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ERROR ~ Cannot get property 'Galgal4' on null object DEBUG

Tichaboni
Sep 13th, 2018
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  1. Sep-13 08:34:25.687 [main] DEBUG nextflow.cli.Launcher - $> /home/bkimathi/miniconda3/bin/nextflow run nf-core/rnaseq --reads *moja_{1,2}.fastq.gz --genome Galgal4 --max_memory 12.GB --aligner hisat2 --hisatBuildMemory 1 --hisat2index /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/kuku_index/kuku_index.1.ht2 /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/kuku_index/kuku_index.2.ht2 /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/kuku_index/kuku_index.3.ht2 /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/kuku_index/kuku_index.4.ht2 /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/kuku_index/kuku_index.5.ht2 /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/kuku_index/kuku_index.6.ht2 /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/kuku_index/kuku_index.7.ht2 /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/kuku_index/kuku_index.8.ht2 --saveReference -profile standard,docker -resume
  2. Sep-13 08:34:25.762 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.31.1
  3. Sep-13 08:34:26.160 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/bkimathi/miniconda3/share/nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
  4. Sep-13 08:34:26.165 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/bkimathi/miniconda3/share/nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
  5. Sep-13 08:34:26.226 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/bkimathi/miniconda3/share/nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
  6. Sep-13 08:34:26.227 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/rnaseq` [wise_khorana] - revision: 44f1525d7a [master]
  7. Sep-13 08:34:26.904 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/bkimathi/miniconda3/share/nextflow/assets/nf-core/rnaseq/nextflow.config
  8. Sep-13 08:34:26.905 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/nextflow.config
  9. Sep-13 08:34:26.906 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/bkimathi/miniconda3/share/nextflow/assets/nf-core/rnaseq/nextflow.config
  10. Sep-13 08:34:26.906 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/nextflow.config
  11. Sep-13 08:34:26.914 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard,docker`
  12. Sep-13 08:34:27.151 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard,docker`
  13. Sep-13 08:34:27.161 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, hebbe, cfc, uppmax_devel, test, uppmax, none, docker, gis, ccga, conda, singularity, uct_hex, awsbatch, uppmax_modules, binac]
  14. Sep-13 08:34:27.182 [main] DEBUG nextflow.Session - Session uuid: 7fea9b89-3931-43e9-ad02-a72c5dd22f2a
  15. Sep-13 08:34:27.183 [main] DEBUG nextflow.Session - Run name: wise_khorana
  16. Sep-13 08:34:27.183 [main] DEBUG nextflow.Session - Executor pool size: 8
  17. Sep-13 08:34:27.189 [main] DEBUG nextflow.cli.CmdRun -
  18. Version: 0.31.1 build 4886
  19. Modified: 07-08-2018 15:53 UTC (10:53 CDT)
  20. System: Linux 4.15.0-33-generic
  21. Runtime: Groovy 2.4.15 on OpenJDK 64-Bit Server VM 1.8.0_121-b15
  22. Encoding: UTF-8 (UTF-8)
  23. Process: 8311@bkimathi-ThinkCentre-M910z [127.0.1.1]
  24. CPUs: 8 - Mem: 15.6 GB (7.7 GB) - Swap: 2 GB (1.7 GB)
  25. Sep-13 08:34:27.201 [main] DEBUG nextflow.Session - Work-dir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work [fuseblk]
  26. Sep-13 08:34:29.882 [main] DEBUG nextflow.Session - Session start invoked
  27. Sep-13 08:34:29.888 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
  28. Sep-13 08:34:29.890 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/results/pipeline_info/pipeline_info/nfcore-rnaseq_trace.txt
  29. Sep-13 08:34:29.896 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
  30. Sep-13 08:34:30.288 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
  31. Sep-13 08:34:30.318 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider
  32. Sep-13 08:34:30.325 [main] DEBUG nextflow.file.FileHelper - AWS S3 config details: {}
  33. Sep-13 08:34:40.776 [main] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: ./; pattern: *moja_{1,2}.fastq.gz; options: [:]
  34. Sep-13 08:34:40.788 [main] INFO nextflow.Nextflow - =======================================================
  35. ,--./,-.
  36. ___ __ __ __ ___ /,-._.--~'
  37. |\ | |__ __ / ` / \ |__) |__ } {
  38. | \| | \__, \__/ | \ |___ \`-._,-`-,
  39. `._,._,'
  40.  
