow.Nextflow - https://bactpipe.readthedocs.io Mar-09 13:54:21.380 [main] INFO nextflow.Nextflow - ============================================================ Mar-09 13:54:21.381 [main] INFO nextflow.Nextflow - Running with the following settings: Mar-09 13:54:21.382 [main] INFO nextflow.Nextflow - clusterOptions: false Mar-09 13:54:21.382 [main] INFO nextflow.Nextflow - output_dir: BACTpipe_results Mar-09 13:54:21.382 [main] INFO nextflow.Nextflow - reads: *R{1,2}.fastq.gz Mar-09 13:54:21.382 [main] INFO nextflow.Nextflow - mashscreen_database: /proj/uppstore2017086/db/refseq.genomes.k21s1000.msh Mar-09 13:54:21.382 [main] INFO nextflow.Nextflow - bbduk_adapters: /home/kaisa/tools/BACTpipe/resources/adapters_w_phiX.fa Mar-09 13:54:21.382 [main] INFO nextflow.Nextflow - bbduk_minlen: 30 Mar-09 13:54:21.383 [main] INFO nextflow.Nextflow - bbduk_qtrim: rl Mar-09 13:54:21.383 [main] INFO nextflow.Nextflow - bbduk_trimq: 10 Mar-09 13:54:21.383 [main] INFO nextflow.Nextflow - bbduk_ktrim: r Mar-09 13:54:21.383 [main] INFO nextflow.Nextflow - bbduk_k: 30 Mar-09 13:54:21.384 [main] INFO nextflow.Nextflow - bbduk_mink: 11 Mar-09 13:54:21.384 [main] INFO nextflow.Nextflow - bbduk_hdist: 1 Mar-09 13:54:21.384 [main] INFO nextflow.Nextflow - bbduk_trimbyoverlap: trimbyoverlap Mar-09 13:54:21.463 [main] INFO nextflow.Nextflow - bbduk_trimpairsevenly: trimpairsevenly Mar-09 13:54:21.464 [main] INFO nextflow.Nextflow - shovill_depth: 100 Mar-09 13:54:21.464 [main] INFO nextflow.Nextflow - shovill_kmers: 31,33,55,77,99,127 Mar-09 13:54:21.464 [main] INFO nextflow.Nextflow - shovill_minlen: 500 Mar-09 13:54:21.465 [main] INFO nextflow.Nextflow - prokka_evalue: 1e-09 Mar-09 13:54:21.465 [main] INFO nextflow.Nextflow - prokka_kingdom: Bacteria Mar-09 13:54:21.465 [main] INFO nextflow.Nextflow - prokka_reference: Mar-09 13:54:21.465 [main] INFO nextflow.Nextflow - prokka_gram_stain: Mar-09 13:54:21.465 [main] INFO nextflow.Nextflow - project: snic2017-7-245 Mar-09 13:54:21.465 [main] INFO nextflow.Nextflow - ============================================================ Mar-09 13:54:21.477 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: ./; pattern: *R{1,2}.fastq.gz; options: null Mar-09 13:54:23.875 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Mar-09 13:54:23.876 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Mar-09 13:54:23.972 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Mar-09 13:54:24.064 [main] INFO nextflow.executor.Executor - [warm up] executor > slurm Mar-09 13:54:24.072 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Mar-09 13:54:24.075 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor Mar-09 13:54:24.076 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Mar-09 13:54:24.078 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: slurm Mar-09 13:54:24.078 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Mar-09 13:54:24.375 [main] DEBUG nextflow.Session - >>> barrier register (process: screen_for_contaminants) Mar-09 13:54:24.567 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [1] Mar-09 13:54:24.575 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > screen_for_contaminants -- maxForks: 40 Mar-09 13:54:25.068 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Mar-09 13:54:25.069 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Mar-09 13:54:25.069 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Mar-09 13:54:25.164 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Mar-09 13:54:25.166 [main] DEBUG nextflow.Session - >>> barrier register (process: bbduk) Mar-09 13:54:25.167 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [1] Mar-09 13:54:25.167 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bbduk -- maxForks: 40 Mar-09 13:54:25.365 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Mar-09 13:54:25.365 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Mar-09 13:54:25.365 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Mar-09 13:54:25.366 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Mar-09 13:54:25.368 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc) Mar-09 13:54:25.369 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 40 Mar-09 13:54:25.464 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Mar-09 13:54:25.464 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Mar-09 13:54:25.466 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Mar-09 13:54:25.466 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Mar-09 13:54:25.467 [main] DEBUG nextflow.Session - >>> barrier register (process: shovill) Mar-09 13:54:25.565 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > shovill -- maxForks: 40 Mar-09 13:54:25.668 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Mar-09 13:54:25.668 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Mar-09 13:54:25.668 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Mar-09 13:54:25.668 