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  1. Jun-03 14:26:36.137 [main] DEBUG nextflow.cli.Launcher - $> /home/msmoot/bin/nextflow run main.nf -process.executor ignite -cluster.join path:/bioscratch/tmp/nextflow -w /bioscratch/tmp/nf-work3 --exp_data=1512_TarClone.yaml --email=msmoot@syntheticgenomics.com
  2. Jun-03 14:26:36.190 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.19.4
  3. Jun-03 14:26:36.190 [main] INFO nextflow.cli.CmdRun - Launching main.nf
  4. Jun-03 14:26:36.205 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: nextflow.config
  5. Jun-03 14:26:36.207 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/msmoot/code/nextflow_resequencing/nextflow.config
  6. Jun-03 14:26:36.480 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'standard'
  7. Jun-03 14:26:36.586 [main] DEBUG nextflow.Session - Session uuid: 4e47cb05-b8b3-44e8-8e48-8f73489552c1
  8. Jun-03 14:26:36.588 [main] DEBUG nextflow.Session - Executor pool size: 24
  9. Jun-03 14:26:36.607 [main] DEBUG nextflow.cli.CmdRun -
  10. Version: 0.19.4 build 3793
  11. Modified: 03-06-2016 17:12 UTC (10:12 PDT)
  12. System: Linux 3.10.0-327.10.1.el7.x86_64
  13. Runtime: Groovy 2.4.5 on OpenJDK 64-Bit Server VM 1.8.0_91-b14
  14. Encoding: UTF-8 (UTF-8)
  15. Process: 20086@asm04.c01.l.synthgeno.global [10.8.101.78]
  16.  
  17. Jun-03 14:26:36.616 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/msmoot/code/nextflow_resequencing/bin
  18. Jun-03 14:26:36.631 [main] DEBUG nextflow.Session - Session start invoked
  19. Jun-03 14:26:36.634 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
  20. Jun-03 14:26:36.635 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/msmoot/code/nextflow_resequencing/trace.tsv
  21. Jun-03 14:26:36.654 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
  22. Jun-03 14:26:37.646 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
  23. Jun-03 14:26:37.670 [main] INFO nextflow.Nextflow -
  24.  
  25. Jun-03 14:26:37.671 [main] INFO nextflow.Nextflow - Resquencing pipeline execution parameters for: 1512_TarClone
  26. Jun-03 14:26:37.671 [main] INFO nextflow.Nextflow -
  27.  
  28. Jun-03 14:26:37.671 [main] INFO nextflow.Nextflow - exp_data : 1512_TarClone.yaml
  29. Jun-03 14:26:37.671 [main] INFO nextflow.Nextflow - ram : 20
  30. Jun-03 14:26:37.671 [main] INFO nextflow.Nextflow - email : msmoot@syntheticgenomics.com
  31. Jun-03 14:26:37.671 [main] INFO nextflow.Nextflow - num cpus : 24
  32. Jun-03 14:26:37.671 [main] INFO nextflow.Nextflow - cpus/process : 4
  33. Jun-03 14:26:37.671 [main] INFO nextflow.Nextflow - max processes : 6
  34. Jun-03 14:26:37.672 [main] INFO nextflow.Nextflow - results dir : results__1512_TarClone
  35. Jun-03 14:26:37.672 [main] INFO nextflow.Nextflow -
  36.  
  37. Jun-03 14:26:37.856 [main] DEBUG nextflow.processor.ProcessFactory - Discovered executor class: nextflow.executor.IgExecutor
  38. Jun-03 14:26:37.912 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  39. Jun-03 14:26:37.912 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  40. Jun-03 14:26:37.912 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  41. Jun-03 14:26:37.919 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  42. Jun-03 14:26:37.920 [main] INFO nextflow.executor.Executor - [warm up] executor > ignite
  43. Jun-03 14:26:37.925 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'ignite' > pollInterval: 5s; dumpInterval: 5m
  44. Jun-03 14:26:37.928 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor
  45. Jun-03 14:26:37.928 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: ignite)
  46. Jun-03 14:26:37.930 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: ignite
  47. Jun-03 14:26:37.968 [main] DEBUG nextflow.executor.IgConnector - Create Ignite master node
  48. Jun-03 14:26:37.988 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: IgFileSystemProvider
  49. Jun-03 14:26:37.993 [main] DEBUG nextflow.daemon.IgGridFactory - Configuration properties for role: 'master' -- [join:path:/bioscratch/tmp/nextflow]
  50. Jun-03 14:26:38.028 [main] DEBUG nextflow.daemon.IgGridFactory - Ignite config > discovery path: /bioscratch/tmp/nextflow
  51. Jun-03 14:26:38.047 [main] DEBUG nextflow.daemon.IgGridFactory - Apache Ignite config > group name: nextflow
  52. Jun-03 14:26:38.135 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Config URL: n/a
  53. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Daemon mode: off
  54. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - OS: Linux 3.10.0-327.10.1.el7.x86_64 amd64
  55. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - OS user: msmoot
  56. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Language runtime: Groovy
  57. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - VM information: OpenJDK Runtime Environment 1.8.0_91-b14 Oracle Corporation OpenJDK 64-Bit Server VM 25.91-b14
  58. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - VM total memory: 27.0GB
  59. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Remote Management [restart: off, REST: on, JMX (remote: off)]
  60. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - IGNITE_HOME=null
  61. Jun-03 14:26:38.136 [main] INFO o.a.i.internal.IgniteKernal%nextflow - VM arguments: [-Xverify:none, -Djava.library.path=/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib, -Dfile.encoding=UTF-8, -Dcapsule.app=nextflow_0.19.4, -Djava.awt.headless=true, -Dcapsule.jar=/home/msmoot/.nextflow/framework/0.19.4/nextflow-0.19.4-one.jar]
  62. Jun-03 14:26:38.137 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Configured caches ['ignite-marshaller-sys-cache', 'ignite-sys-cache', 'ignite-atomics-sys-cache', 'allSessions', 'igfs-data', 'igfs-meta']
  63. Jun-03 14:26:38.140 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Local node user attribute [ROLE=master]
  64. Jun-03 14:26:38.176 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Non-loopback local IPs: 10.8.101.78, 172.17.42.1, fe80:0:0:0:42:beff:fe4a:7e2e%docker0, fe80:0:0:0:92e2:baff:fe04:fd68%p1p1
  65. Jun-03 14:26:38.176 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Enabled local MACs: 0242BE4A7E2E, 90E2BA04FD68
  66. Jun-03 14:26:38.183 [main] INFO o.a.i.i.p.p.IgnitePluginProcessor - Configured plugins:
  67. Jun-03 14:26:38.183 [main] INFO o.a.i.i.p.p.IgnitePluginProcessor - ^-- None
  68. Jun-03 14:26:38.183 [main] INFO o.a.i.i.p.p.IgnitePluginProcessor -
  69. Jun-03 14:26:38.229 [main] INFO o.a.i.s.c.tcp.TcpCommunicationSpi - IPC shared memory server endpoint started [port=48100, tokDir=/tmp/ignite/ipc/shmem/d0b68d67-0099-4407-8689-8342d2e05646-20086]
  70. Jun-03 14:26:38.229 [main] INFO o.a.i.s.c.tcp.TcpCommunicationSpi - Successfully bound shared memory communication to TCP port [port=48100, locHost=0.0.0.0/0.0.0.0]
  71. Jun-03 14:26:38.239 [main] INFO o.a.i.s.c.tcp.TcpCommunicationSpi - Successfully bound to TCP port [port=47100, locHost=0.0.0.0/0.0.0.0]
  72. Jun-03 14:26:38.252 [main] WARN o.a.i.s.c.noop.NoopCheckpointSpi - Checkpoints are disabled (to enable configure any GridCheckpointSpi implementation)
  73. Jun-03 14:26:38.267 [main] DEBUG n.daemon.CustomStealingCollisionSpi - Registered SPI MBean: org.apache:clsLdr=3d4eac69,grid=nextflow,group=SPIs,name=CustomStealingCollisionSpi
  74. Jun-03 14:26:38.267 [main] DEBUG n.daemon.CustomStealingCollisionSpi - SPI started ok [startMs=0, spiMBean=org.apache:clsLdr=3d4eac69,grid=nextflow,group=SPIs,name=CustomStealingCollisionSpi]
  75. Jun-03 14:26:38.269 [main] WARN o.a.i.s.s.noop.NoopSwapSpaceSpi - Swap space is disabled. To enable use FileSwapSpaceSpi.