  41. nf-core/rnaseq : RNA-Seq Best Practice v1.0
  42. =======================================================
  43. Sep-13 08:34:40.792 [main] INFO nextflow.Nextflow - Run Name : wise_khorana
  44. Reads : *moja_{1,2}.fastq.gz
  45. Data Type : Paired-End
  46. Genome : Galgal4
  47. Strandedness : None
  48. Trim R1 : 0
  49. Trim R2 : 0
  50. Trim 3' R1 : 0
  51. Trim 3' R2 : 0
  52. Aligner : HISAT2
  53. Fasta Ref : s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa
  54. GTF Annotation : s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf
  55. BED Annotation : s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed
  56. Save Reference : Yes
  57. Save Trimmed : No
  58. Save Intermeds : No
  59. Max Memory : 12.GB
  60. Max CPUs : 16
  61. Max Time : 10d
  62. Output dir : ./results
  63. Working dir : /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work
  64. Container : nfcore/rnaseq:1.0
  65. Pipeline Release: master
  66. Current home : /home/bkimathi
  67. Current user : bkimathi
  68. Current path : /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation
  69. Script dir : /home/bkimathi/miniconda3/share/nextflow/assets/nf-core/rnaseq
  70. Config Profile : standard,docker
  71. Sep-13 08:34:40.792 [main] INFO nextflow.Nextflow - =========================================
  72. Sep-13 08:34:40.851 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  73. Sep-13 08:34:40.851 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  74. Sep-13 08:34:40.855 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  75. Sep-13 08:34:40.856 [main] INFO nextflow.executor.Executor - [warm up] executor > local
  76. Sep-13 08:34:40.858 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=15.6 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
  77. Sep-13 08:34:40.861 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
  78. Sep-13 08:34:40.861 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
  79. Sep-13 08:34:40.863 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
  80. Sep-13 08:34:40.881 [main] DEBUG nextflow.Session - >>> barrier register (process: makeHisatSplicesites)
  81. Sep-13 08:34:40.882 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeHisatSplicesites -- maxForks: 8
  82. Sep-13 08:34:40.900 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:makeHISATindex` matches process makeHISATindex
  83. Sep-13 08:34:40.902 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  84. Sep-13 08:34:40.902 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  85. Sep-13 08:34:40.902 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  86. Sep-13 08:34:40.904 [main] DEBUG nextflow.Session - >>> barrier register (process: makeHISATindex)
  87. Sep-13 08:34:40.905 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeHISATindex -- maxForks: 8
  88. Sep-13 08:34:40.916 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  89. Sep-13 08:34:40.916 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  90. Sep-13 08:34:40.916 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  91. Sep-13 08:34:40.917 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc)
  92. Sep-13 08:34:40.918 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 8
  93. Sep-13 08:34:40.921 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:trim_galore` matches process trim_galore
  94. Sep-13 08:34:40.922 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  95. Sep-13 08:34:40.922 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  96. Sep-13 08:34:40.922 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  97. Sep-13 08:34:40.926 [main] DEBUG nextflow.Session - >>> barrier register (process: trim_galore)
  98. Sep-13 08:34:40.926 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_galore -- maxForks: 8
  99. Sep-13 08:34:40.943 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:hisat2Align` matches process hisat2Align
  100. Sep-13 08:34:40.944 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  101. Sep-13 08:34:40.944 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  102. Sep-13 08:34:40.944 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  103. Sep-13 08:34:40.945 [main] DEBUG nextflow.Session - >>> barrier register (process: hisat2Align)
  104. Sep-13 08:34:40.946 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > hisat2Align -- maxForks: 8
  105. Sep-13 08:34:40.952 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:hisat2_sortOutput` matches process hisat2_sortOutput
  106. Sep-13 08:34:40.953 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  107. Sep-13 08:34:40.953 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  108. Sep-13 08:34:40.953 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  109. Sep-13 08:34:40.954 [main] DEBUG nextflow.Session - >>> barrier register (process: hisat2_sortOutput)
  110. Sep-13 08:34:40.954 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > hisat2_sortOutput -- maxForks: 8
  111. Sep-13 08:34:40.960 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:rseqc` matches process rseqc
  112. Sep-13 08:34:40.961 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  113. Sep-13 08:34:40.961 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  114. Sep-13 08:34:40.961 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  115. Sep-13 08:34:40.962 [main] DEBUG nextflow.Session - >>> barrier register (process: rseqc)
  116. Sep-13 08:34:40.962 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > rseqc -- maxForks: 8
  117. Sep-13 08:34:40.967 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:createBigWig` matches process createBigWig
