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CI Nextflow Success

vsmalladi
Oct 20th, 2017
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  1. Oct-18 17:25:13.584 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [proxy.swmed.edu, 3128]
  2. Oct-18 17:25:13.631 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [proxy.swmed.edu, 3128]
  3. Oct-18 17:25:13.631 [main] DEBUG nextflow.cli.Launcher - $> /cm/shared/apps/nextflow/0.24.1-SNAPSHOT/bin/nextflow run workflow/main.nf
  4. Oct-18 17:25:13.664 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.24.1-SNAPSHOT
  5. Oct-18 17:25:13.676 [main] INFO nextflow.cli.CmdRun - Launching `workflow/main.nf` [fervent_swanson] - revision: 66ee749850
  6. Oct-18 17:25:13.685 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/workflow/nextflow.config
  7. Oct-18 17:25:13.686 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/workflow/nextflow.config
  8. Oct-18 17:25:13.882 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'standard'
  9. Oct-18 17:25:13.998 [main] DEBUG nextflow.Session - Session uuid: 1c505844-26d5-4b7f-9961-55eeaa26f3ab
  10. Oct-18 17:25:13.998 [main] DEBUG nextflow.Session - Run name: fervent_swanson
  11. Oct-18 17:25:13.999 [main] DEBUG nextflow.Session - Executor pool size: 12
  12. Oct-18 17:25:14.009 [main] DEBUG nextflow.cli.CmdRun -
  13. Version: 0.24.1-SNAPSHOT build 4244
  14. Modified: 24-03-2017 11:25 UTC (06:25 CDT)
  15. System: Linux 2.6.32-696.1.1.el6.x86_64
  16. Runtime: Groovy 2.4.10 on Java HotSpot(TM) 64-Bit Server VM 1.7.0_51-b13
  17. Encoding: UTF-8 (UTF-8)
  18. Process: 4673@biohpcwsc019.biohpc.swmed.edu [198.215.56.19]
  19. CPUs: 12 - Mem: 31.3 GB (26.8 GB) - Swap: 16 GB (15.8 GB)
  20. Oct-18 17:25:14.031 [main] DEBUG nextflow.Session - Work-dir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work [nfs]
  21. Oct-18 17:25:14.031 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/workflow/bin
  22. Oct-18 17:25:14.132 [main] DEBUG nextflow.Session - Session start invoked
  23. Oct-18 17:25:14.136 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
  24. Oct-18 17:25:14.136 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/pipeline_trace.txt
  25. Oct-18 17:25:14.140 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
  26. Oct-18 17:25:14.338 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
  27. Oct-18 17:25:14.417 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/workflow/../test_data/; pattern: *.fastq.gz; options: null
  28. Oct-18 17:25:14.519 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
  29. Oct-18 17:25:14.519 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  30. Oct-18 17:25:14.524 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  31. Oct-18 17:25:14.526 [main] INFO nextflow.executor.Executor - [warm up] executor > local
  32. Oct-18 17:25:14.529 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=12; memory=31.3 GB; capacity=12; pollInterval=100ms; dumpInterval=5m
  33. Oct-18 17:25:14.532 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
  34. Oct-18 17:25:14.533 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
  35. Oct-18 17:25:14.534 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
  36. Oct-18 17:25:14.563 [main] DEBUG nextflow.Session - >>> barrier register (process: checkDesignFile)
  37. Oct-18 17:25:14.572 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > checkDesignFile -- maxForks: 12
  38. Oct-18 17:25:14.601 [Actor Thread 2] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 12; slices: 1; internal sort time: 0.03 s; external sort time: 0.004 s; total time: 0.034 s
  39. Oct-18 17:25:14.608 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  40. Oct-18 17:25:14.608 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  41. Oct-18 17:25:14.614 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  42. Oct-18 17:25:14.614 [main] INFO nextflow.executor.Executor - [warm up] executor > slurm
  43. Oct-18 17:25:14.614 [Actor Thread 2] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/s163035/nextflow-temp/2a70451bb5d371c6de077e43a7d49833.collect-file
  44. Oct-18 17:25:14.617 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
  45. Oct-18 17:25:14.618 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor
  46. Oct-18 17:25:14.618 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm)
