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  1. jul-19 23:28:06.029 [main] DEBUG nextflow.cli.Launcher - $> /home/ska/rafa/bin/nextflow run distiller.nf -params-file project.yml -profile cluster
  2. jul-19 23:28:06.131 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.25.2
  3. jul-19 23:28:06.148 [main] INFO nextflow.cli.CmdRun - Launching `distiller.nf` [awesome_shockley] - revision: d53c36571e
  4. jul-19 23:28:06.159 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: nextflow.config
  5. jul-19 23:28:06.161 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ska/rafa/programs/distiller-nf/nextflow.config
  6. jul-19 23:28:06.413 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'cluster'
  7. jul-19 23:28:06.863 [main] DEBUG nextflow.Session - Session uuid: b30172b6-6596-42ff-862f-4b02c3f90311
  8. jul-19 23:28:06.864 [main] DEBUG nextflow.Session - Run name: awesome_shockley
  9. jul-19 23:28:06.866 [main] DEBUG nextflow.Session - Executor pool size: 16
  10. jul-19 23:28:06.882 [main] DEBUG nextflow.cli.CmdRun -
  11. Version: 0.25.2 build 4462
  12. Modified: 03-07-2017 08:47 UTC (10:47 CEST)
  13. System: Linux 3.10.0-327.10.1.el7.x86_64
  14. Runtime: Groovy 2.4.11 on OpenJDK 64-Bit Server VM 1.8.0_91-b14
  15. Encoding: UTF-8 (UTF-8)
  16. Process: 24543@nodo00.ladon.local [192.168.2.10]
  17. CPUs: 16 - Mem: 125,7 GB (7,7 GB) - Swap: 8 GB (6,4 GB)
  18. jul-19 23:28:06.921 [main] DEBUG nextflow.Session - Work-dir: /home/ska/rafa/programs/distiller-nf/work [nfs]
  19. jul-19 23:28:06.922 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/ska/rafa/programs/distiller-nf/bin
  20. jul-19 23:28:07.142 [main] DEBUG nextflow.Session - Session start invoked
  21. jul-19 23:28:07.145 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
  22. jul-19 23:28:07.146 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/ska/rafa/programs/distiller-nf/trace.txt
  23. jul-19 23:28:07.150 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
  24. jul-19 23:28:07.656 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
  25. jul-19 23:28:07.781 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  26. jul-19 23:28:07.782 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  27. jul-19 23:28:07.790 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  28. jul-19 23:28:07.792 [main] INFO nextflow.executor.Executor - [warm up] executor > slurm
  29. jul-19 23:28:07.798 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
  30. jul-19 23:28:07.800 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor
  31. jul-19 23:28:07.801 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm)
  32. jul-19 23:28:07.802 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: slurm
  33. jul-19 23:28:07.803 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  34. jul-19 23:28:07.828 [main] DEBUG nextflow.Session - >>> barrier register (process: download_sra)
  35. jul-19 23:28:07.836 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > download_sra -- maxForks: 16
  36. jul-19 23:28:07.864 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: download_sra)
  37. jul-19 23:28:07.892 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  38. jul-19 23:28:07.892 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  39. jul-19 23:28:07.892 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  40. jul-19 23:28:07.893 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  41. jul-19 23:28:07.894 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc)
  42. jul-19 23:28:07.900 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 16
  43. jul-19 23:28:07.902 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc)
  44. jul-19 23:28:07.908 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  45. jul-19 23:28:07.908 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  46. jul-19 23:28:07.908 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  47. jul-19 23:28:07.908 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  48. jul-19 23:28:07.909 [main] DEBUG nextflow.Session - >>> barrier register (process: chunk_fastqs)
  49. jul-19 23:28:07.915 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > chunk_fastqs -- maxForks: 16