  118. Sep-13 08:34:40.967 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  119. Sep-13 08:34:40.968 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  120. Sep-13 08:34:40.968 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  121. Sep-13 08:34:40.968 [main] DEBUG nextflow.Session - >>> barrier register (process: createBigWig)
  122. Sep-13 08:34:40.969 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > createBigWig -- maxForks: 8
  123. Sep-13 08:34:40.973 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:genebody_coverage` matches process genebody_coverage
  124. Sep-13 08:34:40.973 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  125. Sep-13 08:34:40.973 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  126. Sep-13 08:34:40.973 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  127. Sep-13 08:34:40.974 [main] DEBUG nextflow.Session - >>> barrier register (process: genebody_coverage)
  128. Sep-13 08:34:40.974 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > genebody_coverage -- maxForks: 8
  129. Sep-13 08:34:40.981 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  130. Sep-13 08:34:40.981 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  131. Sep-13 08:34:40.982 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  132. Sep-13 08:34:40.982 [main] DEBUG nextflow.Session - >>> barrier register (process: preseq)
  133. Sep-13 08:34:40.982 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 8
  134. Sep-13 08:34:40.986 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:markDuplicates` matches process markDuplicates
  135. Sep-13 08:34:40.987 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  136. Sep-13 08:34:40.987 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  137. Sep-13 08:34:40.987 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  138. Sep-13 08:34:40.988 [main] DEBUG nextflow.Session - >>> barrier register (process: markDuplicates)
  139. Sep-13 08:34:40.988 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDuplicates -- maxForks: 8
  140. Sep-13 08:34:40.992 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:dupradar` matches process dupradar
  141. Sep-13 08:34:40.993 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  142. Sep-13 08:34:40.993 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  143. Sep-13 08:34:40.993 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  144. Sep-13 08:34:40.994 [main] DEBUG nextflow.Session - >>> barrier register (process: dupradar)
  145. Sep-13 08:34:40.994 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dupradar -- maxForks: 8
  146. Sep-13 08:34:40.999 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:featureCounts` matches process featureCounts
  147. Sep-13 08:34:40.999 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  148. Sep-13 08:34:40.999 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  149. Sep-13 08:34:41.002 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  150. Sep-13 08:34:41.003 [main] DEBUG nextflow.Session - >>> barrier register (process: featureCounts)
  151. Sep-13 08:34:41.003 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > featureCounts -- maxForks: 8
  152. Sep-13 08:34:41.007 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  153. Sep-13 08:34:41.007 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  154. Sep-13 08:34:41.008 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  155. Sep-13 08:34:41.008 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_featureCounts)
  156. Sep-13 08:34:41.008 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_featureCounts -- maxForks: 8
  157. Sep-13 08:34:41.013 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  158. Sep-13 08:34:41.013 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  159. Sep-13 08:34:41.013 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  160. Sep-13 08:34:41.014 [main] DEBUG nextflow.Session - >>> barrier register (process: stringtieFPKM)
  161. Sep-13 08:34:41.014 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > stringtieFPKM -- maxForks: 8
  162. Sep-13 08:34:41.029 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:sample_correlation` matches process sample_correlation
  163. Sep-13 08:34:41.030 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  164. Sep-13 08:34:41.030 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  165. Sep-13 08:34:41.031 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  166. Sep-13 08:34:41.032 [main] DEBUG nextflow.Session - >>> barrier register (process: sample_correlation)
  167. Sep-13 08:34:41.033 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [25/1cc3ac] Cached process > fastqc (SRR)
  168. Sep-13 08:34:41.033 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > sample_correlation -- maxForks: 8
  169. Sep-13 08:34:41.033 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [1c/fc729c] Cached process > trim_galore (SRR)
  170. Sep-13 08:34:41.038 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:get_software_versions` matches process get_software_versions
  171. Sep-13 08:34:41.038 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  172. Sep-13 08:34:41.038 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  173. Sep-13 08:34:41.038 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  174. Sep-13 08:34:41.039 [main] DEBUG nextflow.Session - >>> barrier register (process: get_software_versions)
  175. Sep-13 08:34:41.039 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 8
  176. Sep-13 08:34:41.042 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:workflow_summary_mqc` matches process workflow_summary_mqc
  177. Sep-13 08:34:41.042 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  178. Sep-13 08:34:41.044 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  179. Sep-13 08:34:41.044 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  180. Sep-13 08:34:41.044 [main] DEBUG nextflow.Session - >>> barrier register (process: workflow_summary_mqc)