  76. Jun-03 14:26:38.270 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Security status [authentication=off, tls/ssl=off]
  77. Jun-03 14:26:38.373 [main] INFO o.a.i.i.p.r.p.t.GridTcpRestProtocol - Command protocol successfully started [name=TCP binary, host=0.0.0.0/0.0.0.0, port=11211]
  78. Jun-03 14:26:38.403 [main] INFO o.a.i.i.u.i.s.IpcSharedMemoryServerEndpoint - IPC shared memory server endpoint started [port=10500, tokDir=/tmp/ignite/ipc/shmem/d0b68d67-0099-4407-8689-8342d2e05646-20086]
  79. Jun-03 14:26:38.404 [main] INFO o.a.i.i.u.i.l.IpcServerTcpEndpoint - IPC server loopback endpoint started [port=11400]
  80. Jun-03 14:26:38.426 [main] INFO o.a.i.s.d.tcp.TcpDiscoverySpi - Successfully bound to TCP port [port=47500, localHost=0.0.0.0/0.0.0.0]
  81. Jun-03 14:26:38.458 [main] WARN o.a.i.i.m.e.GridEventStorageManager - Added listener for disabled event type: TASK_FINISHED
  82. Jun-03 14:26:38.458 [main] WARN o.a.i.i.m.e.GridEventStorageManager - Added listener for disabled event type: TASK_FAILED
  83. Jun-03 14:26:38.458 [main] WARN o.a.i.i.m.e.GridEventStorageManager - Added listener for disabled event type: JOB_MAPPED
  84. Jun-03 14:26:38.609 [main] WARN o.a.i.i.p.c.GridCacheEvictionManager - <igfs-data> Evictions are not synchronized with other nodes in topology which provides 2x-3x better performance but may cause data inconsistency if cache store is not configured (consider changing 'evictSynchronized' configuration property).
  85. Jun-03 14:26:38.639 [main] INFO o.a.i.i.p.cache.GridCacheProcessor - Started cache [name=igfs-data, mode=PARTITIONED]
  86. Jun-03 14:26:38.642 [main] WARN o.a.i.i.p.cache.GridCacheProcessor - Eviction policy not enabled with ONHEAP_TIERED mode for cache (entries will not be moved to off-heap store): allSessions
  87. Jun-03 14:26:38.686 [main] INFO o.a.i.i.p.cache.GridCacheProcessor - Started cache [name=allSessions, mode=PARTITIONED]
  88. Jun-03 14:26:38.689 [main] INFO o.a.i.i.p.cache.GridCacheProcessor - Started cache [name=ignite-sys-cache, mode=REPLICATED]
  89. Jun-03 14:26:38.694 [main] INFO o.a.i.i.p.cache.GridCacheProcessor - Started cache [name=ignite-atomics-sys-cache, mode=PARTITIONED]
  90. Jun-03 14:26:38.698 [main] INFO o.a.i.i.p.cache.GridCacheProcessor - Started cache [name=igfs-meta, mode=REPLICATED]
  91. Jun-03 14:26:38.699 [main] INFO o.a.i.i.p.cache.GridCacheProcessor - Started cache [name=ignite-marshaller-sys-cache, mode=REPLICATED]
  92. Jun-03 14:26:38.809 [exchange-worker-#117%nextflow%] INFO o.a.i.i.p.c.GridCachePartitionExchangeManager - Skipping rebalancing (nothing scheduled) [top=AffinityTopologyVersion [topVer=1, minorTopVer=0], evt=NODE_JOINED, node=d0b68d67-0099-4407-8689-8342d2e05646]
  93. Jun-03 14:26:38.835 [main] INFO o.a.i.internal.IgniteKernal%nextflow - Performance suggestions for grid 'nextflow' (fix if possible)
  94. Jun-03 14:26:38.835 [main] INFO o.a.i.internal.IgniteKernal%nextflow - To disable, set -DIGNITE_PERFORMANCE_SUGGESTIONS_DISABLED=true
  95. Jun-03 14:26:38.835 [main] INFO o.a.i.internal.IgniteKernal%nextflow - ^-- Disable collision resolution (remove 'collisionSpi' from configuration)
  96. Jun-03 14:26:38.835 [main] INFO o.a.i.internal.IgniteKernal%nextflow -
  97. Jun-03 14:26:38.835 [main] INFO o.a.i.internal.IgniteKernal%nextflow - To start Console Management & Monitoring run ignitevisorcmd.{sh|bat}
  98. Jun-03 14:26:38.835 [main] INFO o.a.i.internal.IgniteKernal%nextflow -
  99. Jun-03 14:26:38.836 [main] INFO o.a.i.internal.IgniteKernal%nextflow -
  100.  
  101. >>> +----------------------------------------------------------------------------+
  102. >>> Ignite ver. 1.5.0-final#20151229-sha1:f1f8cda2f3f62231f42a59951bf34c39577c1bec
  103. >>> +----------------------------------------------------------------------------+
  104. >>> OS name: Linux 3.10.0-327.10.1.el7.x86_64 amd64
  105. >>> CPU(s): 24
  106. >>> Heap: 27.0GB
  107. >>> VM name: 20086@asm04.c01.l.synthgeno.global
  108. >>> Grid name: nextflow
  109. >>> Local node [ID=D0B68D67-0099-4407-8689-8342D2E05646, order=1, clientMode=false]
  110. >>> Local node addresses: [172.17.42.1/0:0:0:0:0:0:0:1%lo, asm04.c01.l.synthgeno.global/10.8.101.78, /127.0.0.1, /172.17.42.1]
  111. >>> Local ports: TCP:10500 TCP:11211 TCP:11400 TCP:47100 TCP:47500 TCP:48100
  112.  
  113. Jun-03 14:26:38.837 [main] INFO o.a.i.i.m.d.GridDiscoveryManager - Topology snapshot [ver=1, servers=1, clients=0, CPUs=24, heap=27.0GB]
  114. Jun-03 14:26:38.844 [disco-event-worker-#114%nextflow%] DEBUG n.daemon.CustomStealingCollisionSpi - Computing resources for node: `asm04.c01.l.synthgeno.global` [master] > cpus: 24; mem: 283.2 GB; free disk: 83.5 GB (/tmp)
  115. Jun-03 14:26:38.863 [Topology watcher] DEBUG nextflow.executor.IgConnector - Cluster metrics >> slots: 24
  116. Jun-03 14:26:38.864 [Topology watcher] DEBUG n.processor.TaskPollingMonitor - Monitor current capacity: 34 (after inc: 34)
  117. Jun-03 14:26:38.934 [main] DEBUG nextflow.util.RemoteSession - Packed library (320 files) at path: /tmp/nxf-707940340292782479
  118. Jun-03 14:26:38.992 [main] DEBUG nextflow.executor.IgConnector - Cluster shutdownOnComplete: false
  119. Jun-03 14:26:39.017 [main] DEBUG nextflow.Session - >>> barrier register (process: buildPrimaryReference)
  120. Jun-03 14:26:39.033 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildPrimaryReference -- maxForks: 24
  121. Jun-03 14:26:39.045 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  122. Jun-03 14:26:39.045 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  123. Jun-03 14:26:39.045 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  124. Jun-03 14:26:39.046 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  125. Jun-03 14:26:39.046 [main] DEBUG nextflow.Session - >>> barrier register (process: buildPrimaryAnnotation)
  126. Jun-03 14:26:39.051 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildPrimaryAnnotation -- maxForks: 24
  127. Jun-03 14:26:39.064 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  128. Jun-03 14:26:39.064 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  129. Jun-03 14:26:39.064 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  130. Jun-03 14:26:39.065 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  131. Jun-03 14:26:39.065 [main] DEBUG nextflow.Session - >>> barrier register (process: indexPrimaryFasta)
  132. Jun-03 14:26:39.072 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > indexPrimaryFasta -- maxForks: 24
  133. Jun-03 14:26:39.080 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  134. Jun-03 14:26:39.081 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  135. Jun-03 14:26:39.081 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  136. Jun-03 14:26:39.081 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  137. Jun-03 14:26:39.082 [main] DEBUG nextflow.Session - >>> barrier register (process: buildPrimaryBWAIndex)
  138. Jun-03 14:26:39.091 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildPrimaryBWAIndex -- maxForks: 24
  139. Jun-03 14:26:39.098 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  140. Jun-03 14:26:39.098 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  141. Jun-03 14:26:39.098 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  142. Jun-03 14:26:39.099 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  143. Jun-03 14:26:39.099 [main] DEBUG nextflow.Session - >>> barrier register (process: makeBlastDB)
  144. Jun-03 14:26:39.106 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > makeBlastDB -- maxForks: 24
  145. Jun-03 14:26:39.112 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  146. Jun-03 14:26:39.112 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  147. Jun-03 14:26:39.112 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  148. Jun-03 14:26:39.112 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  149. Jun-03 14:26:39.113 [main] DEBUG nextflow.Session - >>> barrier register (process: computeFastaGCDensity)
  150. Jun-03 14:26:39.119 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > computeFastaGCDensity -- maxForks: 24
  151. Jun-03 14:26:39.125 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  152. Jun-03 14:26:39.125 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  153. Jun-03 14:26:39.125 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  154. Jun-03 14:26:39.125 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  155. Jun-03 14:26:39.126 [main] DEBUG nextflow.Session - >>> barrier register (process: computeFastaGCEntropyDensity)
  156. Jun-03 14:26:39.132 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > computeFastaGCEntropyDensity -- maxForks: 24
  157. Jun-03 14:26:39.139 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  158. Jun-03 14:26:39.139 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  159. Jun-03 14:26:39.139 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  160. Jun-03 14:26:39.139 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  161. Jun-03 14:26:39.140 [main] DEBUG nextflow.Session - >>> barrier register (process: buildSampleReference)
  162. Jun-03 14:26:39.145 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildSampleReference -- maxForks: 24
  163. Jun-03 14:26:39.147 [Actor Thread 7] DEBUG n.processor.ParallelTaskProcessor - <buildSampleReference> Poison pill arrived
  164. Jun-03 14:26:39.149 [Actor Thread 1] DEBUG nextflow.processor.StateObj - <buildSampleReference> State before poison: StateObj[submitted: 2; completed: 0; poisoned: false; allScalar: false]
  165. Jun-03 14:26:39.150 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  166. Jun-03 14:26:39.150 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  167. Jun-03 14:26:39.150 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  168. Jun-03 14:26:39.150 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  169. Jun-03 14:26:39.151 [main] DEBUG nextflow.Session - >>> barrier register (process: buildSampleAnnotation)
  170. Jun-03 14:26:39.157 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildSampleAnnotation -- maxForks: 24
  171. Jun-03 14:26:39.158 [Actor Thread 7] DEBUG n.processor.ParallelTaskProcessor - <buildSampleAnnotation> Poison pill arrived
  172. Jun-03 14:26:39.160 [Actor Thread 1] DEBUG nextflow.processor.StateObj - <buildSampleAnnotation> State before poison: StateObj[submitted: 2; completed: 0; poisoned: false; allScalar: false]
  173. Jun-03 14:26:39.163 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  174. Jun-03 14:26:39.163 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  175. Jun-03 14:26:39.163 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  176. Jun-03 14:26:39.163 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  177. Jun-03 14:26:39.164 [main] DEBUG nextflow.Session - >>> barrier register (process: buildSampleBWAIndex)
  178. Jun-03 14:26:39.170 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildSampleBWAIndex -- maxForks: 24
  179. Jun-03 14:26:39.180 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  180. Jun-03 14:26:39.180 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  181. Jun-03 14:26:39.180 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  182. Jun-03 14:26:39.180 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  183. Jun-03 14:26:39.181 [main] DEBUG nextflow.Session - >>> barrier register (process: calculateGenomeSizes)
  184. Jun-03 14:26:39.186 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > calculateGenomeSizes -- maxForks: 24
  185. Jun-03 14:26:39.193 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  186. Jun-03 14:26:39.193 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  187. Jun-03 14:26:39.193 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  188. Jun-03 14:26:39.193 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  189. Jun-03 14:26:39.194 [main] DEBUG nextflow.Session - >>> barrier register (process: alignPE)
  190. Jun-03 14:26:39.200 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > alignPE -- maxForks: 24
  191. Jun-03 14:26:39.206 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  192. Jun-03 14:26:39.206 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  193. Jun-03 14:26:39.206 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  194. Jun-03 14:26:39.207 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  195. Jun-03 14:26:39.207 [main] DEBUG nextflow.Session - >>> barrier register (process: alignPacBio)
  196. Jun-03 14:26:39.213 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > alignPacBio -- maxForks: 24
  197. Jun-03 14:26:39.222 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  198. Jun-03 14:26:39.222 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  199. Jun-03 14:26:39.222 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  200. Jun-03 14:26:39.222 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  201. Jun-03 14:26:39.223 [main] DEBUG nextflow.Session - >>> barrier register (process: mergeBySample)
