Requeue test log

.nextflow.log

Sep-30 09:01:42.253 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [proxy.swmed.edu, 3128]
Sep-30 09:01:42.354 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [proxy.swmed.edu, 3128]
Sep-30 09:01:42.354 [main] DEBUG nextflow.cli.Launcher - $> ./nextflow -trace nextflow.executor run main.nf
Sep-30 09:01:42.416 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.22.2-SNAPSHOT
Sep-30 09:01:42.428 [main] INFO  nextflow.cli.CmdRun - Launching `main.nf` [reverent_easley] - revision: 8300612e43
Sep-30 09:01:42.437 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: nextflow.config
Sep-30 09:01:42.439 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/nextflow.config
Sep-30 09:01:42.763 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'standard'
Sep-30 09:01:42.828 [main] DEBUG nextflow.Session - Session uuid: 38109f9f-02e8-4363-be75-d76cb141dccb
Sep-30 09:01:42.828 [main] DEBUG nextflow.Session - Run name: reverent_easley
Sep-30 09:01:42.829 [main] DEBUG nextflow.Session - Executor pool size: 12
Sep-30 09:01:42.844 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 0.22.2-SNAPSHOT build 4080
  Modified: 28-09-2016 09:27 UTC (04:27 CDT)
  System: Linux 2.6.32-642.4.2.el6.x86_64
  Runtime: Groovy 2.4.7 on OpenJDK 64-Bit Server VM 1.7.0_101-mockbuild_2016_04_19_08_45-b00
  Encoding: UTF-8 (UTF-8)
  Process: [email protected] [172.18.215.64]
  CPUs: 12 - Mem: 15.6 GB (1.2 GB) - Swap: 31.5 GB (31.2 GB)
Sep-30 09:01:42.862 [main] DEBUG nextflow.Session - Work-dir: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work [nfs]
Sep-30 09:01:42.863 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/bin
Sep-30 09:01:43.008 [main] DEBUG nextflow.Session - Session start invoked
Sep-30 09:01:43.011 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Sep-30 09:01:43.012 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Sep-30 09:01:43.052 [main] DEBUG nextflow.Session - Using default localLib path: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/lib
Sep-30 09:01:43.058 [main] DEBUG nextflow.script.ScriptRunner - Adding to the classpath library: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/lib
Sep-30 09:01:43.195 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Sep-30 09:01:43.354 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
Sep-30 09:01:43.354 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
Sep-30 09:01:43.368 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
Sep-30 09:01:43.371 [main] INFO  nextflow.executor.Executor - [warm up] executor > slurm
Sep-30 09:01:43.377 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 1s; dumpInterval: 5m 
Sep-30 09:01:43.380 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor
Sep-30 09:01:43.380 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm)
Sep-30 09:01:43.383 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: slurm
Sep-30 09:01:43.384 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
Sep-30 09:01:43.440 [main] DEBUG nextflow.Session - >>> barrier register (process: uppercase)
Sep-30 09:01:43.455 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > uppercase -- maxForks: 12
Sep-30 09:01:43.486 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
Sep-30 09:01:43.486 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
Sep-30 09:01:43.486 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
Sep-30 09:01:43.486 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
Sep-30 09:01:43.487 [main] DEBUG nextflow.Session - >>> barrier register (process: tolines)
Sep-30 09:01:43.496 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > tolines -- maxForks: 12
Sep-30 09:01:43.500 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <uppercase> Poison pill arrived
Sep-30 09:01:43.500 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
Sep-30 09:01:43.501 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
Sep-30 09:01:43.501 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
Sep-30 09:01:43.501 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
Sep-30 09:01:43.502 [main] DEBUG nextflow.Session - >>> barrier register (process: wordcounts)
Sep-30 09:01:43.507 [Actor Thread 3] DEBUG nextflow.processor.StateObj - <uppercase> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Sep-30 09:01:43.511 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > wordcounts -- maxForks: 12
Sep-30 09:01:43.512 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
Sep-30 09:01:43.512 [main] DEBUG nextflow.Session - Session await
Sep-30 09:01:43.581 [Actor Thread 2] DEBUG nextflow.executor.GridTaskHandler - Launching process > uppercase (1) -- work folder: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/e1/497e73abe37526b350a255fc66e89b
Sep-30 09:01:43.641 [Actor Thread 2] TRACE nextflow.executor.GridTaskHandler - start process uppercase (1) > cli: [sbatch, .command.run]
Sep-30 09:01:43.654 [Actor Thread 2] TRACE nextflow.executor.GridTaskHandler - submit uppercase (1) > exit: 0
Submitted batch job 242651


