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  1. Oct-27 12:26:48.917 [main] DEBUG nextflow.cli.Launcher - $> nextflow run 2_cache_main.nf -profile charlie -dump-hashes
  2. Oct-27 12:26:49.260 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.3
  3. Oct-27 12:26:49.334 [main] INFO nextflow.cli.CmdRun - Launching `2_cache_main.nf` [curious_pasteur] - revision: 5026b4ae70
  4. Oct-27 12:26:49.373 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/nextflow.config
  5. Oct-27 12:26:49.375 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/nextflow.config
  6. Oct-27 12:26:49.429 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `charlie`
  7. Oct-27 12:26:51.454 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [charlie]
  8. Oct-27 12:26:51.499 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/ggavelis/.nextflow/plugins
  9. Oct-27 12:26:51.501 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
  10. Oct-27 12:26:51.511 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/21921f6807262d1f701978cdf8a1f5c4
  11. Oct-27 12:26:51.528 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
  12. Oct-27 12:26:51.529 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
  13. Oct-27 12:26:51.537 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
  14. Oct-27 12:26:51.565 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.1.0' resolved
  15. Oct-27 12:26:51.581 [main] DEBUG nextflow.plugin.PluginUpdater - Starting plugin nf-tower version: 1.1.0
  16. Oct-27 12:26:51.581 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.1.0'
  17. Oct-27 12:26:51.593 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.1.0
  18. Oct-27 12:26:51.890 [main] DEBUG nextflow.Session - Session uuid: 54be4534-56c1-4680-a355-a511b37fb1f3
  19. Oct-27 12:26:51.890 [main] DEBUG nextflow.Session - Run name: curious_pasteur
  20. Oct-27 12:26:51.890 [main] DEBUG nextflow.Session - Executor pool size: 4
  21. Oct-27 12:26:51.907 [main] DEBUG nextflow.cli.CmdRun -
  22. Version: 21.04.3 build 5560
  23. Created: 21-07-2021 15:09 UTC (11:09 EDT)
  24. System: Linux 3.10.0-1062.9.1.el7.x86_64
  25. Runtime: Groovy 3.0.7 on Java HotSpot(TM) Server VM 1.8.0_73-b02
  26. Encoding: UTF-8 (UTF-8)
  27. Process: 11850@cfe1 [10.2.1.41]
  28. CPUs: 4 - Mem: 7.6 GB (1 GB) - Swap: 2 GB (700 KB)
  29. Oct-27 12:26:51.956 [main] DEBUG nextflow.Session - Work-dir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work [nfs]
  30. Oct-27 12:26:51.957 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/bin
  31. Oct-27 12:26:51.997 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
  32. Oct-27 12:26:52.034 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
  33. Oct-27 12:26:52.042 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
  34. Oct-27 12:26:52.473 [main] DEBUG nextflow.Session - Session start invoked
  35. Oct-27 12:26:52.500 [main] DEBUG io.seqera.tower.plugin.TowerClient - Creating Tower observer -- endpoint=https://api.tower.nf; requestInterval=1s; aliveInterval=1m; maxRetries=5; backOffBase=3; backOffDelay=250
  36. Oct-27 12:26:54.508 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
  37. Oct-27 12:26:54.797 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: trimmomatic, fastqc, bbmerge
  38. Oct-27 12:26:54.956 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:fastqc` matches process fastqc
  39. Oct-27 12:26:54.969 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
  40. Oct-27 12:26:54.969 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
  41. Oct-27 12:26:54.988 [main] DEBUG nextflow.executor.Executor - [warm up] executor > pbspro
  42. Oct-27 12:26:54.995 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'pbspro' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
  43. Oct-27 12:26:55.000 [main] DEBUG n.processor.TaskPollingMonitor - Creating submit rate limit of 10 reqs by 1 seconds
  44. Oct-27 12:26:55.005 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbspro' > queue-stat-interval: 1m
  45. Oct-27 12:26:55.137 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:trimmomatic` matches process trimmomatic