  50. jul-19 23:28:07.953 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - Copying to process workdir foreign file: https://github.com/mirnylab/distiller-test-data/raw/master/fastq/MATalpha_R1/lane2/SRR2601843_1.fastq.gz
  51. jul-19 23:28:07.961 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  52. jul-19 23:28:07.961 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  53. jul-19 23:28:07.961 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  54. jul-19 23:28:07.965 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  55. jul-19 23:28:07.966 [main] DEBUG nextflow.Session - >>> barrier register (process: map_runs)
  56. jul-19 23:28:07.975 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > map_runs -- maxForks: 16
  57. jul-19 23:28:07.981 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  58. jul-19 23:28:07.981 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  59. jul-19 23:28:07.982 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  60. jul-19 23:28:07.982 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  61. jul-19 23:28:07.983 [main] DEBUG nextflow.Session - >>> barrier register (process: parse_runs)
  62. jul-19 23:28:07.988 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > parse_runs -- maxForks: 16
  63. jul-19 23:28:08.027 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  64. jul-19 23:28:08.027 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  65. jul-19 23:28:08.028 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  66. jul-19 23:28:08.028 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  67. jul-19 23:28:08.030 [main] DEBUG nextflow.Session - >>> barrier register (process: premerge_pairsam_chunks)
  68. jul-19 23:28:08.037 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > premerge_pairsam_chunks -- maxForks: 16
  69. jul-19 23:28:08.044 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  70. jul-19 23:28:08.044 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  71. jul-19 23:28:08.044 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  72. jul-19 23:28:08.045 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  73. jul-19 23:28:08.046 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_pairsam_into_runs)
  74. jul-19 23:28:08.051 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_pairsam_into_runs -- maxForks: 16
  75. jul-19 23:28:08.058 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  76. jul-19 23:28:08.059 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  77. jul-19 23:28:08.059 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  78. jul-19 23:28:08.059 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  79. jul-19 23:28:08.060 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_runs_into_libraries)
  80. jul-19 23:28:08.063 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATa_R2 run:lane1) > slurm jobId: 30193; workDir: /home/ska/rafa/programs/distiller-nf/work/8f/409b594275b4f33158af520f89cda4
  81. jul-19 23:28:08.065 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_runs_into_libraries -- maxForks: 16
  82. jul-19 23:28:08.067 [Task submitter] INFO nextflow.Session - [8f/409b59] Submitted process > chunk_fastqs (library:MATa_R2 run:lane1)
  83. jul-19 23:28:08.070 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  84. jul-19 23:28:08.070 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  85. jul-19 23:28:08.071 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  86. jul-19 23:28:08.071 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  87. jul-19 23:28:08.071 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_stats_runs_into_libraries)
  88. jul-19 23:28:08.077 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_stats_runs_into_libraries -- maxForks: 16
  89. jul-19 23:28:08.082 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  90. jul-19 23:28:08.082 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  91. jul-19 23:28:08.082 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  92. jul-19 23:28:08.082 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  93. jul-19 23:28:08.083 [main] DEBUG nextflow.Session - >>> barrier register (process: filter_make_pairs)
  94. jul-19 23:28:08.085 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R1 run:lane1) > slurm jobId: 30194; workDir: /home/ska/rafa/programs/distiller-nf/work/5c/fae72d1dca0e8692f7e77e247f6bd8
  95. jul-19 23:28:08.085 [Task submitter] INFO nextflow.Session - [5c/fae72d] Submitted process > chunk_fastqs (library:MATalpha_R1 run:lane1)
  96. jul-19 23:28:08.088 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > filter_make_pairs -- maxForks: 16
  97. jul-19 23:28:08.093 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  98. jul-19 23:28:08.093 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  99. jul-19 23:28:08.093 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  100. jul-19 23:28:08.094 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  101. jul-19 23:28:08.094 [main] DEBUG nextflow.Session - >>> barrier register (process: index_pairs)
  102. jul-19 23:28:08.099 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > index_pairs -- maxForks: 16
  103. jul-19 23:28:08.100 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATa_R1 run:lane1) > slurm jobId: 30195; workDir: /home/ska/rafa/programs/distiller-nf/work/1c/bacea45dcf0677e37df63533446485
  104. jul-19 23:28:08.100 [Task submitter] INFO nextflow.Session - [1c/bacea4] Submitted process > chunk_fastqs (library:MATa_R1 run:lane1)
  105. jul-19 23:28:08.107 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  106. jul-19 23:28:08.108 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  107. jul-19 23:28:08.108 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  108. jul-19 23:28:08.108 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  109. jul-19 23:28:08.109 [main] DEBUG nextflow.Session - >>> barrier register (process: bin_library_pairs)
  110. jul-19 23:28:08.112 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [1]
  111. jul-19 23:28:08.115 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R2 run:lane1) > slurm jobId: 30196; workDir: /home/ska/rafa/programs/distiller-nf/work/a8/3b8a073464f804f762d5a52a0d5fff
  112. jul-19 23:28:08.116 [Task submitter] INFO nextflow.Session - [a8/3b8a07] Submitted process > chunk_fastqs (library:MATalpha_R2 run:lane1)
  113. jul-19 23:28:08.133 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bin_library_pairs -- maxForks: 16
  114. jul-19 23:28:08.142 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  115. jul-19 23:28:08.142 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  116. jul-19 23:28:08.142 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  117. jul-19 23:28:08.142 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  118. jul-19 23:28:08.143 [main] DEBUG nextflow.Session - >>> barrier register (process: make_library_group_coolers)
  119. jul-19 23:28:08.148 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > make_library_group_coolers -- maxForks: 16
  120. jul-19 23:28:08.156 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm
  121. jul-19 23:28:08.156 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm'
  122. jul-19 23:28:08.157 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm
  123. jul-19 23:28:08.157 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
  124. jul-19 23:28:08.157 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_stats_libraries_into_groups)
  125. jul-19 23:28:08.162 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_stats_libraries_into_groups -- maxForks: 16
  126. jul-19 23:28:08.164 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
  127. jul-19 23:28:08.164 [main] DEBUG nextflow.Session - Session await
  128. jul-19 23:28:09.080 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - Copying to process workdir foreign file: https://github.com/mirnylab/distiller-test-data/raw/master/fastq/MATalpha_R1/lane2/SRR2601843_2.fastq.gz
  129. jul-19 23:28:10.566 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R1 run:lane2) > slurm jobId: 30197; workDir: /home/ska/rafa/programs/distiller-nf/work/7b/f8b6f8ff7cced00df8b5f175358975
  130. jul-19 23:28:10.567 [Task submitter] INFO nextflow.Session - [7b/f8b6f8] Submitted process > chunk_fastqs (library:MATalpha_R1 run:lane2)
  131. jul-19 23:28:12.830 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30193; id: 2; name: chunk_fastqs (library:MATa_R2 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/8f/409b594275b4f33158af520f89cda4 started: 1500499692816; exited: 2017-07-19T21:28:09.034958Z; ]