  181. Sep-13 08:34:41.045 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > workflow_summary_mqc -- maxForks: 8
  182. Sep-13 08:34:41.072 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:multiqc` matches process multiqc
  183. Sep-13 08:34:41.073 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  184. Sep-13 08:34:41.073 [Actor Thread 10] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc)
  185. Sep-13 08:34:41.073 [Actor Thread 11] DEBUG nextflow.Session - <<< barrier arrive (process: trim_galore)
  186. Sep-13 08:34:41.073 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  187. Sep-13 08:34:41.074 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  188. Sep-13 08:34:41.074 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc)
  189. Sep-13 08:34:41.075 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 8
  190. Sep-13 08:34:41.079 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
  191. Sep-13 08:34:41.079 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
  192. Sep-13 08:34:41.079 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
  193. Sep-13 08:34:41.079 [Task submitter] INFO nextflow.Session - [b6/e554e2] Submitted process > workflow_summary_mqc
  194. Sep-13 08:34:41.079 [main] DEBUG nextflow.Session - >>> barrier register (process: output_documentation)
  195. Sep-13 08:34:41.080 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 8
  196. Sep-13 08:34:41.081 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
  197. Sep-13 08:34:41.081 [main] DEBUG nextflow.Session - Session await
  198. Sep-13 08:34:41.088 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [6c/0dae49] Cached process > output_documentation
  199. Sep-13 08:34:41.094 [Actor Thread 10] DEBUG nextflow.Session - <<< barrier arrive (process: output_documentation)
  200. Sep-13 08:34:41.094 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: workflow_summary_mqc; status: COMPLETED; exit: -; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/b6/e554e2873aae059cae6b46e0630301]
  201. Sep-13 08:34:41.128 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -uex .command.run
  202. Sep-13 08:34:41.129 [Task submitter] INFO nextflow.Session - [87/133e01] Submitted process > get_software_versions
  203. Sep-13 08:34:41.136 [Actor Thread 10] DEBUG nextflow.Session - <<< barrier arrive (process: workflow_summary_mqc)
  204. Sep-13 08:34:43.764 [Actor Thread 4] INFO nextflow.processor.TaskProcessor - [26/6f26b7] Cached process > makeHisatSplicesites (genes.gtf)
  205. Sep-13 08:34:43.766 [Actor Thread 11] DEBUG nextflow.Session - <<< barrier arrive (process: makeHisatSplicesites)
  206. Sep-13 08:34:43.768 [Actor Thread 8] INFO nextflow.Nextflow - [HISAT2 index build] Available memory: 12 GB
  207. Sep-13 08:34:43.768 [Actor Thread 8] INFO nextflow.Nextflow - [HISAT2 index build] Over 1 GB available, so using splice sites and exons in HISAT2 index
  208. Sep-13 08:34:47.794 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/87/133e011ed7eaac0ceed56b9d334662]
  209. Sep-13 08:34:47.797 [Actor Thread 11] DEBUG nextflow.Session - <<< barrier arrive (process: get_software_versions)
  210. Sep-13 08:34:50.050 [Actor Thread 8] INFO nextflow.processor.TaskProcessor - [9c/3e947f] Cached process > makeHISATindex (genome.fa)
  211. Sep-13 08:34:50.052 [Actor Thread 10] DEBUG nextflow.Session - <<< barrier arrive (process: makeHISATindex)
  212. Sep-13 08:34:50.072 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -uex .command.run
  213. Sep-13 08:34:50.072 [Task submitter] INFO nextflow.Session - [b2/e63455] Submitted process > hisat2Align (SRRmoja_1)
  214. Sep-13 08:39:40.971 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- pending tasks are shown below
  215. ~> TaskHandler[id: 8; name: hisat2Align (SRRmoja_1); status: RUNNING; exit: -; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/b2/e634552f274f36f854a5ae9142185b]
  216. Sep-13 08:44:41.021 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- pending tasks are shown below
  217. ~> TaskHandler[id: 8; name: hisat2Align (SRRmoja_1); status: RUNNING; exit: -; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/b2/e634552f274f36f854a5ae9142185b]
  218. Sep-13 08:49:41.046 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- pending tasks are shown below
  219. ~> TaskHandler[id: 8; name: hisat2Align (SRRmoja_1); status: RUNNING; exit: -; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/b2/e634552f274f36f854a5ae9142185b]
  220. Sep-13 08:54:41.086 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- pending tasks are shown below
  221. ~> TaskHandler[id: 8; name: hisat2Align (SRRmoja_1); status: RUNNING; exit: -; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/b2/e634552f274f36f854a5ae9142185b]
  222. Sep-13 08:59:41.098 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- pending tasks are shown below
  223. ~> TaskHandler[id: 8; name: hisat2Align (SRRmoja_1); status: RUNNING; exit: -; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/b2/e634552f274f36f854a5ae9142185b]
  224. Sep-13 09:04:41.132 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- pending tasks are shown below
  225. ~> TaskHandler[id: 8; name: hisat2Align (SRRmoja_1); status: RUNNING; exit: -; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/b2/e634552f274f36f854a5ae9142185b]
  226. Sep-13 09:09:41.177 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- pending tasks are shown below
  227. ~> TaskHandler[id: 8; name: hisat2Align (SRRmoja_1); status: RUNNING; exit: -; error: -; workDir: /media/bkimathi/FreeAgentDrive/Reads_Genome_Annotation/work/b2/e634552f274f36f854a5ae9142185b]
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