  46. Oct-27 12:26:55.139 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
  47. Oct-27 12:26:55.139 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
  48. Oct-27 12:26:55.149 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:bbmerge` matches process bbmerge
  49. Oct-27 12:26:55.150 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
  50. Oct-27 12:26:55.150 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
  51. Oct-27 12:26:55.347 [main] INFO io.seqera.tower.plugin.TowerClient - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/3kuXmyGcQCxd8R
  52. Oct-27 12:26:55.350 [main] DEBUG nextflow.Session - Ignite dataflow network (4)
  53. Oct-27 12:26:55.368 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/; pattern: *02_subseq_R{1,2}.fastq.gz; options: [:]
  54. Oct-27 12:26:55.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastqc
  55. Oct-27 12:26:55.371 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > trimmomatic
  56. Oct-27 12:26:55.380 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > bbmerge
  57. Oct-27 12:26:55.380 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
  58. Oct-27 12:26:55.380 [main] DEBUG nextflow.Session - Session await
  59. Oct-27 12:26:55.582 [Actor Thread 6] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1; path=/mnt/scgc_nfs/containers/quay.io-biocontainers-fastqc-0.11.9--hdfd78af_1.img
  60. Oct-27 12:26:55.638 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [fastqc (FASTQC on AH-847-L)] cache hash: e8ce11b03a775c6ffffbc846048203d0; mode: LENIENT; entries:
  61. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  62. 23037893fdd4cef8d4acc5fe82ba1899 [java.lang.String] fastqc
  63. b69439d7f1c9d288f31b7edb83c6985a [java.lang.String] '''
  64. mkdir fastqc_!{sample_id}
  65. fastqc -o fastqc_!{sample_id} -f fastq -q !{reads}
  66. '''
  67.  
  68. 6be004ee9200372fc35619907d08a423 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-fastqc-0.11.9--hdfd78af_1.img
  69. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  70. 27b9c36ff1c3c875fd0a95c97db6ec96 [java.lang.String] AH-847-L
  71. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  72. 4d0d666fa49288036b195bc44287ad65 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-L02_subseq_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-L02_subseq_R1.fastq.gz, stageName:AH-847-L02_subseq_R1.fastq.gz), FileHolder(sourceObj:/mnt/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-L02_subseq_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-L02_subseq_R2.fastq.gz, stageName:AH-847-L02_subseq_R2.fastq.gz)]
  73. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  74. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  75. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  76.  
  77. Oct-27 12:26:55.655 [Actor Thread 1] INFO nextflow.processor.TaskProcessor - [fastqc (FASTQC on AH-847-D)] cache hash: 6ef7564a2531d8ba61e32c1b578b1b88; mode: LENIENT; entries:
  78. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  79. 23037893fdd4cef8d4acc5fe82ba1899 [java.lang.String] fastqc
  80. b69439d7f1c9d288f31b7edb83c6985a [java.lang.String] '''
  81. mkdir fastqc_!{sample_id}
  82. fastqc -o fastqc_!{sample_id} -f fastq -q !{reads}
  83. '''
  84.  
  85. 6be004ee9200372fc35619907d08a423 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-fastqc-0.11.9--hdfd78af_1.img
  86. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  87. 7fff979f0f94ce67d4b135d93e8ce8cc [java.lang.String] AH-847-D
  88. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  89. 4d386428b876f9a98d6ffeda507e9315 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-D02_subseq_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-D02_subseq_R1.fastq.gz, stageName:AH-847-D02_subseq_R1.fastq.gz), FileHolder(sourceObj:/mnt/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-D02_subseq_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-D02_subseq_R2.fastq.gz, stageName:AH-847-D02_subseq_R2.fastq.gz)]
  90. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  91. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  92. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  93.  