  132. jul-19 23:28:12.884 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (1)
  133. jul-19 23:28:12.911 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30194; id: 1; name: chunk_fastqs (library:MATalpha_R1 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/5c/fae72d1dca0e8692f7e77e247f6bd8 started: 1500499692896; exited: 2017-07-19T21:28:08.949957Z; ]
  134. jul-19 23:28:12.914 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATa_R2 run:lane1) > slurm jobId: 30198; workDir: /home/ska/rafa/programs/distiller-nf/work/1b/b405f23567a692084788fc2a5f43e3
  135. jul-19 23:28:12.914 [Task submitter] INFO nextflow.Session - [1b/b405f2] Re-submitted process > chunk_fastqs (library:MATa_R2 run:lane1)
  136. jul-19 23:28:12.920 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (1)
  137. jul-19 23:28:12.927 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30195; id: 5; name: chunk_fastqs (library:MATa_R1 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/1c/bacea45dcf0677e37df63533446485 started: 1500499692924; exited: 2017-07-19T21:28:09.023958Z; ]
  138. jul-19 23:28:12.939 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R1 run:lane1) > slurm jobId: 30199; workDir: /home/ska/rafa/programs/distiller-nf/work/91/5726343beccf53a7bd1acb568dac32
  139. jul-19 23:28:12.940 [Task submitter] INFO nextflow.Session - [91/572634] Re-submitted process > chunk_fastqs (library:MATalpha_R1 run:lane1)
  140. jul-19 23:28:12.944 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (1)
  141. jul-19 23:28:12.952 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30196; id: 4; name: chunk_fastqs (library:MATalpha_R2 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/a8/3b8a073464f804f762d5a52a0d5fff started: 1500499692947; exited: 2017-07-19T21:28:09.124958Z; ]
  142. jul-19 23:28:12.965 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATa_R1 run:lane1) > slurm jobId: 30200; workDir: /home/ska/rafa/programs/distiller-nf/work/dd/173a3136de5c982558bb0f02af92da
  143. jul-19 23:28:12.966 [Task submitter] INFO nextflow.Session - [dd/173a31] Re-submitted process > chunk_fastqs (library:MATa_R1 run:lane1)
  144. jul-19 23:28:12.969 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (1)
  145. jul-19 23:28:12.975 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30197; id: 3; name: chunk_fastqs (library:MATalpha_R1 run:lane2); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/7b/f8b6f8ff7cced00df8b5f175358975 started: 1500499692972; exited: 2017-07-19T21:28:12.374978Z; ]
  146. jul-19 23:28:12.991 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R2 run:lane1) > slurm jobId: 30201; workDir: /home/ska/rafa/programs/distiller-nf/work/a3/17581f5f7b7646fb7e14b1695b843b
  147. jul-19 23:28:12.992 [Task submitter] INFO nextflow.Session - [a3/17581f] Re-submitted process > chunk_fastqs (library:MATalpha_R2 run:lane1)
  148. jul-19 23:28:12.995 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (1)
  149. jul-19 23:28:13.014 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R1 run:lane2) > slurm jobId: 30202; workDir: /home/ska/rafa/programs/distiller-nf/work/ab/e58d32a5ddfc9ec332b78bec6922af
  150. jul-19 23:28:13.014 [Task submitter] INFO nextflow.Session - [ab/e58d32] Re-submitted process > chunk_fastqs (library:MATalpha_R1 run:lane2)
  151. jul-19 23:28:17.814 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30198; id: 6; name: chunk_fastqs (library:MATa_R2 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/1b/b405f23567a692084788fc2a5f43e3 started: 1500499697809; exited: 2017-07-19T21:28:15.478996Z; ]
  152. jul-19 23:28:17.819 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (2)
  153. jul-19 23:28:17.826 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30199; id: 7; name: chunk_fastqs (library:MATalpha_R1 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/91/5726343beccf53a7bd1acb568dac32 started: 1500499697823; exited: 2017-07-19T21:28:15.440996Z; ]
  154. jul-19 23:28:17.843 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATa_R2 run:lane1) > slurm jobId: 30203; workDir: /home/ska/rafa/programs/distiller-nf/work/65/0134876397edbe096431a888e58a65
  155. jul-19 23:28:17.844 [Task submitter] INFO nextflow.Session - [65/013487] Re-submitted process > chunk_fastqs (library:MATa_R2 run:lane1)
  156. jul-19 23:28:17.847 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (2)
  157. jul-19 23:28:17.854 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30200; id: 8; name: chunk_fastqs (library:MATa_R1 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/dd/173a3136de5c982558bb0f02af92da started: 1500499697851; exited: 2017-07-19T21:28:15.466996Z; ]
  158. jul-19 23:28:17.869 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R1 run:lane1) > slurm jobId: 30204; workDir: /home/ska/rafa/programs/distiller-nf/work/a9/6b1599b73f42604a0169c2d2eeebe1
  159. jul-19 23:28:17.869 [Task submitter] INFO nextflow.Session - [a9/6b1599] Re-submitted process > chunk_fastqs (library:MATalpha_R1 run:lane1)
  160. jul-19 23:28:17.873 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (2)
  161. jul-19 23:28:17.880 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30201; id: 9; name: chunk_fastqs (library:MATalpha_R2 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/a3/17581f5f7b7646fb7e14b1695b843b started: 1500499697877; exited: 2017-07-19T21:28:15.566997Z; ]
  162. jul-19 23:28:17.891 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATa_R1 run:lane1) > slurm jobId: 30205; workDir: /home/ska/rafa/programs/distiller-nf/work/48/135367a39969af1b4a72adb679da4a
  163. jul-19 23:28:17.891 [Task submitter] INFO nextflow.Session - [48/135367] Re-submitted process > chunk_fastqs (library:MATa_R1 run:lane1)
  164. jul-19 23:28:17.894 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (2)
  165. jul-19 23:28:17.901 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30202; id: 10; name: chunk_fastqs (library:MATalpha_R1 run:lane2); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/ab/e58d32a5ddfc9ec332b78bec6922af started: 1500499697898; exited: 2017-07-19T21:28:15.546997Z; ]
  166. jul-19 23:28:17.912 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R2 run:lane1) > slurm jobId: 30206; workDir: /home/ska/rafa/programs/distiller-nf/work/9a/1ae2b8220cb69a4875df5209aa0b1a
  167. jul-19 23:28:17.912 [Task submitter] INFO nextflow.Session - [9a/1ae2b8] Re-submitted process > chunk_fastqs (library:MATalpha_R2 run:lane1)
  168. jul-19 23:28:17.915 [Task monitor] WARN nextflow.processor.TaskProcessor - Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks' -- Execution is retried (2)
  169. jul-19 23:28:17.933 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - Submitted process chunk_fastqs (library:MATalpha_R1 run:lane2) > slurm jobId: 30207; workDir: /home/ska/rafa/programs/distiller-nf/work/99/c4f329338120c6212774491e43428a
  170. jul-19 23:28:17.933 [Task submitter] INFO nextflow.Session - [99/c4f329] Re-submitted process > chunk_fastqs (library:MATalpha_R1 run:lane2)
  171. jul-19 23:28:22.813 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30203; id: 11; name: chunk_fastqs (library:MATa_R2 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/65/0134876397edbe096431a888e58a65 started: 1500499702809; exited: 2017-07-19T21:28:18.478014Z; ]
  172. jul-19 23:28:22.838 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'chunk_fastqs (library:MATa_R2 run:lane1)'
  173.  
  174. Caused by:
  175. /home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks
  176.  
  177. Command executed:
  178.  
  179. zcat SRR2601851_1.fastq.gz | split -l 20000 -d --filter 'pbgzip -c -n 2 > $FILE.1.fastq.gz' - MATa_R2.lane1.
  180.  
  181. zcat SRR2601851_2.fastq.gz | split -l 20000 -d --filter 'pbgzip -c -n 2 > $FILE.2.fastq.gz' - MATa_R2.lane1.
  182.  
  183. Command exit status:
  184. 0
  185.  
  186. Command output:
  187. (empty)
  188.  
  189. Work dir:
  190. /home/ska/rafa/programs/distiller-nf/work/65/0134876397edbe096431a888e58a65
  191.  
  192. Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
  193. jul-19 23:28:22.845 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Cannot access folder: '/home/ska/rafa/programs/distiller-nf/test/intermediates/fastq_chunks'
  194. jul-19 23:28:22.884 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
  195. [process] map_runs
  196. status=ACTIVE
  197. port 0: (queue) OPEN; channel: -
  198. port 1: (value) - ; channel: -
  199. port 2: (cntrl) OPEN; channel: $
  200.  
