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failed Nextflow Log

vsmalladi
Oct 20th, 2017
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  1. Oct-20 08:55:20.668 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [proxy.swmed.edu, 3128]
  2. Oct-20 08:55:20.715 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [proxy.swmed.edu, 3128]
  3. Oct-20 08:55:20.715 [main] DEBUG nextflow.cli.Launcher - $> /cm/shared/apps/nextflow/0.24.1-SNAPSHOT/bin/nextflow run workflow/main.nf
  4. Oct-20 08:55:20.758 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.24.1-SNAPSHOT
  5. Oct-20 08:55:20.794 [main] INFO nextflow.cli.CmdRun - Launching `workflow/main.nf` [stupefied_visvesvaraya] - revision: 66ee749850
  6. Oct-20 08:55:20.802 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /work/BICF/s163035/chipseq_analysis/workflow/nextflow.config
  7. Oct-20 08:55:20.803 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /work/BICF/s163035/chipseq_analysis/workflow/nextflow.config
  8. Oct-20 08:55:20.998 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'standard'
  9. Oct-20 08:55:21.128 [main] DEBUG nextflow.Session - Session uuid: 69e8091d-ccd2-4b8d-b797-e621e17670ee
  10. Oct-20 08:55:21.128 [main] DEBUG nextflow.Session - Run name: stupefied_visvesvaraya
  11. Oct-20 08:55:21.128 [main] DEBUG nextflow.Session - Executor pool size: 12
  12. Oct-20 08:55:21.138 [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: 32321@biohpcwsc019.biohpc.swmed.edu [198.215.56.19]
  19. CPUs: 12 - Mem: 31.3 GB (17.3 GB) - Swap: 16 GB (15.7 GB)
  20. Oct-20 08:55:21.156 [main] DEBUG nextflow.Session - Work-dir: /work/BICF/s163035/chipseq_analysis/work [nfs]
  21. Oct-20 08:55:21.157 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /work/BICF/s163035/chipseq_analysis/workflow/bin
  22. Oct-20 08:55:21.274 [main] DEBUG nextflow.Session - Session start invoked
  23. Oct-20 08:55:21.279 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
  24. Oct-20 08:55:21.280 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /work/BICF/s163035/chipseq_analysis/pipeline_trace.txt
  25. Oct-20 08:55:21.287 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
  26. Oct-20 08:55:21.484 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
  27. Oct-20 08:55:21.559 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: /work/BICF/s163035/chipseq_analysis/workflow/../test_data/; pattern: *.fastq.gz; options: null
  28. Oct-20 08:55:21.652 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
  29. Oct-20 08:55:21.652 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  30. Oct-20 08:55:21.657 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  31. Oct-20 08:55:21.658 [main] INFO nextflow.executor.Executor - [warm up] executor > local
  32. Oct-20 08:55:21.661 [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-20 08:55:21.664 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
  34. Oct-20 08:55:21.665 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
  35. Oct-20 08:55:21.666 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
  36. Oct-20 08:55:21.692 [main] DEBUG nextflow.Session - >>> barrier register (process: checkDesignFile)
  37. Oct-20 08:55:21.700 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > checkDesignFile -- maxForks: 12
  38. Oct-20 08:55:21.732 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  39. Oct-20 08:55:21.732 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  40. Oct-20 08:55:21.737 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  41. Oct-20 08:55:21.737 [main] INFO nextflow.executor.Executor - [warm up] executor > slurm
  42. Oct-20 08:55:21.740 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
  43. Oct-20 08:55:21.741 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor
  44. Oct-20 08:55:21.741 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm)
  45. Oct-20 08:55:21.741 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: slurm
  46. Oct-20 08:55:21.741 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  47. Oct-20 08:55:21.742 [main] DEBUG nextflow.Session - >>> barrier register (process: trimReads)
  48. Oct-20 08:55:21.747 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trimReads -- maxForks: 12
  49. Oct-20 08:55:21.754 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  50. Oct-20 08:55:21.754 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  51. Oct-20 08:55:21.754 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  52. Oct-20 08:55:21.755 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  53. Oct-20 08:55:21.755 [main] DEBUG nextflow.Session - >>> barrier register (process: alignReads)
  54. Oct-20 08:55:21.761 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > alignReads -- maxForks: 12
  55. Oct-20 08:55:21.767 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  56. Oct-20 08:55:21.768 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  57. Oct-20 08:55:21.768 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  58. Oct-20 08:55:21.768 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  59. Oct-20 08:55:21.768 [main] DEBUG nextflow.Session - >>> barrier register (process: filterReads)
  60. Oct-20 08:55:21.774 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > filterReads -- maxForks: 12
  61. Oct-20 08:55:22.129 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
  62. Oct-20 08:55:22.129 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  63. Oct-20 08:55:22.129 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  64. Oct-20 08:55:22.130 [main] DEBUG nextflow.Session - >>> barrier register (process: experimentQC)
  65. Oct-20 08:55:22.136 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > experimentQC -- maxForks: 12