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Mar-09 13:54:25.669 [main] DEBUG nextflow.Session - >>> barrier register (process: prokka) Mar-09 13:54:25.670 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > prokka -- maxForks: 40 Mar-09 13:54:25.869 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Mar-09 13:54:25.870 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Mar-09 13:54:25.870 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Mar-09 13:54:25.870 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Mar-09 13:54:25.964 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc) Mar-09 13:54:25.964 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 40 Mar-09 13:54:25.967 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Mar-09 13:54:25.967 [main] DEBUG nextflow.Session - Session await Mar-09 13:54:26.873 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC5587-u) > jobId: 2398774; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/c3/5845c7247fb8bb1f010acd782f9085 Mar-09 13:54:26.877 [Task submitter] INFO nextflow.Session - [c3/5845c7] Submitted process > screen_for_contaminants (PC5587-u) Mar-09 13:54:27.253 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC2022III) > jobId: 2398775; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/d4/50eb2d7de5f9e8b454e5980b7bf532 Mar-09 13:54:27.263 [Task submitter] INFO nextflow.Session - [d4/50eb2d] Submitted process > screen_for_contaminants (PC2022III) Mar-09 13:54:27.480 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC3714II) > jobId: 2398776; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/07/61ad4b71d746b4f5be0d15acf661e1 Mar-09 13:54:27.480 [Task submitter] INFO nextflow.Session - [07/61ad4b] Submitted process > screen_for_contaminants (PC3714II) Mar-09 13:54:27.641 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC5538III) > jobId: 2398777; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/56/2cc35079ef4f47d92563cc24c2e20e Mar-09 13:54:27.641 [Task submitter] INFO nextflow.Session - [56/2cc350] Submitted process > screen_for_contaminants (PC5538III) Mar-09 13:54:27.808 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC4580III) > jobId: 2398778; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/64/550c41b2a774957b957bd48f6d1b15 Mar-09 13:54:27.808 [Task submitter] INFO nextflow.Session - [64/550c41] Submitted process > screen_for_contaminants (PC4580III) Mar-09 13:54:27.990 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC4597II) > jobId: 2398779; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/6c/addad18d3d9ab26723d286e870ee2c Mar-09 13:54:27.990 [Task submitter] INFO nextflow.Session - [6c/addad1] Submitted process > screen_for_contaminants (PC4597II) Mar-09 13:54:28.158 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC390II) > jobId: 2398780; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/b1/b30297616789ad99aaf629aa97c2c8 Mar-09 13:54:28.159 [Task submitter] INFO nextflow.Session - [b1/b30297] Submitted process > screen_for_contaminants (PC390II) Mar-09 13:54:28.408 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC3997IV) > jobId: 2398781; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/b5/ee7c6bd7eae3caff1774e93e83a229 Mar-09 13:54:28.408 [Task submitter] INFO nextflow.Session - [b5/ee7c6b] Submitted process > screen_for_contaminants (PC3997IV) Mar-09 13:54:28.568 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC4226IV) > jobId: 2398782; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/ad/6dc1334c188c75ce881bdcded51ffa Mar-09 13:54:28.569 [Task submitter] INFO nextflow.Session - [ad/6dc133] Submitted process > screen_for_contaminants (PC4226IV) Mar-09 13:54:28.738 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (W1090330) > jobId: 2398783; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/e9/7d9402ae79ea1445fdb89bb3e96b16 Mar-09 13:54:28.738 [Task submitter] INFO nextflow.Session - [e9/7d9402] Submitted process > screen_for_contaminants (W1090330) Mar-09 13:54:28.906 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC5587-p) > jobId: 2398784; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/f8/6e735c6407f5fb8cdf8458fe334daf Mar-09 13:54:28.906 [Task submitter] INFO nextflow.Session - [f8/6e735c] Submitted process > screen_for_contaminants (PC5587-p) Mar-09 13:54:29.070 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC3053II) > jobId: 2398785; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/22/4d34dbc8ef7df3367a043596fbacb3 Mar-09 13:54:29.071 [Task submitter] INFO nextflow.Session - [22/4d34db] Submitted process > screen_for_contaminants (PC3053II) Mar-09 13:54:29.251 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC2777IV) > jobId: 2398786; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/b5/53a82ae20bedf470f71936b880a5ba Mar-09 13:54:29.252 [Task submitter] INFO nextflow.Session - [b5/53a82a] Submitted process > screen_for_contaminants (PC2777IV) Mar-09 