  201. [process] parse_runs
  202. status=ACTIVE
  203. port 0: (queue) OPEN; channel: -
  204. port 1: (value) - ; channel: chrom_sizes
  205. port 2: (cntrl) OPEN; channel: $
  206.  
  207. [process] premerge_pairsam_chunks
  208. status=ACTIVE
  209. port 0: (queue) OPEN; channel: -
  210. port 1: (cntrl) OPEN; channel: $
  211.  
  212. [process] merge_pairsam_into_runs
  213. status=ACTIVE
  214. port 0: (queue) OPEN; channel: -
  215. port 1: (cntrl) OPEN; channel: $
  216.  
  217. [process] merge_runs_into_libraries
  218. status=ACTIVE
  219. port 0: (queue) OPEN; channel: -
  220. port 1: (cntrl) OPEN; channel: $
  221.  
  222. [process] merge_stats_runs_into_libraries
  223. status=ACTIVE
  224. port 0: (queue) OPEN; channel: -
  225. port 1: (cntrl) OPEN; channel: $
  226.  
  227. [process] filter_make_pairs
  228. status=ACTIVE
  229. port 0: (queue) OPEN; channel: -
  230. port 1: (cntrl) OPEN; channel: $
  231.  
  232. [process] index_pairs
  233. status=ACTIVE
  234. port 0: (queue) OPEN; channel: -
  235. port 1: (cntrl) OPEN; channel: $
  236.  
  237. [process] bin_library_pairs
  238. status=ACTIVE
  239. port 0: (queue) OPEN; channel: -
  240. port 1: (value) - ; channel: __$eachinparam<1>
  241. port 2: (value) - ; channel: chrom_sizes
  242. port 3: (cntrl) OPEN; channel: $
  243.  
  244. [process] make_library_group_coolers
  245. status=ACTIVE
  246. port 0: (queue) OPEN; channel: -
  247. port 1: (cntrl) OPEN; channel: $
  248.  
  249. [process] merge_stats_libraries_into_groups
  250. status=ACTIVE
  251. port 0: (queue) OPEN; channel: -
  252. port 1: (cntrl) OPEN; channel: $
  253.  
  254. jul-19 23:28:22.889 [main] DEBUG nextflow.Session - Session await > all process finished
  255. jul-19 23:28:22.889 [main] DEBUG nextflow.Session - Session await > all barriers passed
  256. jul-19 23:28:22.898 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30204; id: 12; name: chunk_fastqs (library:MATalpha_R1 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/a9/6b1599b73f42604a0169c2d2eeebe1 started: 1500499702895; exited: 2017-07-19T21:28:18.457014Z; ]
  257. jul-19 23:28:22.906 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30205; id: 13; name: chunk_fastqs (library:MATa_R1 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/48/135367a39969af1b4a72adb679da4a started: 1500499702903; exited: 2017-07-19T21:28:18.491014Z; ]
  258. jul-19 23:28:22.907 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (2)
  259. jul-19 23:28:22.914 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30206; id: 14; name: chunk_fastqs (library:MATalpha_R2 run:lane1); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/9a/1ae2b8220cb69a4875df5209aa0b1a started: 1500499702911; exited: 2017-07-19T21:28:18.567015Z; ]
  260. jul-19 23:28:22.920 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30207; id: 15; name: chunk_fastqs (library:MATalpha_R1 run:lane2); status: COMPLETED; exit: 0; error: -; workDir: /home/ska/rafa/programs/distiller-nf/work/99/c4f329338120c6212774491e43428a started: 1500499702917; exited: 2017-07-19T21:28:18.520014Z; ]
  261. jul-19 23:28:22.923 [Actor Thread 9] DEBUG nextflow.Session - <<< barrier arrive (process: chunk_fastqs)
  262. jul-19 23:28:22.925 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
  263. jul-19 23:28:22.925 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm)
  264. jul-19 23:28:22.928 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
  265. jul-19 23:28:22.955 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
  266. jul-19 23:28:22.968 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
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