  202. Jun-03 14:26:39.229 [Actor Thread 5] INFO nextflow.processor.TaskDispatcher - [bc/326e57] Submitted process > buildPrimaryReference (1)
  203. Jun-03 14:26:39.231 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > mergeBySample -- maxForks: 24
  204. Jun-03 14:26:39.233 [Actor Thread 2] INFO nextflow.processor.TaskDispatcher - [55/3335b9] Submitted process > buildPrimaryAnnotation (1)
  205. Jun-03 14:26:39.237 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  206. Jun-03 14:26:39.237 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  207. Jun-03 14:26:39.237 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  208. Jun-03 14:26:39.237 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  209. Jun-03 14:26:39.238 [main] DEBUG nextflow.Session - >>> barrier register (process: alignStats)
  210. Jun-03 14:26:39.241 [Actor Thread 6] INFO nextflow.processor.TaskDispatcher - [1a/a0b757] Submitted process > buildSampleReference (Cen9)
  211. Jun-03 14:26:39.242 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > alignStats -- maxForks: 24
  212. Jun-03 14:26:39.245 [Actor Thread 4] INFO nextflow.processor.TaskDispatcher - [0b/93bbbd] Submitted process > buildSampleReference (Cen2)
  213. Jun-03 14:26:39.248 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  214. Jun-03 14:26:39.248 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  215. Jun-03 14:26:39.248 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  216. Jun-03 14:26:39.249 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  217. Jun-03 14:26:39.251 [Actor Thread 3] INFO nextflow.processor.TaskDispatcher - [9e/498127] Submitted process > buildSampleAnnotation (Cen2)
  218. Jun-03 14:26:39.252 [main] DEBUG nextflow.Session - >>> barrier register (process: sampleSamView)
  219. Jun-03 14:26:39.256 [Actor Thread 8] INFO nextflow.processor.TaskDispatcher - [a6/154670] Submitted process > buildSampleAnnotation (Cen9)
  220. Jun-03 14:26:39.258 [pub-#11%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildSampleAnnotation (Cen2) - workdir: /bioscratch/tmp/nf-work3/9e/4981270a1f08465fb8e153aaeee734 - remote: false
  221. Jun-03 14:26:39.258 [pub-#7%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildPrimaryReference (1) - workdir: /bioscratch/tmp/nf-work3/bc/326e573f1661531ad6b8bc17f8f3f9 - remote: false
  222. Jun-03 14:26:39.258 [pub-#9%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildSampleReference (Cen9) - workdir: /bioscratch/tmp/nf-work3/1a/a0b757617aba24a6b08fbdd7b1f43b - remote: false
  223. Jun-03 14:26:39.258 [pub-#10%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildSampleReference (Cen2) - workdir: /bioscratch/tmp/nf-work3/0b/93bbbd01cef9e5e05f682dfeee37ff - remote: false
  224. Jun-03 14:26:39.259 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > sampleSamView -- maxForks: 24
  225. Jun-03 14:26:39.263 [pub-#12%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildSampleAnnotation (Cen9) - workdir: /bioscratch/tmp/nf-work3/a6/154670e8cb6b01313668355ff04419 - remote: false
  226. Jun-03 14:26:39.267 [pub-#8%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildPrimaryAnnotation (1) - workdir: /bioscratch/tmp/nf-work3/55/3335b96ada65b63fab4d1dfb475d33 - remote: false
  227. Jun-03 14:26:39.269 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  228. Jun-03 14:26:39.269 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  229. Jun-03 14:26:39.269 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  230. Jun-03 14:26:39.270 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  231. Jun-03 14:26:39.270 [main] DEBUG nextflow.Session - >>> barrier register (process: sampleSamDepth)
  232. Jun-03 14:26:39.278 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > sampleSamDepth -- maxForks: 24
  233. Jun-03 14:26:39.287 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  234. Jun-03 14:26:39.288 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  235. Jun-03 14:26:39.288 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  236. Jun-03 14:26:39.288 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  237. Jun-03 14:26:39.288 [main] DEBUG nextflow.Session - >>> barrier register (process: findBrokenMatePairsPE)
  238. Jun-03 14:26:39.295 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > findBrokenMatePairsPE -- maxForks: 24
  239. Jun-03 14:26:39.302 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  240. Jun-03 14:26:39.302 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  241. Jun-03 14:26:39.302 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  242. Jun-03 14:26:39.302 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  243. Jun-03 14:26:39.302 [main] DEBUG nextflow.Session - >>> barrier register (process: calculateCoverage)
  244. Jun-03 14:26:39.309 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > calculateCoverage -- maxForks: 24
  245. Jun-03 14:26:39.314 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  246. Jun-03 14:26:39.314 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  247. Jun-03 14:26:39.314 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  248. Jun-03 14:26:39.314 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  249. Jun-03 14:26:39.315 [main] DEBUG nextflow.Session - >>> barrier register (process: findSplitReadsPacBio)
  250. Jun-03 14:26:39.321 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > findSplitReadsPacBio -- maxForks: 24
  251. Jun-03 14:26:39.331 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  252. Jun-03 14:26:39.332 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  253. Jun-03 14:26:39.332 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  254. Jun-03 14:26:39.332 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  255. Jun-03 14:26:39.332 [main] DEBUG nextflow.Session - >>> barrier register (process: reuseAssembly)
  256. Jun-03 14:26:39.337 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > reuseAssembly -- maxForks: 24
  257. Jun-03 14:26:39.338 [Actor Thread 8] DEBUG n.processor.ParallelTaskProcessor - <reuseAssembly> Poison pill arrived
  258. Jun-03 14:26:39.338 [Actor Thread 1] DEBUG nextflow.processor.StateObj - <reuseAssembly> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
  259. Jun-03 14:26:39.338 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <reuseAssembly> Sending poison pills and terminating process
  260. Jun-03 14:26:39.339 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: reuseAssembly)
  261. Jun-03 14:26:39.340 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  262. Jun-03 14:26:39.340 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  263. Jun-03 14:26:39.340 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  264. Jun-03 14:26:39.340 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  265. Jun-03 14:26:39.340 [Actor Thread 8] DEBUG n.processor.ParallelTaskProcessor - <reuseAssembly> After stop
  266. Jun-03 14:26:39.340 [main] DEBUG nextflow.Session - >>> barrier register (process: contigsOfInterest)
  267. Jun-03 14:26:39.345 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > contigsOfInterest -- maxForks: 24
  268. Jun-03 14:26:39.360 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  269. Jun-03 14:26:39.360 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  270. Jun-03 14:26:39.360 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  271. Jun-03 14:26:39.361 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  272. Jun-03 14:26:39.361 [main] DEBUG nextflow.Session - >>> barrier register (process: denovoReassembly)
  273. Jun-03 14:26:39.366 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > denovoReassembly -- maxForks: 24
  274. Jun-03 14:26:39.373 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  275. Jun-03 14:26:39.373 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  276. Jun-03 14:26:39.373 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  277. Jun-03 14:26:39.373 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  278. Jun-03 14:26:39.374 [main] DEBUG nextflow.Session - >>> barrier register (process: brokenBlast)
  279. Jun-03 14:26:39.378 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > brokenBlast -- maxForks: 24
  280. Jun-03 14:26:39.382 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  281. Jun-03 14:26:39.382 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  282. Jun-03 14:26:39.382 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  283. Jun-03 14:26:39.382 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  284. Jun-03 14:26:39.383 [main] DEBUG nextflow.Session - >>> barrier register (process: buildReassemblyBWAIndex)