13:54:29.409 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC5099IV) > jobId: 2398787; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/cc/d46f51b050cccbdb6b6d21a4ab61f9 Mar-09 13:54:29.409 [Task submitter] INFO nextflow.Session - [cc/d46f51] Submitted process > screen_for_contaminants (PC5099IV) Mar-09 13:54:29.569 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC3517II) > jobId: 2398788; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/e2/ee9e724f1ebabcb1b52889d4f4a84c Mar-09 13:54:29.569 [Task submitter] INFO nextflow.Session - [e2/ee9e72] Submitted process > screen_for_contaminants (PC3517II) Mar-09 13:54:29.743 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (PC3939II) > jobId: 2398789; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/0a/7aaf5e11a87046d666182fce855fd2 Mar-09 13:54:29.743 [Task submitter] INFO nextflow.Session - [0a/7aaf5e] Submitted process > screen_for_contaminants (PC3939II) Mar-09 13:54:29.908 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process screen_for_contaminants (513A) > jobId: 2398790; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/dd/cbbb51efe8cb538db49edaf0019ecd Mar-09 13:54:29.909 [Task submitter] INFO nextflow.Session - [dd/cbbb51] Submitted process > screen_for_contaminants (513A) Mar-09 13:59:09.141 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 2398782; id: 5; name: screen_for_contaminants (PC4226IV); status: COMPLETED; exit: 0; error: -; workDir: /crex1/proj/uppstore2017086/projects/WGS/kaisa_projects/Brachyspira/work/ad/6dc1334c188c75ce881bdcded51ffa started: 1520600169120; exited: 2018-03-09T12:59:04Z; ] Mar-09 13:59:09.155 [Actor Thread 2] ERROR n.extension.DataflowExtensions - @unknown java.lang.ArrayIndexOutOfBoundsException: 1 at org.codehaus.groovy.runtime.dgmimpl.arrays.ObjectArrayGetAtMetaMethod.invoke(ObjectArrayGetAtMetaMethod.java:41) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.invoke(PojoMetaMethodSite.java:51) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56) 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:125) at _nf_script_b5d5167f$_run_closure6.doCall(_nf_script_b5d5167f:208) 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: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:1022) 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:125) at nextflow.extension.DataflowExtensions$_filter_closure6.doCall(DataflowExtensions.groovy:363) 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: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:1022) at groovy.lang.Closure.call(Closure.java:414) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108) at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43) at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293) at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30) at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93) at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Mar-09 13:59:09.161 [Actor Thread 2] DEBUG nextflow.Session - Session aborted -- Cause: 1 Mar-09 13:59:09.176 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) Mar-09 13:59:09.272 [Actor Thread 2] DEBUG nextflow.Session - The following nodes are still active: [process] bbduk status=ACTIVE port 0: (queue) OPEN; channel: - port 1: (value) - ; channel: __$eachinparam<1> port 2: (cntrl) OPEN; channel: $ [process] fastqc status=ACTIVE port 0: (queue) OPEN; channel: - port 1: (cntrl) OPEN; channel: $ [process] shovill status=ACTIVE port 0: (queue) OPEN; channel: - port 1: (cntrl) OPEN; channel: $ [process] prokka status=ACTIVE port 0: (queue) OPEN; channel: - port 1: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: fastqc port 1: (value) - ; channel: prokka port 2: (cntrl) OPEN; channel: $ Mar-09 13:59:09.365 [main] DEBUG nextflow.Session - Session await > all process finished Mar-09 13:59:09.365 [main] DEBUG nextflow.Session - Session await > all barriers passed Mar-09 13:59:09.367 [main] INFO nextflow.Nextflow - ============================================================ Mar-09 13:59:09.368 [main] ERROR nextflow.Nextflow - Oops .. something went wrong! Mar-09 13:59:09.368 [main] INFO nextflow.Nextflow - Check output files in folder: Mar-09 13:59:09.369 [main] INFO nextflow.Nextflow - BACTpipe_results Mar-09 13:59:09.369 [main] INFO nextflow.Nextflow - ============================================================ Mar-09 13:59:09.470 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (16) Mar-09 13:59:09.988 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=1; failedCount=16; ignoredCount=0; cachedCount=0; succeedDuration=5m 52s; failedDuration=0ms; cachedDuration=0ms] Mar-09 13:59:09.988 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Mar-09 13:59:11.394 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline Mar-09 13:59:11.487 [main] DEBUG nextflow.CacheDB - Closing CacheDB done Mar-09 13:59:11.495 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye