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  1. Oct-27 12:26:14.702 [main] DEBUG nextflow.cli.Launcher - $> nextflow run 2_cache_main.nf -profile charlie -dump-hashes
  2. Oct-27 12:26:14.831 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.3
  3. Oct-27 12:26:14.874 [main] INFO nextflow.cli.CmdRun - Launching `2_cache_main.nf` [gigantic_banach] - revision: 5026b4ae70
  4. Oct-27 12:26:14.895 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/nextflow.config
  5. Oct-27 12:26:14.896 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/nextflow.config
  6. Oct-27 12:26:14.926 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `charlie`
  7. Oct-27 12:26:16.307 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [charlie]
  8. Oct-27 12:26:16.322 [main] WARN nextflow.config.ConfigBuilder - It appears you have never run this project before -- Option `-resume` is ignored
  9. Oct-27 12:26:16.352 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/ggavelis/.nextflow/plugins
  10. Oct-27 12:26:16.354 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
  11. Oct-27 12:26:16.363 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/21921f6807262d1f701978cdf8a1f5c4
  12. Oct-27 12:26:16.383 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
  13. Oct-27 12:26:16.385 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
  14. Oct-27 12:26:16.392 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
  15. Oct-27 12:26:16.410 [main] INFO org.pf4j.AbstractPluginManager - No plugins
  16. Oct-27 12:26:16.410 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.1.0
  17. Oct-27 12:26:16.420 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.1.0' resolved
  18. Oct-27 12:26:16.421 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.1.0'
  19. Oct-27 12:26:16.434 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.1.0
  20. Oct-27 12:26:16.670 [main] DEBUG nextflow.Session - Session uuid: 54be4534-56c1-4680-a355-a511b37fb1f3
  21. Oct-27 12:26:16.670 [main] DEBUG nextflow.Session - Run name: gigantic_banach
  22. Oct-27 12:26:16.671 [main] DEBUG nextflow.Session - Executor pool size: 4
  23. Oct-27 12:26:16.689 [main] DEBUG nextflow.cli.CmdRun -
  24. Version: 21.04.3 build 5560
  25. Created: 21-07-2021 15:09 UTC (11:09 EDT)
  26. System: Linux 3.10.0-1062.9.1.el7.x86_64
  27. Runtime: Groovy 3.0.7 on Java HotSpot(TM) Server VM 1.8.0_73-b02
  28. Encoding: UTF-8 (UTF-8)
  29. Process: 11503@cfe1 [10.2.1.41]
  30. CPUs: 4 - Mem: 7.6 GB (1 GB) - Swap: 2 GB (700 KB)
  31. Oct-27 12:26:16.727 [main] DEBUG nextflow.Session - Work-dir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work [nfs]
  32. Oct-27 12:26:16.728 [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
  33. Oct-27 12:26:16.743 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
  34. Oct-27 12:26:16.759 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
  35. Oct-27 12:26:16.762 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
  36. Oct-27 12:26:16.948 [main] DEBUG nextflow.Session - Session start invoked
  37. Oct-27 12:26:16.962 [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
  38. Oct-27 12:26:18.715 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
  39. Oct-27 12:26:19.080 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: trimmomatic, fastqc, bbmerge
  40. Oct-27 12:26:19.236 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:fastqc` matches process fastqc
  41. Oct-27 12:26:19.258 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
  42. Oct-27 12:26:19.258 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
  43. Oct-27 12:26:19.277 [main] DEBUG nextflow.executor.Executor - [warm up] executor > pbspro
  44. Oct-27 12:26:19.284 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'pbspro' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
  45. Oct-27 12:26:19.290 [main] DEBUG n.processor.TaskPollingMonitor - Creating submit rate limit of 10 reqs by 1 seconds
  46. Oct-27 12:26:19.297 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbspro' > queue-stat-interval: 1m
  47. Oct-27 12:26:19.445 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:trimmomatic` matches process trimmomatic
  48. Oct-27 12:26:19.447 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
  49. Oct-27 12:26:19.447 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
  50. Oct-27 12:26:19.456 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:bbmerge` matches process bbmerge
  51. Oct-27 12:26:19.457 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
  52. Oct-27 12:26:19.457 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
  53. Oct-27 12:26:19.672 [main] INFO io.seqera.tower.plugin.TowerClient - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/2Cj1Uenk1QvSzx
  54. Oct-27 12:26:19.677 [main] DEBUG nextflow.Session - Ignite dataflow network (4)
  55. Oct-27 12:26:19.697 [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: [:]
  56. Oct-27 12:26:19.698 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastqc
  57. Oct-27 12:26:19.710 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > trimmomatic
  58. Oct-27 12:26:19.712 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > bbmerge
  59. Oct-27 12:26:19.713 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
  60. Oct-27 12:26:19.713 [main] DEBUG nextflow.Session - Session await
  61. Oct-27 12:26:20.090 [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
  62. Oct-27 12:26:20.202 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [fastqc (FASTQC on AH-847-C)] cache hash: f786147ee48887f6100faf608beafb91; mode: LENIENT; entries:
  63. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  64. 23037893fdd4cef8d4acc5fe82ba1899 [java.lang.String] fastqc
  65. b69439d7f1c9d288f31b7edb83c6985a [java.lang.String] '''
  66. mkdir fastqc_!{sample_id}
  67. fastqc -o fastqc_!{sample_id} -f fastq -q !{reads}
  68. '''
  69.  
  70. 6be004ee9200372fc35619907d08a423 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-fastqc-0.11.9--hdfd78af_1.img
  71. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  72. d6605b4a6bd1a0e61b59db8b86ecc713 [java.lang.String] AH-847-C
  73. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  74. 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)]
  75. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  76. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  77. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  78.  
  79. Oct-27 12:26:20.203 [Actor Thread 1] INFO nextflow.processor.TaskProcessor - [fastqc (FASTQC on AH-847-D)] cache hash: 6ef7564a2531d8ba61e32c1b578b1b88; mode: LENIENT; entries:
  80. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  81. 23037893fdd4cef8d4acc5fe82ba1899 [java.lang.String] fastqc
  82. b69439d7f1c9d288f31b7edb83c6985a [java.lang.String] '''
  83. mkdir fastqc_!{sample_id}
  84. fastqc -o fastqc_!{sample_id} -f fastq -q !{reads}
  85. '''
  86.  
  87. 6be004ee9200372fc35619907d08a423 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-fastqc-0.11.9--hdfd78af_1.img
  88. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  89. 7fff979f0f94ce67d4b135d93e8ce8cc [java.lang.String] AH-847-D
  90. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  91. 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)]
  92. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  93. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  94. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  95.  
  96. Oct-27 12:26:20.207 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [fastqc (FASTQC on AH-847-L)] cache hash: e8ce11b03a775c6ffffbc846048203d0; mode: LENIENT; entries:
  97. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  98. 23037893fdd4cef8d4acc5fe82ba1899 [java.lang.String] fastqc
  99. b69439d7f1c9d288f31b7edb83c6985a [java.lang.String] '''
  100. mkdir fastqc_!{sample_id}
  101. fastqc -o fastqc_!{sample_id} -f fastq -q !{reads}
  102. '''
  103.  
  104. 6be004ee9200372fc35619907d08a423 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-fastqc-0.11.9--hdfd78af_1.img
  105. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  106. 27b9c36ff1c3c875fd0a95c97db6ec96 [java.lang.String] AH-847-L
  107. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  108. 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)]
  109. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  110. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  111. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  112.  