  47. Oct-18 17:25:14.618 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: slurm
  48. Oct-18 17:25:14.618 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  49. Oct-18 17:25:14.619 [main] DEBUG nextflow.Session - >>> barrier register (process: trimReads)
  50. Oct-18 17:25:14.621 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - <checkDesignFile> Poison pill arrived
  51. Oct-18 17:25:14.623 [Actor Thread 1] DEBUG nextflow.processor.StateObj - <checkDesignFile> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
  52. Oct-18 17:25:14.626 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trimReads -- maxForks: 12
  53. Oct-18 17:25:14.628 [Actor Thread 2] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/s163035/nextflow-temp/nxf-910729976172583810
  54. Oct-18 17:25:14.634 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  55. Oct-18 17:25:14.634 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  56. Oct-18 17:25:14.634 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  57. Oct-18 17:25:14.634 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  58. Oct-18 17:25:14.635 [main] DEBUG nextflow.Session - >>> barrier register (process: alignReads)
  59. Oct-18 17:25:14.642 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > alignReads -- maxForks: 12
  60. Oct-18 17:25:14.650 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  61. Oct-18 17:25:14.650 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  62. Oct-18 17:25:14.650 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  63. Oct-18 17:25:14.651 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  64. Oct-18 17:25:14.651 [main] DEBUG nextflow.Session - >>> barrier register (process: filterReads)
  65. Oct-18 17:25:14.658 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > filterReads -- maxForks: 12
  66. Oct-18 17:25:14.669 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
  67. Oct-18 17:25:14.669 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  68. Oct-18 17:25:14.669 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  69. Oct-18 17:25:14.670 [main] DEBUG nextflow.Session - >>> barrier register (process: experimentQC)
  70. Oct-18 17:25:14.676 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > experimentQC -- maxForks: 12
  71. Oct-18 17:25:14.678 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
  72. Oct-18 17:25:14.679 [main] DEBUG nextflow.Session - Session await
  73. Oct-18 17:25:14.745 [Actor Thread 4] INFO nextflow.Session - [3c/f33f6a] Submitted process > checkDesignFile (1)
  74. Oct-18 17:25:14.752 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - <checkDesignFile> After stop
  75. Oct-18 17:25:16.001 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <checkDesignFile> Sending poison pills and terminating process
  76. Oct-18 17:25:16.005 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: checkDesignFile)
  77. Oct-18 17:25:16.006 [Actor Thread 10] DEBUG nextflow.processor.TaskProcessor - <trimReads> Poison pill arrived
  78. Oct-18 17:25:16.007 [Actor Thread 1] DEBUG nextflow.processor.StateObj - <trimReads> State before poison: StateObj[submitted: 4; completed: 0; poisoned: false ]
  79. Oct-18 17:25:16.016 [Actor Thread 7] DEBUG nextflow.executor.GridTaskHandler - Launching process > trimReads (ENCLB304SBJ-1) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/e3/7e9ff0ef8f1642dd0051a61a15b536
  80. Oct-18 17:25:16.053 [Actor Thread 5] DEBUG nextflow.executor.GridTaskHandler - Launching process > trimReads (ENCLB144FDT-1) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/00/e313a7101b85daf8e5400090bb47bd
  81. Oct-18 17:25:16.053 [Actor Thread 7] INFO nextflow.Session - [e3/7e9ff0] Submitted process > trimReads (ENCLB304SBJ-1)
  82. Oct-18 17:25:16.088 [Actor Thread 4] DEBUG nextflow.executor.GridTaskHandler - Launching process > trimReads (ENCLB410VVO-2) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/1f/257d0f12966601370b568edfc1f7f7
  83. Oct-18 17:25:16.088 [Actor Thread 5] INFO nextflow.Session - [00/e313a7] Submitted process > trimReads (ENCLB144FDT-1)
  84. Oct-18 17:25:16.117 [Actor Thread 6] DEBUG nextflow.executor.GridTaskHandler - Launching process > trimReads (ENCLB831RUI-2) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/ba/56f9cfed1e2b4a41e89c4bb2ce41af