  285. Jun-03 14:26:39.387 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildReassemblyBWAIndex -- maxForks: 24
  286. Jun-03 14:26:39.392 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  287. Jun-03 14:26:39.392 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  288. Jun-03 14:26:39.392 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  289. Jun-03 14:26:39.393 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  290. Jun-03 14:26:39.393 [main] DEBUG nextflow.Session - >>> barrier register (process: alignReassemblyPE)
  291. Jun-03 14:26:39.398 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > alignReassemblyPE -- maxForks: 24
  292. Jun-03 14:26:39.402 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  293. Jun-03 14:26:39.402 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  294. Jun-03 14:26:39.402 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  295. Jun-03 14:26:39.403 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  296. Jun-03 14:26:39.403 [main] DEBUG nextflow.Session - >>> barrier register (process: alignReassemblyPacBio)
  297. Jun-03 14:26:39.407 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > alignReassemblyPacBio -- maxForks: 24
  298. Jun-03 14:26:39.413 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  299. Jun-03 14:26:39.413 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  300. Jun-03 14:26:39.413 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  301. Jun-03 14:26:39.414 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  302. Jun-03 14:26:39.414 [main] DEBUG nextflow.Session - >>> barrier register (process: mergeReassemblyBySample)
  303. Jun-03 14:26:39.418 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > mergeReassemblyBySample -- maxForks: 24
  304. Jun-03 14:26:39.424 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  305. Jun-03 14:26:39.424 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  306. Jun-03 14:26:39.424 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  307. Jun-03 14:26:39.424 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  308. Jun-03 14:26:39.425 [main] DEBUG nextflow.Session - >>> barrier register (process: mergeByType)
  309. Jun-03 14:26:39.431 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > mergeByType -- maxForks: 24
  310. Jun-03 14:26:39.435 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  311. Jun-03 14:26:39.435 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  312. Jun-03 14:26:39.435 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  313. Jun-03 14:26:39.435 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  314. Jun-03 14:26:39.436 [main] DEBUG nextflow.Session - >>> barrier register (process: runFreebayes)
  315. Jun-03 14:26:39.440 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > runFreebayes -- maxForks: 24
  316. Jun-03 14:26:39.443 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  317. Jun-03 14:26:39.443 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  318. Jun-03 14:26:39.443 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  319. Jun-03 14:26:39.443 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  320. Jun-03 14:26:39.443 [main] DEBUG nextflow.Session - >>> barrier register (process: buildSNPEffConfig)
  321. Jun-03 14:26:39.448 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildSNPEffConfig -- maxForks: 24
  322. Jun-03 14:26:39.450 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  323. Jun-03 14:26:39.450 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  324. Jun-03 14:26:39.450 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  325. Jun-03 14:26:39.450 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  326. Jun-03 14:26:39.450 [main] DEBUG nextflow.Session - >>> barrier register (process: buildSNPEffDb)
  327. Jun-03 14:26:39.454 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildSNPEffDb -- maxForks: 24
  328. Jun-03 14:26:39.458 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  329. Jun-03 14:26:39.458 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  330. Jun-03 14:26:39.458 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  331. Jun-03 14:26:39.458 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  332. Jun-03 14:26:39.458 [main] DEBUG nextflow.Session - >>> barrier register (process: runSNPEff)
  333. Jun-03 14:26:39.464 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > runSNPEff -- maxForks: 24
  334. Jun-03 14:26:39.466 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  335. Jun-03 14:26:39.467 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  336. Jun-03 14:26:39.467 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  337. Jun-03 14:26:39.467 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  338. Jun-03 14:26:39.467 [main] DEBUG nextflow.Session - >>> barrier register (process: indexSampleBam)
  339. Jun-03 14:26:39.472 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > indexSampleBam -- maxForks: 24
  340. Jun-03 14:26:39.475 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  341. Jun-03 14:26:39.475 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  342. Jun-03 14:26:39.475 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  343. Jun-03 14:26:39.475 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  344. Jun-03 14:26:39.476 [main] DEBUG nextflow.Session - >>> barrier register (process: runTEMP)
  345. Jun-03 14:26:39.480 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > runTEMP -- maxForks: 24
  346. Jun-03 14:26:39.483 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  347. Jun-03 14:26:39.483 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  348. Jun-03 14:26:39.483 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  349. Jun-03 14:26:39.484 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  350. Jun-03 14:26:39.484 [main] DEBUG nextflow.Session - >>> barrier register (process: runKraken)
  351. Jun-03 14:26:39.488 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > runKraken -- maxForks: 24
  352. Jun-03 14:26:39.489 [Actor Thread 8] DEBUG n.processor.ParallelTaskProcessor - <runKraken> Poison pill arrived
  353. Jun-03 14:26:39.490 [Actor Thread 1] DEBUG nextflow.processor.StateObj - <runKraken> State before poison: StateObj[submitted: 6; completed: 0; poisoned: false; allScalar: false]
  354. Jun-03 14:26:39.494 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  355. Jun-03 14:26:39.494 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  356. Jun-03 14:26:39.494 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  357. Jun-03 14:26:39.494 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  358. Jun-03 14:26:39.495 [main] DEBUG nextflow.Session - >>> barrier register (process: buildStatsRDataImage)
  359. Jun-03 14:26:39.502 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildStatsRDataImage -- maxForks: 24
  360. Jun-03 14:26:39.506 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  361. Jun-03 14:26:39.506 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  362. Jun-03 14:26:39.506 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  363. Jun-03 14:26:39.507 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  364. Jun-03 14:26:39.507 [main] DEBUG nextflow.Session - >>> barrier register (process: buildContaminationRDataImage)
  365. Jun-03 14:26:39.512 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildContaminationRDataImage -- maxForks: 24
  366. Jun-03 14:26:39.519 [Actor Thread 4] INFO nextflow.processor.TaskDispatcher - [1a/d28204] Submitted process > runKraken (G2-41 - 0)
  367. Jun-03 14:26:39.523 [Actor Thread 9] INFO nextflow.processor.TaskDispatcher - [f2/404afe] Submitted process > runKraken (G9-56 - 0)
  368. Jun-03 14:26:39.526 [pub-#13%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: runKraken (G2-41 - 0) - workdir: /bioscratch/tmp/nf-work3/1a/d28204f4c696618c2580cb683f36f8 - remote: false
  369. Jun-03 14:26:39.526 [Actor Thread 3] INFO nextflow.processor.TaskDispatcher - [a9/43707d] Submitted process > runKraken (G2-23 - 0)
  370. Jun-03 14:26:39.526 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  371. Jun-03 14:26:39.526 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  372. Jun-03 14:26:39.526 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  373. Jun-03 14:26:39.527 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  374. Jun-03 14:26:39.527 [main] DEBUG nextflow.Session - >>> barrier register (process: buildBreakPlotRDataImage)
  375. Jun-03 14:26:39.528 [Actor Thread 5] INFO nextflow.processor.TaskDispatcher - [cf/a38215] Submitted process > runKraken (G9-38 - 0)