  113. Oct-27 12:26:20.476 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process fastqc (FASTQC on AH-847-D) > jobId: 570576.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c2/5c9f48e802e9dae31d5a1bedbc6485
  114. Oct-27 12:26:20.487 [Task submitter] INFO nextflow.Session - [c2/5c9f48] Submitted process > fastqc (FASTQC on AH-847-D)
  115. Oct-27 12:26:20.533 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process fastqc (FASTQC on AH-847-C) > jobId: 570577.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c6/c42a40801e4bff9272751286f75e10
  116. Oct-27 12:26:20.533 [Task submitter] INFO nextflow.Session - [c6/c42a40] Submitted process > fastqc (FASTQC on AH-847-C)
  117. Oct-27 12:26:20.573 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process fastqc (FASTQC on AH-847-L) > jobId: 570578.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/e5/7ce398ec539da1beba30a410de7ec3
  118. Oct-27 12:26:20.573 [Task submitter] INFO nextflow.Session - [e5/7ce398] Submitted process > fastqc (FASTQC on AH-847-L)
  119. Oct-27 12:26:29.314 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570576.cfe1; id: 2; name: fastqc (FASTQC on AH-847-D); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c2/5c9f48e802e9dae31d5a1bedbc6485 started: 1635351984317; exited: 2021-10-27T16:26:25Z; ]
  120. Oct-27 12:26:29.419 [Actor Thread 5] 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
  121. Oct-27 12:26:29.512 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570577.cfe1; id: 1; name: fastqc (FASTQC on AH-847-C); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/c6/c42a40801e4bff9272751286f75e10 started: 1635351984409; exited: 2021-10-27T16:26:25Z; ]
  122. Oct-27 12:26:29.518 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [trimmomatic (TRIMMOMATIC on AH-847-D)] cache hash: fa858092327bac8939b6716c3ee76128; mode: LENIENT; entries:
  123. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  124. 87fa86fc60107e6a421ff93ad5d42064 [java.lang.String] trimmomatic
  125. d003529244513f5a86e2088a109bf8c2 [java.lang.String] '''
  126. trimmomatic \
  127. PE \
  128. -phred33 \
  129. -threads !{task.cpus} \
  130. !{reads} \
  131. !{sample_id}_trimmed_R1.fastq.gz \
  132. !{sample_id}_orphan_R1.fastq.gz \
  133. !{sample_id}_trimmed_R2.fastq.gz \
  134. !{sample_id}_orphan_R2.fastq.gz \
  135. LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
  136.  
  137. '''
  138.  
  139. 242b8faf69f88989b8d685442210a97e [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-trimmomatic-0.32--hdfd78af_4.img
  140. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  141. 7fff979f0f94ce67d4b135d93e8ce8cc [java.lang.String] AH-847-D
  142. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  143. 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)]
  144. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  145. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  146. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  147.  
  148. Oct-27 12:26:29.547 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [trimmomatic (TRIMMOMATIC on AH-847-C)] cache hash: fb9937382f140bffd10cecab962c3ae6; mode: LENIENT; entries:
  149. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  150. 87fa86fc60107e6a421ff93ad5d42064 [java.lang.String] trimmomatic
  151. d003529244513f5a86e2088a109bf8c2 [java.lang.String] '''
  152. trimmomatic \
  153. PE \
  154. -phred33 \
  155. -threads !{task.cpus} \
  156. !{reads} \
  157. !{sample_id}_trimmed_R1.fastq.gz \
  158. !{sample_id}_orphan_R1.fastq.gz \
  159. !{sample_id}_trimmed_R2.fastq.gz \
  160. !{sample_id}_orphan_R2.fastq.gz \
  161. LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
  162.  
  163. '''
  164.  
  165. 242b8faf69f88989b8d685442210a97e [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-trimmomatic-0.32--hdfd78af_4.img
  166. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  167. d6605b4a6bd1a0e61b59db8b86ecc713 [java.lang.String] AH-847-C
  168. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  169. 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)]
  170. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  171. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  172. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  173.  
  174. Oct-27 12:26:29.570 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570578.cfe1; id: 3; name: fastqc (FASTQC on AH-847-L); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/e5/7ce398ec539da1beba30a410de7ec3 started: 1635351984416; exited: 2021-10-27T16:26:25Z; ]
  175. Oct-27 12:26:29.618 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process trimmomatic (TRIMMOMATIC on AH-847-D) > jobId: 570579.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/92/6ebb982f34b1a56bbaeac1b462a5b9
  176. Oct-27 12:26:29.618 [Task submitter] INFO nextflow.Session - [92/6ebb98] Submitted process > trimmomatic (TRIMMOMATIC on AH-847-D)
  177. Oct-27 12:26:29.649 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [trimmomatic (TRIMMOMATIC on AH-847-L)] cache hash: 1a926ece4b978f84b5303ba757b53bcb; mode: LENIENT; entries:
  178. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  179. 87fa86fc60107e6a421ff93ad5d42064 [java.lang.String] trimmomatic
  180. d003529244513f5a86e2088a109bf8c2 [java.lang.String] '''
  181. trimmomatic \
  182. PE \
  183. -phred33 \
  184. -threads !{task.cpus} \
  185. !{reads} \
  186. !{sample_id}_trimmed_R1.fastq.gz \
  187. !{sample_id}_orphan_R1.fastq.gz \
  188. !{sample_id}_trimmed_R2.fastq.gz \
  189. !{sample_id}_orphan_R2.fastq.gz \
  190. LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
  191.  