  85. Oct-18 17:25:16.117 [Actor Thread 4] INFO nextflow.Session - [1f/257d0f] Submitted process > trimReads (ENCLB410VVO-2)
  86. Oct-18 17:25:16.150 [Actor Thread 6] INFO nextflow.Session - [ba/56f9cf] Submitted process > trimReads (ENCLB831RUI-2)
  87. Oct-18 17:25:16.153 [Actor Thread 10] DEBUG nextflow.processor.TaskProcessor - <trimReads> After stop
  88. Oct-18 17:30:14.672 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  89. Oct-18 17:30:19.642 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483788; id: 4; name: trimReads (ENCLB304SBJ-1); status: SUBMITTED; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/e3/7e9ff0ef8f1642dd0051a61a15b536 started: -; exited: -; ]
  90. Oct-18 17:35:14.686 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  91. Oct-18 17:35:19.654 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483788; id: 4; name: trimReads (ENCLB304SBJ-1); status: SUBMITTED; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/e3/7e9ff0ef8f1642dd0051a61a15b536 started: -; exited: -; ]
  92. Oct-18 17:40:14.744 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  93. Oct-18 17:40:19.671 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483788; id: 4; name: trimReads (ENCLB304SBJ-1); status: SUBMITTED; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/e3/7e9ff0ef8f1642dd0051a61a15b536 started: -; exited: -; ]
  94. Oct-18 17:45:14.811 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  95. Oct-18 17:45:19.686 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483788; id: 4; name: trimReads (ENCLB304SBJ-1); status: SUBMITTED; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/e3/7e9ff0ef8f1642dd0051a61a15b536 started: -; exited: -; ]
  96. Oct-18 17:50:14.880 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  97. Oct-18 17:50:19.701 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483788; id: 4; name: trimReads (ENCLB304SBJ-1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/e3/7e9ff0ef8f1642dd0051a61a15b536 started: 1508366754702; exited: -; ]
  98. Oct-18 17:55:14.909 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  99. Oct-18 17:55:19.714 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483788; id: 4; name: trimReads (ENCLB304SBJ-1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/e3/7e9ff0ef8f1642dd0051a61a15b536 started: 1508366754702; exited: -; ]
  100. Oct-18 18:00:14.916 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  101. Oct-18 18:00:19.724 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483788; id: 4; name: trimReads (ENCLB304SBJ-1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/e3/7e9ff0ef8f1642dd0051a61a15b536 started: 1508366754702; exited: -; ]
  102. Oct-18 18:03:29.792 [Actor Thread 11] DEBUG nextflow.executor.GridTaskHandler - Launching process > alignReads (ENCLB304SBJ-1) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/bb/784fe847d35675aa045432d3595502
  103. Oct-18 18:03:29.829 [Actor Thread 11] INFO nextflow.Session - [bb/784fe8] Submitted process > alignReads (ENCLB304SBJ-1)
  104. Oct-18 18:04:44.864 [Actor Thread 13] DEBUG nextflow.executor.GridTaskHandler - Launching process > alignReads (ENCLB144FDT-1) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/20/7b8962ee6256bdfdfce02b26a096d2
  105. Oct-18 18:04:45.253 [Actor Thread 13] INFO nextflow.Session - [20/7b8962] Submitted process > alignReads (ENCLB144FDT-1)
  106. Oct-18 18:05:15.002 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  107. Oct-18 18:05:19.737 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483790; id: 5; name: trimReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/1f/257d0f12966601370b568edfc1f7f7 started: 1508366819733; exited: -; ]
  108. Oct-18 18:10:15.009 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  109. Oct-18 18:10:19.754 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483790; id: 5; name: trimReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/1f/257d0f12966601370b568edfc1f7f7 started: 1508366819733; exited: -; ]
  110. Oct-18 18:10:54.806 [Actor Thread 15] DEBUG nextflow.executor.GridTaskHandler - Launching process > alignReads (ENCLB831RUI-2) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/21/76ca1a72d1f878c33d59cbf2b0c9a7
  111. Oct-18 18:10:54.893 [Actor Thread 15] INFO nextflow.Session - [21/76ca1a] Submitted process > alignReads (ENCLB831RUI-2)