  94. Oct-27 12:26:55.663 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [fastqc (FASTQC on AH-847-C)] cache hash: f786147ee48887f6100faf608beafb91; mode: LENIENT; entries:
  95. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  96. 23037893fdd4cef8d4acc5fe82ba1899 [java.lang.String] fastqc
  97. b69439d7f1c9d288f31b7edb83c6985a [java.lang.String] '''
  98. mkdir fastqc_!{sample_id}
  99. fastqc -o fastqc_!{sample_id} -f fastq -q !{reads}
  100. '''
  101.  
  102. 6be004ee9200372fc35619907d08a423 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-fastqc-0.11.9--hdfd78af_1.img
  103. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  104. d6605b4a6bd1a0e61b59db8b86ecc713 [java.lang.String] AH-847-C
  105. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  106. 949f5ba0a0c6d736ab5f61c9516e17bb [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-C02_subseq_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-C02_subseq_R1.fastq.gz, stageName:AH-847-C02_subseq_R1.fastq.gz), FileHolder(sourceObj:/mnt/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-C02_subseq_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-C02_subseq_R2.fastq.gz, stageName:AH-847-C02_subseq_R2.fastq.gz)]
  107. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  108. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  109. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  110.  
  111. Oct-27 12:26:55.843 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [e5/7ce398] Cached process > fastqc (FASTQC on AH-847-L)
  112. Oct-27 12:26:55.846 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [c6/c42a40] Cached process > fastqc (FASTQC on AH-847-C)
  113. Oct-27 12:26:55.848 [Actor Thread 1] INFO nextflow.processor.TaskProcessor - [c2/5c9f48] Cached process > fastqc (FASTQC on AH-847-D)
  114. Oct-27 12:26:55.952 [Actor Thread 1] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://quay.io/biocontainers/trimmomatic:0.32--hdfd78af_4; path=/mnt/scgc_nfs/containers/quay.io-biocontainers-trimmomatic-0.32--hdfd78af_4.img
  115. Oct-27 12:26:55.965 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [trimmomatic (TRIMMOMATIC on AH-847-D)] cache hash: fa858092327bac8939b6716c3ee76128; mode: LENIENT; entries:
  116. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  117. 87fa86fc60107e6a421ff93ad5d42064 [java.lang.String] trimmomatic
  118. d003529244513f5a86e2088a109bf8c2 [java.lang.String] '''
  119. trimmomatic \
  120. PE \
  121. -phred33 \
  122. -threads !{task.cpus} \
  123. !{reads} \
  124. !{sample_id}_trimmed_R1.fastq.gz \
  125. !{sample_id}_orphan_R1.fastq.gz \
  126. !{sample_id}_trimmed_R2.fastq.gz \
  127. !{sample_id}_orphan_R2.fastq.gz \
  128. LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
  129.  
  130. '''
  131.  
  132. 242b8faf69f88989b8d685442210a97e [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-trimmomatic-0.32--hdfd78af_4.img
  133. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  134. 7fff979f0f94ce67d4b135d93e8ce8cc [java.lang.String] AH-847-D
  135. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  136. 22db743f7be48d6885bb0840b15aae4b [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c2/5c9f48e802e9dae31d5a1bedbc6485/AH-847-D02_subseq_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-D02_subseq_R1.fastq.gz, stageName:AH-847-D02_subseq_R1.fastq.gz), FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c2/5c9f48e802e9dae31d5a1bedbc6485/AH-847-D02_subseq_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-D02_subseq_R2.fastq.gz, stageName:AH-847-D02_subseq_R2.fastq.gz)]
  137. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  138. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  139. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  140.  