  192. '''
  193.  
  194. 242b8faf69f88989b8d685442210a97e [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-trimmomatic-0.32--hdfd78af_4.img
  195. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  196. 27b9c36ff1c3c875fd0a95c97db6ec96 [java.lang.String] AH-847-L
  197. 553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  198. 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)]
  199. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  200. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  201. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  202.  
  203. Oct-27 12:26:29.691 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process trimmomatic (TRIMMOMATIC on AH-847-C) > jobId: 570580.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/63/fbf46b73d7fae2aea7e601b72a8a73
  204. Oct-27 12:26:29.692 [Task submitter] INFO nextflow.Session - [63/fbf46b] Submitted process > trimmomatic (TRIMMOMATIC on AH-847-C)
  205. Oct-27 12:26:29.730 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process trimmomatic (TRIMMOMATIC on AH-847-L) > jobId: 570581.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/d0/737d25453727a3363bf9ef8b3dba3b
  206. Oct-27 12:26:29.731 [Task submitter] INFO nextflow.Session - [d0/737d25] Submitted process > trimmomatic (TRIMMOMATIC on AH-847-L)
  207. Oct-27 12:26:34.317 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570579.cfe1; id: 4; name: trimmomatic (TRIMMOMATIC on AH-847-D); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/92/6ebb982f34b1a56bbaeac1b462a5b9 started: 1635351994307; exited: 2021-10-27T16:26:30Z; ]
  208. Oct-27 12:26:34.361 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570580.cfe1; id: 5; name: trimmomatic (TRIMMOMATIC on AH-847-C); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/63/fbf46b73d7fae2aea7e601b72a8a73 started: 1635351994349; exited: 2021-10-27T16:26:30Z; ]
  209. Oct-27 12:26:34.377 [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
  210. Oct-27 12:26:34.393 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [bbmerge (MERGING on AH-847-C)] cache hash: 16d0fbcbeb6e2a1c6c3d0f48ca719b73; mode: LENIENT; entries:
  211. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  212. 32b35978c0e945d35b9517e471531a43 [java.lang.String] bbmerge
  213. ac6a8e72f7200e7195858d7ce9672180 [java.lang.String] '''
  214. reformat.sh in1=!{trimmed_R1_paired} in2=!{trimmed_R2_paired} out=!{sample_id}_merged.fastq
  215. '''
  216.  
  217. 5632241bf34f0acad52a76595c250798 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-bbmap-38.90--he522d1c_3.img
  218. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  219. d6605b4a6bd1a0e61b59db8b86ecc713 [java.lang.String] AH-847-C
  220. dc8c1aa13de7a405386d52144e08bb54 [java.lang.String] trimmed_R1_paired
  221. 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)]
  222. fb235e59786e747b345ebb94cba36e73 [java.lang.String] trimmed_R2_paired
  223. 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)]
  224. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  225. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  226. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  227.  
  228. Oct-27 12:26:34.403 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [bbmerge (MERGING on AH-847-D)] cache hash: b71d711c76cb4768f9c41f43ecc3388d; mode: LENIENT; entries:
  229. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  230. 32b35978c0e945d35b9517e471531a43 [java.lang.String] bbmerge
  231. ac6a8e72f7200e7195858d7ce9672180 [java.lang.String] '''
  232. reformat.sh in1=!{trimmed_R1_paired} in2=!{trimmed_R2_paired} out=!{sample_id}_merged.fastq
  233. '''
  234.  
  235. 5632241bf34f0acad52a76595c250798 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-bbmap-38.90--he522d1c_3.img
  236. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  237. 7fff979f0f94ce67d4b135d93e8ce8cc [java.lang.String] AH-847-D
  238. dc8c1aa13de7a405386d52144e08bb54 [java.lang.String] trimmed_R1_paired
  239. 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)]
  240. fb235e59786e747b345ebb94cba36e73 [java.lang.String] trimmed_R2_paired
  241. 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)]
  242. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  243. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  244. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  245.  