  112. Oct-18 18:15:15.099 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  113. Oct-18 18:15:19.768 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483790; id: 5; name: trimReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/1f/257d0f12966601370b568edfc1f7f7 started: 1508366819733; exited: -; ]
  114. Oct-18 18:20:15.111 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  115. Oct-18 18:20:19.787 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483790; id: 5; name: trimReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/1f/257d0f12966601370b568edfc1f7f7 started: 1508366819733; exited: -; ]
  116. Oct-18 18:24:49.839 [Actor Thread 16] DEBUG nextflow.processor.TaskProcessor - <trimReads> Sending poison pills and terminating process
  117. Oct-18 18:24:49.841 [Actor Thread 16] DEBUG nextflow.Session - <<< barrier arrive (process: trimReads)
  118. Oct-18 18:24:49.841 [Actor Thread 15] DEBUG nextflow.processor.TaskProcessor - <alignReads> Poison pill arrived
  119. Oct-18 18:24:49.842 [Actor Thread 16] DEBUG nextflow.processor.StateObj - <alignReads> State before poison: StateObj[submitted: 4; completed: 0; poisoned: false ]
  120. Oct-18 18:24:49.847 [Actor Thread 17] DEBUG nextflow.executor.GridTaskHandler - Launching process > alignReads (ENCLB410VVO-2) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/84/ee9220417091806ad1121934a4132a
  121. Oct-18 18:24:49.963 [Actor Thread 17] INFO nextflow.Session - [84/ee9220] Submitted process > alignReads (ENCLB410VVO-2)
  122. Oct-18 18:24:49.966 [Actor Thread 15] DEBUG nextflow.processor.TaskProcessor - <alignReads> After stop
  123. Oct-18 18:25:15.205 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  124. Oct-18 18:25:19.804 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483805; id: 6; name: alignReads (ENCLB304SBJ-1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/bb/784fe847d35675aa045432d3595502 started: 1508368029813; exited: -; ]
  125. Oct-18 18:30:15.218 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  126. Oct-18 18:30:19.822 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483805; id: 6; name: alignReads (ENCLB304SBJ-1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/bb/784fe847d35675aa045432d3595502 started: 1508368029813; exited: -; ]
  127. Oct-18 18:35:15.316 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  128. Oct-18 18:35:19.828 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483805; id: 6; name: alignReads (ENCLB304SBJ-1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/bb/784fe847d35675aa045432d3595502 started: 1508368029813; exited: -; ]
  129. Oct-18 18:40:15.413 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  130. Oct-18 18:40:19.845 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483805; id: 6; name: alignReads (ENCLB304SBJ-1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/bb/784fe847d35675aa045432d3595502 started: 1508368029813; exited: -; ]
  131. Oct-18 18:41:29.847 [Thread-3] DEBUG nextflow.file.FileHelper - NFS path (true): /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work
  132. Oct-18 18:41:29.915 [Actor Thread 19] DEBUG nextflow.executor.GridTaskHandler - Launching process > filterReads (ENCLB304SBJ-1) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/f8/ec5789af9a6003fd01fc3528871fa3
  133. Oct-18 18:41:30.018 [Actor Thread 19] INFO nextflow.Session - [f8/ec5789] Submitted process > filterReads (ENCLB304SBJ-1)
  134. Oct-18 18:43:24.902 [Actor Thread 21] DEBUG nextflow.executor.GridTaskHandler - Launching process > filterReads (ENCLB144FDT-1) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/2b/e768917e507fe839a71e47966957a9
  135. Oct-18 18:43:26.304 [Actor Thread 21] INFO nextflow.Session - [2b/e76891] Submitted process > filterReads (ENCLB144FDT-1)
  136. Oct-18 18:45:15.492 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  137. Oct-18 18:45:19.857 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483809; id: 8; name: alignReads (ENCLB831RUI-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/21/76ca1a72d1f878c33d59cbf2b0c9a7 started: 1508368409775; exited: -; ]
  138. Oct-18 18:50:15.584 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  139. Oct-18 18:50:19.868 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483809; id: 8; name: alignReads (ENCLB831RUI-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/21/76ca1a72d1f878c33d59cbf2b0c9a7 started: 1508368409775; exited: -; ]