  376. Jun-03 14:26:39.531 [pub-#14%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: runKraken (G9-56 - 0) - workdir: /bioscratch/tmp/nf-work3/f2/404afe164a3d37d65a1bacfef0a511 - remote: false
  377. Jun-03 14:26:39.531 [Actor Thread 2] INFO nextflow.processor.TaskDispatcher - [e2/b53778] Submitted process > runKraken (G9-25 - 0)
  378. Jun-03 14:26:39.532 [pub-#15%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: runKraken (G2-23 - 0) - workdir: /bioscratch/tmp/nf-work3/a9/43707d22721b4d067f890c40f95f44 - remote: false
  379. Jun-03 14:26:39.533 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildBreakPlotRDataImage -- maxForks: 24
  380. Jun-03 14:26:39.534 [Actor Thread 6] INFO nextflow.processor.TaskDispatcher - [57/d4dcdb] Submitted process > runKraken (G2-9 - 0)
  381. Jun-03 14:26:39.535 [pub-#16%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: runKraken (G9-38 - 0) - workdir: /bioscratch/tmp/nf-work3/cf/a382151a5ca64d0e0d57c712bf3037 - remote: false
  382. Jun-03 14:26:39.539 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: ignite
  383. Jun-03 14:26:39.539 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'ignite'
  384. Jun-03 14:26:39.539 [main] DEBUG nextflow.processor.ProcessFactory - Loading executor class: nextflow.executor.IgExecutor
  385. Jun-03 14:26:39.539 [main] DEBUG nextflow.executor.Executor - Initializing executor: ignite
  386. Jun-03 14:26:39.540 [main] DEBUG nextflow.Session - >>> barrier register (process: buildSNPRDataImage)
  387. Jun-03 14:26:39.542 [pub-#18%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: runKraken (G2-9 - 0) - workdir: /bioscratch/tmp/nf-work3/57/d4dcdbe97c6a98eb817740c02f3171 - remote: false
  388. Jun-03 14:26:39.545 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > buildSNPRDataImage -- maxForks: 24
  389. Jun-03 14:26:39.547 [pub-#17%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: runKraken (G9-25 - 0) - workdir: /bioscratch/tmp/nf-work3/e2/b537789043c1b1b0ec4abed8adc289 - remote: false
  390. Jun-03 14:26:39.547 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
  391. Jun-03 14:26:39.547 [main] DEBUG nextflow.Session - Session await
  392. Jun-03 14:26:42.310 [pub-#9%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildSampleReference (Cen9) - exitStatus: 0
  393. Jun-03 14:26:42.323 [Thread-2] DEBUG nextflow.file.FileHelper - NFS path (true): /bioscratch/tmp/nf-work3
  394. Jun-03 14:26:42.352 [Actor Thread 2] INFO nextflow.processor.TaskDispatcher - [0c/110705] Submitted process > buildSampleBWAIndex (Cen9)
  395. Jun-03 14:26:42.357 [pub-#19%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildSampleBWAIndex (Cen9) - workdir: /bioscratch/tmp/nf-work3/0c/110705167e0428c55cd5a3dc614200 - remote: false
  396. Jun-03 14:26:42.440 [pub-#10%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildSampleReference (Cen2) - exitStatus: 0
  397. Jun-03 14:26:42.452 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <buildSampleReference> Sending poison pills and terminating process
  398. Jun-03 14:26:42.452 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: buildSampleReference)
  399. Jun-03 14:26:42.452 [Actor Thread 2] DEBUG n.processor.ParallelTaskProcessor - <buildSampleBWAIndex> Poison pill arrived
  400. Jun-03 14:26:42.452 [Actor Thread 5] DEBUG n.processor.ParallelTaskProcessor - <buildSampleReference> After stop
  401. Jun-03 14:26:42.453 [Actor Thread 10] DEBUG nextflow.processor.StateObj - <buildSampleBWAIndex> State before poison: StateObj[submitted: 2; completed: 0; poisoned: false; allScalar: false]
  402. Jun-03 14:26:42.456 [Actor Thread 6] INFO nextflow.processor.TaskDispatcher - [ac/fb3814] Submitted process > buildSampleBWAIndex (Cen2)
  403. Jun-03 14:26:42.461 [pub-#20%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildSampleBWAIndex (Cen2) - workdir: /bioscratch/tmp/nf-work3/ac/fb38146e0b0550ad74dbdd1beb4d25 - remote: false
  404. Jun-03 14:26:44.675 [pub-#7%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildPrimaryReference (1) - exitStatus: 0
  405. Jun-03 14:26:44.687 [Actor Thread 10] DEBUG nextflow.processor.TaskProcessor - <buildPrimaryReference> Sending poison pills and terminating process
  406. Jun-03 14:26:44.687 [Actor Thread 10] DEBUG nextflow.Session - <<< barrier arrive (process: buildPrimaryReference)
  407. Jun-03 14:26:44.687 [Actor Thread 7] DEBUG n.processor.ParallelTaskProcessor - <buildPrimaryBWAIndex> Poison pill arrived
  408. Jun-03 14:26:44.687 [Actor Thread 6] DEBUG n.processor.ParallelTaskProcessor - <indexPrimaryFasta> Poison pill arrived
  409. Jun-03 14:26:44.688 [Actor Thread 16] DEBUG n.processor.ParallelTaskProcessor - <buildPrimaryReference> After stop
  410. Jun-03 14:26:44.688 [Actor Thread 3] DEBUG n.processor.ParallelTaskProcessor - <makeBlastDB> Poison pill arrived
  411. Jun-03 14:26:44.688 [Actor Thread 10] DEBUG nextflow.processor.StateObj - <buildPrimaryBWAIndex> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
  412. Jun-03 14:26:44.688 [Actor Thread 7] DEBUG n.processor.ParallelTaskProcessor - <computeFastaGCEntropyDensity> Poison pill arrived
  413. Jun-03 14:26:44.688 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <computeFastaGCDensity> Poison pill arrived
  414. Jun-03 14:26:44.688 [Actor Thread 11] DEBUG nextflow.processor.StateObj - <indexPrimaryFasta> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
  415. Jun-03 14:26:44.688 [Actor Thread 12] DEBUG nextflow.processor.StateObj - <computeFastaGCDensity> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
  416. Jun-03 14:26:44.688 [Actor Thread 14] DEBUG nextflow.processor.StateObj - <makeBlastDB> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
  417. Jun-03 14:26:44.689 [Actor Thread 13] DEBUG nextflow.processor.StateObj - <computeFastaGCEntropyDensity> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
  418. Jun-03 14:26:44.695 [Actor Thread 8] INFO nextflow.processor.TaskDispatcher - [fe/ca872b] Submitted process > buildPrimaryBWAIndex (1)
  419. Jun-03 14:26:44.700 [pub-#21%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildPrimaryBWAIndex (1) - workdir: /bioscratch/tmp/nf-work3/fe/ca872bebda213198de8a1a2077b69d - remote: false
  420. Jun-03 14:26:44.701 [Actor Thread 5] INFO nextflow.processor.TaskDispatcher - [68/3ed084] Submitted process > indexPrimaryFasta (1)
  421. Jun-03 14:26:44.704 [Actor Thread 2] INFO nextflow.processor.TaskDispatcher - [45/082bc5] Submitted process > computeFastaGCEntropyDensity (1)
  422. Jun-03 14:26:44.706 [Actor Thread 4] INFO nextflow.processor.TaskDispatcher - [18/446c46] Submitted process > computeFastaGCDensity (1)
  423. Jun-03 14:26:44.710 [pub-#22%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: indexPrimaryFasta (1) - workdir: /bioscratch/tmp/nf-work3/68/3ed0845a06c45c654c08361aa7a939 - remote: false
  424. Jun-03 14:26:44.710 [Actor Thread 17] INFO nextflow.processor.TaskDispatcher - [02/3f3d62] Submitted process > makeBlastDB (1)
  425. Jun-03 14:26:44.721 [pub-#24%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: computeFastaGCDensity (1) - workdir: /bioscratch/tmp/nf-work3/18/446c46fb8e63a2c5ee8dbbe042274c - remote: false
  426. Jun-03 14:26:44.734 [pub-#23%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: computeFastaGCEntropyDensity (1) - workdir: /bioscratch/tmp/nf-work3/45/082bc56d38a576dd2be96ca6299c02 - remote: false
  427. Jun-03 14:26:44.737 [pub-#25%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: makeBlastDB (1) - workdir: /bioscratch/tmp/nf-work3/02/3f3d621f9672e152fb9e30e0abe101 - remote: false
  428. Jun-03 14:26:46.353 [pub-#8%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildPrimaryAnnotation (1) - exitStatus: 0
  429. Jun-03 14:26:46.365 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - <buildPrimaryAnnotation> Sending poison pills and terminating process
  430. Jun-03 14:26:46.365 [Actor Thread 14] DEBUG nextflow.Session - <<< barrier arrive (process: buildPrimaryAnnotation)
  431. Jun-03 14:26:46.365 [Actor Thread 2] DEBUG n.processor.ParallelTaskProcessor - <buildPrimaryAnnotation> After stop
  432. Jun-03 14:26:46.380 [pub-#12%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildSampleAnnotation (Cen9) - exitStatus: 0
  433. Jun-03 14:26:49.274 [pub-#11%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildSampleAnnotation (Cen2) - exitStatus: 0
  434. Jun-03 14:26:49.283 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - <buildSampleAnnotation> Sending poison pills and terminating process
  435. Jun-03 14:26:49.283 [Actor Thread 14] DEBUG nextflow.Session - <<< barrier arrive (process: buildSampleAnnotation)
  436. Jun-03 14:26:49.283 [Actor Thread 2] DEBUG n.processor.ParallelTaskProcessor - <buildSampleAnnotation> After stop