  246. Oct-27 12:26:34.423 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570581.cfe1; id: 6; name: trimmomatic (TRIMMOMATIC on AH-847-L); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/d0/737d25453727a3363bf9ef8b3dba3b started: 1635351994407; exited: 2021-10-27T16:26:30Z; ]
  247. Oct-27 12:26:34.458 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [bbmerge (MERGING on AH-847-L)] cache hash: f2a495accf263c5a92c5b23934bbce24; mode: LENIENT; entries:
  248. 8c6296beba786eb720043a479abd03b2 [java.util.UUID] 54be4534-56c1-4680-a355-a511b37fb1f3
  249. 32b35978c0e945d35b9517e471531a43 [java.lang.String] bbmerge
  250. ac6a8e72f7200e7195858d7ce9672180 [java.lang.String] '''
  251. reformat.sh in1=!{trimmed_R1_paired} in2=!{trimmed_R2_paired} out=!{sample_id}_merged.fastq
  252. '''
  253.  
  254. 5632241bf34f0acad52a76595c250798 [java.lang.String] /mnt/scgc_nfs/containers/quay.io-biocontainers-bbmap-38.90--he522d1c_3.img
  255. 7ec7cbd71ff757f5fcdbaa760c9ce6de [java.lang.String] sample_id
  256. 27b9c36ff1c3c875fd0a95c97db6ec96 [java.lang.String] AH-847-L
  257. dc8c1aa13de7a405386d52144e08bb54 [java.lang.String] trimmed_R1_paired
  258. 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)]
  259. fb235e59786e747b345ebb94cba36e73 [java.lang.String] trimmed_R2_paired
  260. 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)]
  261. 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  262. 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  263. c7cc2659d6dfdb0ac1e240cbdfcdb31d [java.lang.String] singularity/3.8.0
  264.  
  265. Oct-27 12:26:34.472 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process bbmerge (MERGING on AH-847-C) > jobId: 570582.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/5b/c211837272db6cc7e14ab3c093c55e
  266. Oct-27 12:26:34.473 [Task submitter] INFO nextflow.Session - [5b/c21183] Submitted process > bbmerge (MERGING on AH-847-C)
  267. Oct-27 12:26:34.507 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process bbmerge (MERGING on AH-847-D) > jobId: 570583.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/05/190f2939361d62b8fdd37cdae522e4
  268. Oct-27 12:26:34.508 [Task submitter] INFO nextflow.Session - [05/190f29] Submitted process > bbmerge (MERGING on AH-847-D)
  269. Oct-27 12:26:34.538 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBSPRO] submitted process bbmerge (MERGING on AH-847-L) > jobId: 570584.cfe1; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/a7/6a5b4094da871a7ac60f2d66ce6ef0
  270. Oct-27 12:26:34.539 [Task submitter] INFO nextflow.Session - [a7/6a5b40] Submitted process > bbmerge (MERGING on AH-847-L)
  271. Oct-27 12:26:39.327 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570582.cfe1; id: 8; name: bbmerge (MERGING on AH-847-C); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/5b/c211837272db6cc7e14ab3c093c55e started: 1635351999307; exited: 2021-10-27T16:26:35Z; ]
  272. Oct-27 12:26:39.342 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570583.cfe1; id: 7; name: bbmerge (MERGING on AH-847-D); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/05/190f2939361d62b8fdd37cdae522e4 started: 1635351999337; exited: 2021-10-27T16:26:35Z; ]
  273. Oct-27 12:26:39.356 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 570584.cfe1; id: 9; name: bbmerge (MERGING on AH-847-L); status: COMPLETED; exit: 0; error: -; workDir: /mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/cache_2/work/a7/6a5b4094da871a7ac60f2d66ce6ef0 started: 1635351999350; exited: 2021-10-27T16:26:35Z; ]
  274. Oct-27 12:26:39.361 [main] DEBUG nextflow.Session - Session await > all process finished
  275. Oct-27 12:26:39.367 [main] DEBUG nextflow.Session - Session await > all barriers passed
  276. Oct-27 12:26:39.387 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=9; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=26s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=4; peakMemory=0; ]
  277. Oct-27 12:26:39.929 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
  278. Oct-27 12:26:39.930 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.1.0'
  279. Oct-27 12:26:39.930 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
  280. Oct-27 12:26:39.995 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
  281.  
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