  140. Oct-18 18:55:15.596 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  141. Oct-18 18:55:19.879 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483809; id: 8; name: alignReads (ENCLB831RUI-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/21/76ca1a72d1f878c33d59cbf2b0c9a7 started: 1508368409775; exited: -; ]
  142. Oct-18 19:00:15.684 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  143. Oct-18 19:00:19.888 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483809; id: 8; name: alignReads (ENCLB831RUI-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/21/76ca1a72d1f878c33d59cbf2b0c9a7 started: 1508368409775; exited: -; ]
  144. Oct-18 19:00:59.941 [Actor Thread 23] DEBUG nextflow.executor.GridTaskHandler - Launching process > filterReads (ENCLB831RUI-2) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/28/14541ddaf2153e5b1e2f8e30c224d8
  145. Oct-18 19:01:00.712 [Actor Thread 23] INFO nextflow.Session - [28/14541d] Submitted process > filterReads (ENCLB831RUI-2)
  146. Oct-18 19:05:15.743 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  147. Oct-18 19:05:19.897 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- first: TaskHandler[jobId: 483811; id: 9; name: alignReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/84/ee9220417091806ad1121934a4132a started: 1508369184818; exited: -; ]
  148. Oct-18 19:10:15.825 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  149. Oct-18 19:10:19.912 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- first: TaskHandler[jobId: 483811; id: 9; name: alignReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/84/ee9220417091806ad1121934a4132a started: 1508369184818; exited: -; ]
  150. Oct-18 19:15:15.910 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  151. Oct-18 19:15:19.922 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- first: TaskHandler[jobId: 483811; id: 9; name: alignReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/84/ee9220417091806ad1121934a4132a started: 1508369184818; exited: -; ]
  152. Oct-18 19:15:59.970 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - <alignReads> Sending poison pills and terminating process
  153. Oct-18 19:15:59.971 [Actor Thread 28] DEBUG nextflow.Session - <<< barrier arrive (process: alignReads)
  154. Oct-18 19:15:59.971 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - <filterReads> Poison pill arrived
  155. Oct-18 19:15:59.971 [Actor Thread 28] DEBUG nextflow.processor.StateObj - <filterReads> State before poison: StateObj[submitted: 4; completed: 2; poisoned: false ]
  156. Oct-18 19:15:59.975 [Actor Thread 29] DEBUG nextflow.executor.GridTaskHandler - Launching process > filterReads (ENCLB410VVO-2) -- work folder: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/6c/a6ad0077597fb9a10e543d338159a2
  157. Oct-18 19:16:00.411 [Actor Thread 29] INFO nextflow.Session - [6c/a6ad00] Submitted process > filterReads (ENCLB410VVO-2)
  158. Oct-18 19:16:00.414 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - <filterReads> After stop
  159. Oct-18 19:20:15.985 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  160. Oct-18 19:20:19.935 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- first: TaskHandler[jobId: 483833; id: 12; name: filterReads (ENCLB831RUI-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/28/14541ddaf2153e5b1e2f8e30c224d8 started: 1508371266420; exited: -; ]
  161. Oct-18 19:25:16.078 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  162. Oct-18 19:25:19.951 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- first: TaskHandler[jobId: 483833; id: 12; name: filterReads (ENCLB831RUI-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/28/14541ddaf2153e5b1e2f8e30c224d8 started: 1508371266420; exited: -; ]
  163. Oct-18 19:30:16.081 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  164. Oct-18 19:30:19.966 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- first: TaskHandler[jobId: 483833; id: 12; name: filterReads (ENCLB831RUI-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/28/14541ddaf2153e5b1e2f8e30c224d8 started: 1508371266420; exited: -; ]