  141. Oct-27 12:26:55.977 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [92/6ebb98] Cached process > trimmomatic (TRIMMOMATIC on AH-847-D)
  142. Oct-27 12:26:55.981 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [trimmomatic (TRIMMOMATIC on AH-847-C)] cache hash: fb9937382f140bffd10cecab962c3ae6; mode: LENIENT; entries:
  143. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  144. 87fa86fc60107e6a421ff93ad5d42064 [java.lang.String] trimmomatic
  145. d003529244513f5a86e2088a109bf8c2 [java.lang.String] '''
  146. trimmomatic \
  147. PE \
  148. -phred33 \
  149. -threads !{task.cpus} \
  150. !{reads} \
  151. !{sample_id}_trimmed_R1.fastq.gz \
  152. !{sample_id}_orphan_R1.fastq.gz \
  153. !{sample_id}_trimmed_R2.fastq.gz \
  154. !{sample_id}_orphan_R2.fastq.gz \
  155. LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
  156.  
  157. '''
  158.  
  159. 242b8faf69f88989b8d685442210a97e [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-trimmomatic-0.32--hdfd78af_4.img
  160. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  161. d6605b4a6bd1a0e61b59db8b86ecc713 [java.lang.String] AH-847-C
  162. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  163. 76b1bb6924427f97157e0e27a5b00dbb [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c6/c42a40801e4bff9272751286f75e10/AH-847-C02_subseq_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-C02_subseq_R1.fastq.gz, stageName:AH-847-C02_subseq_R1.fastq.gz), FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c6/c42a40801e4bff9272751286f75e10/AH-847-C02_subseq_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-C02_subseq_R2.fastq.gz, stageName:AH-847-C02_subseq_R2.fastq.gz)]
  164. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  165. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  166. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  167.  
  168. Oct-27 12:26:55.981 [Actor Thread 9] INFO nextflow.processor.TaskProcessor - [trimmomatic (TRIMMOMATIC on AH-847-L)] cache hash: 1a926ece4b978f84b5303ba757b53bcb; mode: LENIENT; entries:
  169. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  170. 87fa86fc60107e6a421ff93ad5d42064 [java.lang.String] trimmomatic
  171. d003529244513f5a86e2088a109bf8c2 [java.lang.String] '''
  172. trimmomatic \
  173. PE \
  174. -phred33 \
  175. -threads !{task.cpus} \
  176. !{reads} \
  177. !{sample_id}_trimmed_R1.fastq.gz \
  178. !{sample_id}_orphan_R1.fastq.gz \
  179. !{sample_id}_trimmed_R2.fastq.gz \
  180. !{sample_id}_orphan_R2.fastq.gz \
  181. LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
  182.  
  183. '''
  184.  
  185. 242b8faf69f88989b8d685442210a97e [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-trimmomatic-0.32--hdfd78af_4.img
  186. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  187. 27b9c36ff1c3c875fd0a95c97db6ec96 [java.lang.String] AH-847-L
  188. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  189. c0c1b7f48214b881300d4c212397ab01 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/e5/7ce398ec539da1beba30a410de7ec3/AH-847-L02_subseq_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-L02_subseq_R1.fastq.gz, stageName:AH-847-L02_subseq_R1.fastq.gz), FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/e5/7ce398ec539da1beba30a410de7ec3/AH-847-L02_subseq_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/sample_data/smallest_subset/AH-847-L02_subseq_R2.fastq.gz, stageName:AH-847-L02_subseq_R2.fastq.gz)]
  190. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  191. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  192. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  193.  
  194. Oct-27 12:26:55.995 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [63/fbf46b] Cached process > trimmomatic (TRIMMOMATIC on AH-847-C)
  195. Oct-27 12:26:56.002 [Actor Thread 9] INFO nextflow.processor.TaskProcessor - [d0/737d25] Cached process > trimmomatic (TRIMMOMATIC on AH-847-L)
  196. Oct-27 12:26:56.039 [Actor Thread 2] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://quay.io/biocontainers/bbmap:38.90--he522d1c_3; path=/mnt/scgc_nfs/containers/quay.io-biocontainers-bbmap-38.90--he522d1c_3.img
  197. Oct-27 12:26:56.056 [Actor Thread 1] INFO nextflow.processor.TaskProcessor - [bbmerge (MERGING on AH-847-D)] cache hash: e7539a632e1cf91b97b9ce6922ffd64e; mode: LENIENT; entries:
  198. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  199. 32b35978c0e945d35b9517e471531a43 [java.lang.String] bbmerge
  200. ac6a8e72f7200e7195858d7ce9672180 [java.lang.String] '''
  201. reformat.sh in1=!{trimmed_R1_paired} in2=!{trimmed_R2_paired} out=!{sample_id}_merged.fastq
  202. '''
  203.  