Sep-30 09:01:43.664 [Actor Thread 2] INFO  nextflow.Session - [e1/497e73] Submitted process > uppercase (1)
Sep-30 09:01:43.666 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <uppercase> After stop
Sep-30 09:01:44.409 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - <uppercase> Sending poison pills and terminating process
Sep-30 09:01:44.410 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <tolines> Poison pill arrived
Sep-30 09:01:44.411 [Actor Thread 3] DEBUG nextflow.Session - <<< barrier arrive (process: uppercase)
Sep-30 09:01:44.411 [Actor Thread 6] DEBUG nextflow.processor.StateObj - <tolines> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Sep-30 09:01:44.415 [Actor Thread 2] DEBUG nextflow.executor.GridTaskHandler - Launching process > tolines (1) -- work folder: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e
Sep-30 09:01:44.427 [Actor Thread 2] TRACE nextflow.executor.GridTaskHandler - start process tolines (1) > cli: [sbatch, .command.run]
Sep-30 09:01:44.436 [Actor Thread 2] TRACE nextflow.executor.GridTaskHandler - submit tolines (1) > exit: 0
Submitted batch job 242652


Sep-30 09:01:44.437 [Actor Thread 2] INFO  nextflow.Session - [4b/68f2de] Submitted process > tolines (1)
Sep-30 09:01:44.437 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <tolines> After stop
Sep-30 09:01:45.390 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:45.394 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:46.388 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:46.389 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:47.388 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:47.388 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:48.388 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:48.389 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:49.388 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:49.388 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:50.388 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:50.389 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:51.388 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:51.388 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:52.389 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:52.389 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:53.389 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:53.389 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:54.389 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:54.390 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:55.390 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:55.390 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:56.391 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:56.391 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:57.392 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:57.393 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:58.391 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:58.391 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:01:59.391 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:01:59.392 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:00.392 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:00.392 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:01.391 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:01.391 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:02.392 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:02.392 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:03.392 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:03.393 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:04.393 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:04.393 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:05.393 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:05.393 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:06.393 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:06.394 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:07.394 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:07.395 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:08.395 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:08.395 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:09.394 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:09.395 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:10.395 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:10.395 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:11.395 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:11.395 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:12.394 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:12.395 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:13.395 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:13.395 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:14.396 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:14.396 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:15.396 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:15.397 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:16.396 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:16.396 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:17.396 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:17.396 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:18.396 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:18.397 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:19.397 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:19.397 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:20.397 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:20.398 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:21.398 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:21.398 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:22.398 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:22.398 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:23.397 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:23.397 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:24.397 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:24.398 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:25.398 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:25.398 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:26.398 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:26.398 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:27.398 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:27.399 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:28.398 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:28.398 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:29.398 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:29.399 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:30.398 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:30.399 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:31.399 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:31.399 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:32.399 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:32.399 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:33.400 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:33.400 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:34.401 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:34.401 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:35.401 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:35.402 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:36.402 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:36.403 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:37.402 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:37.402 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:38.401 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:38.402 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:39.402 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:39.402 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:40.402 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:40.402 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:41.402 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:41.403 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:42.403 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:42.403 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:43.403 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:43.403 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:44.403 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:44.403 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status map is null -- return true
Sep-30 09:02:45.403 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:45.404 [Thread-1] TRACE n.executor.AbstractGridExecutor - Getting grid queue status: squeue -h -o %i %t -t all -u dtrudgian
Sep-30 09:02:45.422 [Thread-1] TRACE n.executor.AbstractGridExecutor - SLURM status result > exit: 0
242651 CD
242652 PD
242648 R