  165. Oct-18 19:35:16.155 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  166. Oct-18 19:35:19.994 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- first: TaskHandler[jobId: 483835; id: 13; name: filterReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/6c/a6ad0077597fb9a10e543d338159a2 started: 1508372167679; exited: -; ]
  167. Oct-18 19:40:16.243 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
  168. Oct-18 19:40:20.006 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- first: TaskHandler[jobId: 483835; id: 13; name: filterReads (ENCLB410VVO-2); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/6c/a6ad0077597fb9a10e543d338159a2 started: 1508372167679; exited: -; ]
  169. Oct-18 19:43:15.071 [Actor Thread 32] DEBUG nextflow.processor.TaskProcessor - <filterReads> Sending poison pills and terminating process
  170. Oct-18 19:43:15.072 [Actor Thread 32] DEBUG nextflow.Session - <<< barrier arrive (process: filterReads)
  171. Oct-18 19:43:15.097 [Actor Thread 33] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 4; slices: 1; internal sort time: 0.019 s; external sort time: 0.001 s; total time: 0.02 s
  172. Oct-18 19:43:15.382 [Actor Thread 33] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/s163035/nextflow-temp/080541c40b3bd0d6d3fefbea02b555b3.collect-file
  173. Oct-18 19:43:15.383 [Actor Thread 31] DEBUG nextflow.processor.TaskProcessor - <experimentQC> Poison pill arrived
  174. Oct-18 19:43:15.383 [Actor Thread 34] DEBUG nextflow.processor.StateObj - <experimentQC> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
  175. Oct-18 19:43:15.385 [Actor Thread 33] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/s163035/nextflow-temp/nxf-2371203334718193445
  176. Oct-18 19:43:15.742 [Actor Thread 35] INFO nextflow.Session - [c1/ade01f] Submitted process > experimentQC (1)
  177. Oct-18 19:43:15.750 [Actor Thread 31] DEBUG nextflow.processor.TaskProcessor - <experimentQC> After stop
  178. Oct-18 19:45:16.293 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- first: TaskHandler[id: 14; name: experimentQC (1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/c1/ade01f8688fef0042147b061c0fe64]
  179. Oct-18 19:45:20.014 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 0 -- first: null
  180. Oct-18 19:50:16.350 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- first: TaskHandler[id: 14; name: experimentQC (1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/c1/ade01f8688fef0042147b061c0fe64]
  181. Oct-18 19:50:20.020 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 0 -- first: null
  182. Oct-18 19:55:16.364 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- first: TaskHandler[id: 14; name: experimentQC (1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/c1/ade01f8688fef0042147b061c0fe64]
  183. Oct-18 19:55:20.025 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 0 -- first: null
  184. Oct-18 20:00:16.412 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- first: TaskHandler[id: 14; name: experimentQC (1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/c1/ade01f8688fef0042147b061c0fe64]
  185. Oct-18 20:00:20.029 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 0 -- first: null
  186. Oct-18 20:05:16.449 [Thread-2] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- first: TaskHandler[id: 14; name: experimentQC (1); status: RUNNING; exit: -; workDir: /work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/work/c1/ade01f8688fef0042147b061c0fe64]
  187. Oct-18 20:05:20.035 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 0 -- first: null
  188. Oct-18 20:07:34.711 [Actor Thread 34] DEBUG nextflow.processor.TaskProcessor - <experimentQC> Sending poison pills and terminating process
  189. Oct-18 20:07:34.712 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: experimentQC)
  190. Oct-18 20:07:34.712 [main] DEBUG nextflow.Session - Session await > all process finished
  191. Oct-18 20:07:34.714 [Thread-2] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
  192. Oct-18 20:07:35.037 [Thread-3] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm)
  193. Oct-18 20:07:35.037 [main] DEBUG nextflow.Session - Session await > all barriers passed
  194. Oct-18 20:07:35.042 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
  195. Oct-18 20:07:35.076 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
  196. Oct-18 20:07:35.097 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
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