  204. 5632241bf34f0acad52a76595c250798 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-bbmap-38.90--he522d1c_3.img
  205. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  206. 7fff979f0f94ce67d4b135d93e8ce8cc [java.lang.String] AH-847-D
  207. dc8c1aa13de7a405386d52144e08bb54 [java.lang.String] trimmed_R1_paired
  208. 94fc8996dac2a0fcf366580009e5c2f2 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/d0/737d25453727a3363bf9ef8b3dba3b/AH-847-L_trimmed_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/d0/737d25453727a3363bf9ef8b3dba3b/AH-847-L_trimmed_R1.fastq.gz, stageName:AH-847-L_trimmed_R1.fastq.gz)]
  209. fb235e59786e747b345ebb94cba36e73 [java.lang.String] trimmed_R2_paired
  210. 25f4374348e1ac05fce2dddec0c9b6d6 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/d0/737d25453727a3363bf9ef8b3dba3b/AH-847-L_trimmed_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/d0/737d25453727a3363bf9ef8b3dba3b/AH-847-L_trimmed_R2.fastq.gz, stageName:AH-847-L_trimmed_R2.fastq.gz)]
  211. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  212. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  213. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  214.  
  215. Oct-27 12:26:56.059 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [bbmerge (MERGING on AH-847-L)] cache hash: a686d714fe9c6318b7d9b24789c01615; mode: LENIENT; entries:
  216. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  217. 32b35978c0e945d35b9517e471531a43 [java.lang.String] bbmerge
  218. ac6a8e72f7200e7195858d7ce9672180 [java.lang.String] '''
  219. reformat.sh in1=!{trimmed_R1_paired} in2=!{trimmed_R2_paired} out=!{sample_id}_merged.fastq
  220. '''
  221.  
  222. 5632241bf34f0acad52a76595c250798 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-bbmap-38.90--he522d1c_3.img
  223. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  224. 27b9c36ff1c3c875fd0a95c97db6ec96 [java.lang.String] AH-847-L
  225. dc8c1aa13de7a405386d52144e08bb54 [java.lang.String] trimmed_R1_paired
  226. 9d8d1cc26cc46f441c08203f2aeb13ab [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/63/fbf46b73d7fae2aea7e601b72a8a73/AH-847-C_trimmed_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/63/fbf46b73d7fae2aea7e601b72a8a73/AH-847-C_trimmed_R1.fastq.gz, stageName:AH-847-C_trimmed_R1.fastq.gz)]
  227. fb235e59786e747b345ebb94cba36e73 [java.lang.String] trimmed_R2_paired
  228. 9a5bff8efb92ff77857c39a12121bacc [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/63/fbf46b73d7fae2aea7e601b72a8a73/AH-847-C_trimmed_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/63/fbf46b73d7fae2aea7e601b72a8a73/AH-847-C_trimmed_R2.fastq.gz, stageName:AH-847-C_trimmed_R2.fastq.gz)]
  229. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  230. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  231. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  232.  
  233. Oct-27 12:26:56.066 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [bbmerge (MERGING on AH-847-C)] cache hash: fedcaeceb20bfa3e7e541f78686d48fe; mode: LENIENT; entries:
  234. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  235. 32b35978c0e945d35b9517e471531a43 [java.lang.String] bbmerge
  236. ac6a8e72f7200e7195858d7ce9672180 [java.lang.String] '''
  237. reformat.sh in1=!{trimmed_R1_paired} in2=!{trimmed_R2_paired} out=!{sample_id}_merged.fastq
  238. '''
  239.  