Sep-30 09:02:45.428 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:45.429 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:46.404 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:46.405 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:46.405 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:47.405 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:47.405 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:47.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:48.405 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:48.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:48.407 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:49.405 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:49.405 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:49.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:50.405 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:50.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:50.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:51.404 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:51.405 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:51.405 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:52.405 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:52.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:52.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:53.406 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:53.407 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:53.407 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:54.406 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:54.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:54.406 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:55.407 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:55.408 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:55.408 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:56.408 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:56.409 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:56.409 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:57.409 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:57.410 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:57.410 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:58.408 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:58.409 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:58.409 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:02:59.409 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:02:59.410 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:02:59.410 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:00.409 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:00.410 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:00.410 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:01.410 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:01.411 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:01.411 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:02.411 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:02.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:02.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:03.412 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:03.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:03.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:04.412 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:04.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:04.413 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:05.412 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:05.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:05.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:06.412 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:06.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:06.412 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:07.412 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:07.413 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:07.413 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:08.413 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:08.414 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:08.414 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:09.414 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:09.415 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:09.415 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:10.415 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:10.415 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:10.416 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:11.415 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:11.416 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:11.416 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:12.414 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:12.415 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:12.415 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:13.415 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:13.416 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:13.416 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:14.416 [Thread-1] TRACE nextflow.executor.GridTaskHandler - JobId `242652` exit file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e/.exitcode - lastModified: null - size: null
Sep-30 09:03:14.417 [Thread-1] TRACE n.executor.AbstractGridExecutor - Queue status:
  job: 242651: DONE
  job: 242652: PENDING
  job: 242648: RUNNING

Sep-30 09:03:14.417 [Thread-1] TRACE n.executor.AbstractGridExecutor - JobId `242652` active status: true
Sep-30 09:03:15.447 [Thread-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'tolines (1)'

Caused by:
  Process `tolines (1)` terminated with an error exit status (143)

Command executed:

  cat "mobydick.txt.uppercase" | tr -cs "A-Z'" "
  "  > "mobydick.txt.uppercase.tolines"
      sleep 3600

Command exit status:
  143

Command output:
  (empty)

Work dir:
  /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/work/4b/68f2dee5b8fc018fafc7cd8ffa026e

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named: '.command.sh'
Sep-30 09:03:15.449 [Thread-1] DEBUG nextflow.Session - Session aborted -- Cause: Process `tolines (1)` terminated with an error exit status (143)
Sep-30 09:03:15.449 [Actor Thread 5] DEBUG nextflow.processor.TaskProcessor - <tolines> Sending poison pills and terminating process
Sep-30 09:03:15.449 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: tolines)
Sep-30 09:03:15.450 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <wordcounts> Poison pill arrived
Sep-30 09:03:15.450 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <wordcounts> After stop
Sep-30 09:03:15.450 [Actor Thread 5] DEBUG nextflow.processor.StateObj - <wordcounts> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false ]
Sep-30 09:03:15.450 [Actor Thread 5] DEBUG nextflow.processor.TaskProcessor - <wordcounts> Sending poison pills and terminating process
Sep-30 09:03:15.450 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: wordcounts)
Sep-30 09:03:15.451 [main] DEBUG nextflow.Session - Session await > processes completed
Sep-30 09:03:15.454 [main] DEBUG nextflow.Session - Session await > done
Sep-30 09:03:15.454 [Thread-1] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm)
Sep-30 09:03:15.510 [main] DEBUG nextflow.Session - Session destroyed