  437. Jun-03 14:26:53.136 [pub-#19%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildSampleBWAIndex (Cen9) - exitStatus: 0
  438. Jun-03 14:26:53.180 [Actor Thread 9] INFO nextflow.processor.TaskDispatcher - [ef/c11c3c] Submitted process > contigsOfInterest (G9-25)
  439. Jun-03 14:26:53.186 [Actor Thread 16] INFO nextflow.processor.TaskDispatcher - [6b/fd8aa8] Submitted process > calculateGenomeSizes (G9-56)
  440. Jun-03 14:26:53.186 [pub-#26%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: contigsOfInterest (G9-25) - workdir: /bioscratch/tmp/nf-work3/ef/c11c3c236ae8750f97ffa6f2e6f6c6 - remote: false
  441. Jun-03 14:26:53.189 [Actor Thread 4] INFO nextflow.processor.TaskDispatcher - [34/04f673] Submitted process > calculateGenomeSizes (G9-25)
  442. Jun-03 14:26:53.191 [Actor Thread 17] INFO nextflow.processor.TaskDispatcher - [95/4839a6] Submitted process > contigsOfInterest (G9-56)
  443. Jun-03 14:26:53.194 [pub-#27%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: calculateGenomeSizes (G9-56) - workdir: /bioscratch/tmp/nf-work3/6b/fd8aa8b33e4790a80622df42474943 - remote: false
  444. Jun-03 14:26:53.195 [pub-#28%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: calculateGenomeSizes (G9-25) - workdir: /bioscratch/tmp/nf-work3/34/04f6735b658608e5752f3e2582b13d - remote: false
  445. Jun-03 14:26:53.196 [pub-#29%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: contigsOfInterest (G9-56) - workdir: /bioscratch/tmp/nf-work3/95/4839a648336f6be1f2577e3cc9c8be - remote: false
  446. Jun-03 14:26:53.200 [Actor Thread 6] INFO nextflow.processor.TaskDispatcher - [18/c91b3a] Submitted process > contigsOfInterest (G9-38)
  447. Jun-03 14:26:53.204 [Actor Thread 3] INFO nextflow.processor.TaskDispatcher - [88/72e18e] Submitted process > calculateGenomeSizes (G9-38)
  448. Jun-03 14:26:53.206 [pub-#30%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: contigsOfInterest (G9-38) - workdir: /bioscratch/tmp/nf-work3/18/c91b3a4dff65c4cb9436bd44cd77ba - remote: false
  449. Jun-03 14:26:53.210 [pub-#31%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: calculateGenomeSizes (G9-38) - workdir: /bioscratch/tmp/nf-work3/88/72e18ede95ac113759bba2b20cb33a - remote: false
  450. Jun-03 14:26:53.226 [Actor Thread 2] INFO nextflow.processor.TaskDispatcher - [8c/f3c011] Submitted process > alignPE (G9-38 - 0)
  451. Jun-03 14:26:53.235 [Actor Thread 7] INFO nextflow.processor.TaskDispatcher - [68/e28e5e] Submitted process > alignPE (G9-25 - 0)
  452. Jun-03 14:26:53.238 [pub-#32%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: alignPE (G9-38 - 0) - workdir: /bioscratch/tmp/nf-work3/8c/f3c01166b2b5f0437260758b25dd48 - remote: false
  453. Jun-03 14:26:53.241 [pub-#33%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: alignPE (G9-25 - 0) - workdir: /bioscratch/tmp/nf-work3/68/e28e5e059cd1eb30924a796665954f - remote: false
  454. Jun-03 14:26:53.263 [Actor Thread 8] INFO nextflow.processor.TaskDispatcher - [d6/187c7c] Submitted process > alignPE (G9-56 - 0)
  455. Jun-03 14:26:53.267 [pub-#34%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: alignPE (G9-56 - 0) - workdir: /bioscratch/tmp/nf-work3/d6/187c7ce6a9e815760771bdd8aa4c80 - remote: false
  456. Jun-03 14:26:54.223 [pub-#20%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildSampleBWAIndex (Cen2) - exitStatus: 0
  457. Jun-03 14:26:54.237 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - <buildSampleBWAIndex> Sending poison pills and terminating process
  458. Jun-03 14:26:54.237 [Actor Thread 14] DEBUG nextflow.Session - <<< barrier arrive (process: buildSampleBWAIndex)
  459. Jun-03 14:26:54.238 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <buildSampleBWAIndex> After stop
  460. Jun-03 14:26:54.240 [Actor Thread 5] DEBUG n.processor.ParallelTaskProcessor - <contigsOfInterest> Poison pill arrived
  461. Jun-03 14:26:54.240 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <alignPacBio> Poison pill arrived
  462. Jun-03 14:26:54.243 [Actor Thread 14] DEBUG nextflow.processor.StateObj - <contigsOfInterest> State before poison: StateObj[submitted: 6; completed: 0; poisoned: false; allScalar: false]
  463. Jun-03 14:26:54.243 [Actor Thread 12] DEBUG nextflow.processor.StateObj - <alignPacBio> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
  464. Jun-03 14:26:54.243 [Actor Thread 8] DEBUG n.processor.ParallelTaskProcessor - <calculateGenomeSizes> Poison pill arrived
  465. Jun-03 14:26:54.243 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <alignPacBio> Sending poison pills and terminating process
  466. Jun-03 14:26:54.245 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: alignPacBio)
  467. Jun-03 14:26:54.245 [Actor Thread 14] DEBUG nextflow.processor.StateObj - <calculateGenomeSizes> State before poison: StateObj[submitted: 6; completed: 0; poisoned: false; allScalar: false]
  468. Jun-03 14:26:54.245 [Actor Thread 8] DEBUG n.processor.ParallelTaskProcessor - <alignPacBio> After stop
  469. Jun-03 14:26:54.246 [Actor Thread 20] DEBUG n.processor.ParallelTaskProcessor - <alignPE> Poison pill arrived
  470. Jun-03 14:26:54.246 [Actor Thread 12] DEBUG nextflow.processor.StateObj - <alignPE> State before poison: StateObj[submitted: 6; completed: 0; poisoned: false; allScalar: false]
  471. Jun-03 14:26:54.250 [Actor Thread 2] INFO nextflow.processor.TaskDispatcher - [1b/4d8c80] Submitted process > contigsOfInterest (G2-23)
  472. Jun-03 14:26:54.253 [Actor Thread 17] INFO nextflow.processor.TaskDispatcher - [62/f409f5] Submitted process > calculateGenomeSizes (G2-23)
  473. Jun-03 14:26:54.256 [Actor Thread 9] INFO nextflow.processor.TaskDispatcher - [1e/6faf85] Submitted process > contigsOfInterest (G2-9)
  474. Jun-03 14:26:54.257 [pub-#35%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: contigsOfInterest (G2-23) - workdir: /bioscratch/tmp/nf-work3/1b/4d8c809e33272cc0c5532d2b0ea165 - remote: false
  475. Jun-03 14:26:54.261 [pub-#36%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: calculateGenomeSizes (G2-23) - workdir: /bioscratch/tmp/nf-work3/62/f409f5ab39447ffe2cac5a962615d0 - remote: false
  476. Jun-03 14:26:54.267 [pub-#38%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: contigsOfInterest (G2-41) - workdir: /bioscratch/tmp/nf-work3/cb/954b1290fabf155ae4ef33b7dff19c - remote: false
  477. Jun-03 14:26:54.277 [Actor Thread 3] INFO nextflow.processor.TaskDispatcher - [5c/896007] Submitted process > calculateGenomeSizes (G2-9)
  478. Jun-03 14:26:54.284 [Actor Thread 18] INFO nextflow.processor.TaskDispatcher - [83/cfae5f] Submitted process > calculateGenomeSizes (G2-41)
  479. Jun-03 14:26:54.288 [Actor Thread 7] INFO nextflow.processor.TaskDispatcher - [cb/954b12] Submitted process > contigsOfInterest (G2-41)
  480. Jun-03 14:26:54.293 [Actor Thread 15] INFO nextflow.processor.TaskDispatcher - [f0/034a77] Submitted process > alignPE (G2-41 - 0)
  481. Jun-03 14:26:54.294 [pub-#37%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: contigsOfInterest (G2-9) - workdir: /bioscratch/tmp/nf-work3/1e/6faf85beaba768ce7db069af66cbc2 - remote: false
  482. Jun-03 14:26:54.296 [Actor Thread 6] INFO nextflow.processor.TaskDispatcher - [ae/62d21b] Submitted process > alignPE (G2-9 - 0)
  483. Jun-03 14:26:54.303 [Actor Thread 19] INFO nextflow.processor.TaskDispatcher - [42/9f04db] Submitted process > alignPE (G2-23 - 0)
  484. Jun-03 14:26:54.907 [pub-#23%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > computeFastaGCEntropyDensity (1) - exitStatus: 0
  485. Jun-03 14:26:54.919 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <computeFastaGCEntropyDensity> Sending poison pills and terminating process
  486. Jun-03 14:26:54.920 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: computeFastaGCEntropyDensity)
  487. Jun-03 14:26:54.920 [Actor Thread 6] DEBUG n.processor.ParallelTaskProcessor - <computeFastaGCEntropyDensity> After stop
  488. Jun-03 14:26:55.036 [pub-#24%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > computeFastaGCDensity (1) - exitStatus: 0
  489. Jun-03 14:26:55.048 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <computeFastaGCDensity> Sending poison pills and terminating process
  490. Jun-03 14:26:55.048 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: computeFastaGCDensity)
  491. Jun-03 14:26:55.048 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <computeFastaGCDensity> After stop
  492. Jun-03 14:26:55.051 [pub-#39%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: calculateGenomeSizes (G2-9) - workdir: /bioscratch/tmp/nf-work3/5c/896007bd9fc1294801acf51cf89b51 - remote: false