  240. 5632241bf34f0acad52a76595c250798 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-bbmap-38.90--he522d1c_3.img
  241. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  242. d6605b4a6bd1a0e61b59db8b86ecc713 [java.lang.String] AH-847-C
  243. dc8c1aa13de7a405386d52144e08bb54 [java.lang.String] trimmed_R1_paired
  244. 318f814f5a001b51b9567188e693449e [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/92/6ebb982f34b1a56bbaeac1b462a5b9/AH-847-D_trimmed_R1.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/92/6ebb982f34b1a56bbaeac1b462a5b9/AH-847-D_trimmed_R1.fastq.gz, stageName:AH-847-D_trimmed_R1.fastq.gz)]
  245. fb235e59786e747b345ebb94cba36e73 [java.lang.String] trimmed_R2_paired
  246. b4c1ed2959917236ac8a2a8b442e9cd7 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/92/6ebb982f34b1a56bbaeac1b462a5b9/AH-847-D_trimmed_R2.fastq.gz, storePath:/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/92/6ebb982f34b1a56bbaeac1b462a5b9/AH-847-D_trimmed_R2.fastq.gz, stageName:AH-847-D_trimmed_R2.fastq.gz)]
  247. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  248. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  249. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  250.  
  251. Oct-27 12:26:56.199 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process bbmerge (MERGING on AH-847-C) > jobId: 570585.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c6/94eca8cdcd9baf42096d44e4ce1967
  252. Oct-27 12:26:56.204 [Task submitter] INFO nextflow.Session - [c6/94eca8] Submitted process > bbmerge (MERGING on AH-847-C)
  253. Oct-27 12:26:56.252 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process bbmerge (MERGING on AH-847-D) > jobId: 570586.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/e9/8bf6b8d7bb718f595a0a04862436a5
  254. Oct-27 12:26:56.252 [Task submitter] INFO nextflow.Session - [e9/8bf6b8] Submitted process > bbmerge (MERGING on AH-847-D)
  255. Oct-27 12:26:56.274 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process bbmerge (MERGING on AH-847-L) > jobId: 570587.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/7a/d8fb625a789e8fc1942cd139459cab
  256. Oct-27 12:26:56.275 [Task submitter] INFO nextflow.Session - [7a/d8fb62] Submitted process > bbmerge (MERGING on AH-847-L)
  257. Oct-27 12:27:00.039 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570585.cfe1; id: 7; name: bbmerge (MERGING on AH-847-C); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c6/94eca8cdcd9baf42096d44e4ce1967 started: 1635352020027; exited: 2021-10-27T16:26:57Z; ]
  258. Oct-27 12:27:00.083 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570586.cfe1; id: 9; name: bbmerge (MERGING on AH-847-D); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/e9/8bf6b8d7bb718f595a0a04862436a5 started: 1635352020058; exited: 2021-10-27T16:26:57Z; ]
  259. Oct-27 12:27:00.107 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570587.cfe1; id: 8; name: bbmerge (MERGING on AH-847-L); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/7a/d8fb625a789e8fc1942cd139459cab started: 1635352020094; exited: 2021-10-27T16:26:57Z; ]
  260. Oct-27 12:27:00.114 [main] DEBUG nextflow.Session - Session await > all process finished
  261. Oct-27 12:27:00.116 [main] DEBUG nextflow.Session - Session await > all barriers passed
  262. Oct-27 12:27:00.139 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=3; failedCount=0; ignoredCount=0; cachedCount=6; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=12s; failedDuration=0ms; cachedDuration=14s;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=4; peakMemory=0; ]
  263. Oct-27 12:27:00.753 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
  264. Oct-27 12:27:00.753 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.1.0'
  265. Oct-27 12:27:00.753 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
  266. Oct-27 12:27:01.384 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
  267.  
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