  66. Oct-20 08:55:22.138 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
  67. Oct-20 08:55:22.138 [main] DEBUG nextflow.Session - Session await
  68. Oct-20 08:55:22.182 [Actor Thread 3] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 12; slices: 1; internal sort time: 0.02 s; external sort time: 0.002 s; total time: 0.022 s
  69. Oct-20 08:55:22.192 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/s163035/nextflow-temp/3ae5d65f1340cb7428e20dce4eb9126b.collect-file
  70. Oct-20 08:55:22.197 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - <checkDesignFile> Poison pill arrived
  71. Oct-20 08:55:22.199 [Actor Thread 1] DEBUG nextflow.processor.StateObj - <checkDesignFile> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
  72. Oct-20 08:55:22.202 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/s163035/nextflow-temp/nxf-1777879847362874938
  73. Oct-20 08:55:22.350 [Actor Thread 2] INFO nextflow.Session - [27/822df0] Submitted process > checkDesignFile (1)
  74. Oct-20 08:55:22.355 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - <checkDesignFile> After stop
  75. Oct-20 08:55:46.223 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <checkDesignFile> Sending poison pills and terminating process
  76. Oct-20 08:55:46.225 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: checkDesignFile)
  77. Oct-20 08:55:46.226 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - <trimReads> Poison pill arrived
  78. Oct-20 08:55:46.227 [Actor Thread 11] DEBUG nextflow.processor.StateObj - <trimReads> State before poison: StateObj[submitted: 4; completed: 0; poisoned: false ]
  79. Oct-20 08:55:46.237 [Actor Thread 7] DEBUG nextflow.executor.GridTaskHandler - Launching process > trimReads (ENCLB144FDT-1) -- work folder: /work/BICF/s163035/chipseq_analysis/work/b6/fabb10450a5f13e370bbd0ff1a802a
  80. Oct-20 08:55:46.272 [Actor Thread 7] INFO nextflow.Session - [b6/fabb10] Submitted process > trimReads (ENCLB144FDT-1)
  81. Oct-20 08:55:46.272 [Actor Thread 8] DEBUG nextflow.executor.GridTaskHandler - Launching process > trimReads (ENCLB831RUI-2) -- work folder: /work/BICF/s163035/chipseq_analysis/work/58/74cf363f840b50c4d35fb2382bfb57
  82. Oct-20 08:55:46.296 [Actor Thread 8] INFO nextflow.Session - [58/74cf36] Submitted process > trimReads (ENCLB831RUI-2)
  83. Oct-20 08:55:46.296 [Actor Thread 5] DEBUG nextflow.executor.GridTaskHandler - Launching process > trimReads (ENCLB410VVO-2) -- work folder: /work/BICF/s163035/chipseq_analysis/work/81/d718d8f1bfcc44faf99f00428c2d75
  84. Oct-20 08:55:46.315 [Actor Thread 4] DEBUG nextflow.executor.GridTaskHandler - Launching process > trimReads (ENCLB304SBJ-1) -- work folder: /work/BICF/s163035/chipseq_analysis/work/f1/1a25b48bd0a38d3234ab9eb35fc464
  85. Oct-20 08:55:46.315 [Actor Thread 5] INFO nextflow.Session - [81/d718d8] Submitted process > trimReads (ENCLB410VVO-2)
  86. Oct-20 08:55:46.337 [Actor Thread 4] INFO nextflow.Session - [f1/1a25b4] Submitted process > trimReads (ENCLB304SBJ-1)
  87. Oct-20 08:55:46.340 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - <trimReads> After stop
  88. Oct-20 08:56:16.802 [Thread-3] ERROR nextflow.processor.TaskProcessor - Error executing process > 'trimReads (ENCLB144FDT-1)'
  89.  
  90. Caused by:
  91. Process `trimReads (ENCLB144FDT-1)` terminated with an error exit status (127)
  92.  
  93. Command executed:
  94.  
  95. python3 /work/BICF/s163035/chipseq_analysis/workflow/scripts/trim_reads.py -f /work/BICF/s163035/chipseq_analysis/test_data/ENCFF833BLU.fastq.gz
  96.  
  97. Command exit status:
  98. 127
  99.  
  100. Command output:
  101. (empty)
  102.  
  103. Command error:
  104. .command.sh: line 2: python3: command not found
  105.  
  106. Work dir:
  107. /work/BICF/s163035/chipseq_analysis/work/b6/fabb10450a5f13e370bbd0ff1a802a
  108.  
  109. Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
  110. Oct-20 08:56:16.810 [Thread-3] DEBUG nextflow.Session - Session aborted -- Cause: Process `trimReads (ENCLB144FDT-1)` terminated with an error exit status (127)
  111. Oct-20 08:56:16.813 [Thread-2] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
  112. Oct-20 08:56:16.815 [main] DEBUG nextflow.Session - Session await > all process finished
  113. Oct-20 08:56:16.815 [main] DEBUG nextflow.Session - Session await > all barriers passed
  114. Oct-20 08:56:16.815 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - <alignReads> After stop
  115. Oct-20 08:56:16.815 [Actor Thread 13] DEBUG nextflow.processor.TaskProcessor - <filterReads> After stop
  116. Oct-20 08:56:16.816 [Actor Thread 16] DEBUG nextflow.processor.TaskProcessor - <experimentQC> After stop
  117. Oct-20 08:56:16.817 [Actor Thread 15] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
  118. Oct-20 08:56:16.822 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (3)
  119. Oct-20 08:56:16.857 [main] DEBUG n.executor.AbstractGridExecutor - Unable to killing pending jobs
  120. - cmd executed: scancel 485403 485404 485405
  121. - exit status : 1
  122. - output :
  123. scancel: error: Kill job error on job id 485403: Invalid job id specified
  124. scancel: error: Kill job error on job id 485404: Invalid job id specified
  125. scancel: error: Kill job error on job id 485405: Invalid job id specified
  126.  
  127. Oct-20 08:56:16.858 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
  128. Oct-20 08:56:16.862 [Thread-3] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm)
  129. Oct-20 08:56:16.875 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
  130. Oct-20 08:56:16.892 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
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