  493. Jun-03 14:26:56.512 [pub-#40%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: calculateGenomeSizes (G2-41) - workdir: /bioscratch/tmp/nf-work3/83/cfae5f9ea7fb5727a3687f059cfb95 - remote: false
  494. Jun-03 14:27:07.352 [pub-#30%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > contigsOfInterest (G9-38) - exitStatus: 0
  495. Jun-03 14:27:07.496 [pub-#29%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > contigsOfInterest (G9-56) - exitStatus: 0
  496. Jun-03 14:27:07.511 [pub-#41%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: alignPE (G2-41 - 0) - workdir: /bioscratch/tmp/nf-work3/f0/034a773cb3af75bae0b734f59e07d1 - remote: false
  497. Jun-03 14:27:08.557 [pub-#42%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: alignPE (G2-9 - 0) - workdir: /bioscratch/tmp/nf-work3/ae/62d21bd63c1a8e1ea959a3dfc2956c - remote: false
  498. Jun-03 14:27:10.404 [pub-#26%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > contigsOfInterest (G9-25) - exitStatus: 0
  499. Jun-03 14:27:10.594 [pub-#43%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: alignPE (G2-23 - 0) - workdir: /bioscratch/tmp/nf-work3/42/9f04dbff8060eba882b8c037a35678 - remote: false
  500. Jun-03 14:27:17.911 [pub-#22%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > indexPrimaryFasta (1) - exitStatus: 0
  501. Jun-03 14:27:17.934 [pub-#21%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildPrimaryBWAIndex (1) - exitStatus: 0
  502. Jun-03 14:27:17.938 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <indexPrimaryFasta> Sending poison pills and terminating process
  503. Jun-03 14:27:17.938 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: indexPrimaryFasta)
  504. Jun-03 14:27:17.938 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <indexPrimaryFasta> After stop
  505. Jun-03 14:27:17.938 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <buildSNPEffConfig> Poison pill arrived
  506. Jun-03 14:27:17.939 [Actor Thread 12] DEBUG nextflow.processor.StateObj - <buildSNPEffConfig> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
  507. Jun-03 14:27:17.975 [Actor Thread 23] INFO nextflow.processor.TaskDispatcher - [88/f9b442] Submitted process > buildSNPEffConfig (1)
  508. Jun-03 14:27:17.983 [pub-#44%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildSNPEffConfig (1) - workdir: /bioscratch/tmp/nf-work3/88/f9b44276b09718b7f2d32fcaa199cb - remote: false
  509. Jun-03 14:27:22.937 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <buildPrimaryBWAIndex> Sending poison pills and terminating process
  510. Jun-03 14:27:22.937 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: buildPrimaryBWAIndex)
  511. Jun-03 14:27:22.938 [Actor Thread 23] DEBUG n.processor.ParallelTaskProcessor - <buildPrimaryBWAIndex> After stop
  512. Jun-03 14:27:31.678 [pub-#18%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > runKraken (G2-9 - 0) - exitStatus: 0
  513. Jun-03 14:27:38.842 [grid-timeout-worker-#97%nextflow%] INFO o.a.i.internal.IgniteKernal%nextflow -
  514. Metrics for local node (to disable set 'metricsLogFrequency' to 0)
  515. ^-- Node [id=d0b68d67, name=nextflow]
  516. ^-- H/N/C [hosts=1, nodes=1, CPUs=24]
  517. ^-- CPU [cur=0.17%, avg=0.37%, GC=0%]
  518. ^-- Heap [used=501MB, free=98.16%, comm=2201MB]
  519. ^-- Public thread pool [active=22, idle=26, qSize=0]
  520. ^-- System thread pool [active=0, idle=48, qSize=0]
  521. ^-- Outbound messages queue [size=0]
  522. Jun-03 14:27:39.483 [pub-#13%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > runKraken (G2-41 - 0) - exitStatus: 0
  523. Jun-03 14:27:41.150 [pub-#25%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > makeBlastDB (1) - exitStatus: 0
  524. Jun-03 14:27:41.166 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <makeBlastDB> Sending poison pills and terminating process
  525. Jun-03 14:27:41.167 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: makeBlastDB)
  526. Jun-03 14:27:41.167 [Actor Thread 25] DEBUG n.processor.ParallelTaskProcessor - <makeBlastDB> After stop
  527. Jun-03 14:27:49.154 [pub-#35%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > contigsOfInterest (G2-23) - exitStatus: 0
  528. Jun-03 14:27:49.261 [pub-#17%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > runKraken (G9-25 - 0) - exitStatus: 0
  529. Jun-03 14:27:49.445 [pub-#14%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > runKraken (G9-56 - 0) - exitStatus: 0
  530. Jun-03 14:27:49.534 [pub-#16%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > runKraken (G9-38 - 0) - exitStatus: 0
  531. Jun-03 14:27:50.055 [pub-#38%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > contigsOfInterest (G2-41) - exitStatus: 0
  532. Jun-03 14:27:59.114 [pub-#37%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > contigsOfInterest (G2-9) - exitStatus: 0
  533. Jun-03 14:27:59.125 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <contigsOfInterest> Sending poison pills and terminating process
  534. Jun-03 14:27:59.125 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: contigsOfInterest)
  535. Jun-03 14:27:59.126 [Actor Thread 28] DEBUG n.processor.ParallelTaskProcessor - <contigsOfInterest> After stop
  536. Jun-03 14:28:02.218 [pub-#15%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > runKraken (G2-23 - 0) - exitStatus: 0
  537. Jun-03 14:28:02.227 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <runKraken> Sending poison pills and terminating process
  538. Jun-03 14:28:02.227 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: runKraken)
  539. Jun-03 14:28:02.227 [Actor Thread 26] DEBUG n.processor.ParallelTaskProcessor - <runKraken> After stop
  540. Jun-03 14:28:02.245 [Actor Thread 26] INFO nextflow.processor.TaskDispatcher - [6d/1d0ba2] Submitted process > buildContaminationRDataImage (1)
  541. Jun-03 14:28:02.251 [pub-#45%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildContaminationRDataImage (1) - workdir: /bioscratch/tmp/nf-work3/6d/1d0ba2495e96d3c256a1673b7eb7af - remote: false
  542. Jun-03 14:28:34.976 [pub-#28%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > calculateGenomeSizes (G9-25) - exitStatus: 0
  543. Jun-03 14:28:36.604 [pub-#27%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > calculateGenomeSizes (G9-56) - exitStatus: 0
  544. Jun-03 14:28:38.848 [grid-timeout-worker-#97%nextflow%] INFO o.a.i.internal.IgniteKernal%nextflow -
  545. Metrics for local node (to disable set 'metricsLogFrequency' to 0)
  546. ^-- Node [id=d0b68d67, name=nextflow]
  547. ^-- H/N/C [hosts=1, nodes=1, CPUs=24]
  548. ^-- CPU [cur=0.07%, avg=0.23%, GC=0%]
  549. ^-- Heap [used=522MB, free=98.09%, comm=2201MB]
  550. ^-- Public thread pool [active=12, idle=36, qSize=0]
  551. ^-- System thread pool [active=0, idle=48, qSize=0]
  552. ^-- Outbound messages queue [size=0]
  553. Jun-03 14:28:59.953 [pub-#44%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > buildSNPEffConfig (1) - exitStatus: 0
  554. Jun-03 14:28:59.966 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - <buildSNPEffConfig> Sending poison pills and terminating process
  555. Jun-03 14:28:59.967 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: buildSNPEffConfig)
  556. Jun-03 14:28:59.967 [Actor Thread 30] DEBUG n.processor.ParallelTaskProcessor - <buildSNPEffDb> Poison pill arrived
  557. Jun-03 14:28:59.968 [Actor Thread 32] DEBUG n.processor.ParallelTaskProcessor - <buildSNPEffConfig> After stop
  558. Jun-03 14:28:59.968 [Actor Thread 30] DEBUG n.processor.ParallelTaskProcessor - <buildSNPEffDb> Poison pill arrived
  559. Jun-03 14:28:59.969 [Actor Thread 31] DEBUG nextflow.processor.StateObj - <buildSNPEffDb> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
  560. Jun-03 14:28:59.969 [Actor Thread 31] DEBUG nextflow.processor.StateObj - <buildSNPEffDb> State before poison: StateObj[submitted: 1; completed: 0; poisoned: true; allScalar: false]
  561. Jun-03 14:28:59.982 [Actor Thread 33] INFO nextflow.processor.TaskDispatcher - [b4/92aabc] Submitted process > buildSNPEffDb (1)
  562. Jun-03 14:29:00.010 [pub-#46%nextflow%] DEBUG nextflow.executor.IgScriptTask - Running task > name: buildSNPEffDb (1) - workdir: /bioscratch/tmp/nf-work3/b4/92aabcc38f0d03abda2a8db62f1e10 - remote: false
  563. Jun-03 14:29:00.019 [pub-#34%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > alignPE (G9-56 - 0) - exitStatus: 0
  564. Jun-03 14:29:00.881 [pub-#31%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > calculateGenomeSizes (G9-38) - exitStatus: 0
  565. Jun-03 14:29:01.825 [pub-#33%nextflow%] DEBUG nextflow.executor.IgScriptTask - Completed task > alignPE (G9-25 - 0) - exitStatus: 0
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