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nf-core / vipr

Assembly and intrahost / low-frequency variant calling for viral samples
https://nf-co.re/vipr
MIT License
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Error executing process > gap_fill_assembly #34

Open ahmedmoustafa opened 5 years ago

ahmedmoustafa commented 5 years ago

The pipeline throws an error gap_fill_assembly with the following info:

Caused by:
  Process `gap_fill_assembly (Orienting and gap filling contigs for Naive)` terminated with an error exit status (127)

Command executed:

  set +e;
  log=Naive-gap-filled-assembly.log;
  simple_contig_joiner.py -c Naive_contigs.fa -r HBV.fa           -s "Naive-gap-filled-assembly" -o Naive-gap-filled-assembly.fa           -b "Naive-gap-filled-assembly.gaps.bed" >& $log;

  rc=$?
  if [ $rc -ne 0 ]; then
      # nothing to join, means we cannot continue. so stop here.
      grep 'Nothing to join' $log && exit 3;
      exit $rc;
  fi

Command exit status:
  127

It is not clear what could be the issue. Your help will be greatly appreciated.

The complete log can be found below:

Jun-16 20:42:31.376 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/vipr -params-file params.yaml -profile docker
Jun-16 20:42:31.753 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 19.04.1
Jun-16 20:42:33.610 [main] WARN  nextflow.config.Manifest - Invalid config manifest attribute `pipelineVersion`
Jun-16 20:42:33.610 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/nf-core/vipr/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/vipr.git
Jun-16 20:42:33.623 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/nf-core/vipr/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/vipr.git
Jun-16 20:42:34.150 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/nf-core/vipr/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/vipr.git
Jun-16 20:42:34.151 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/vipr` [sick_morse] - revision: 6eef3b32ea [master]
Jun-16 20:42:35.648 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /root/.nextflow/assets/nf-core/vipr/nextflow.config
Jun-16 20:42:35.650 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /root/.nextflow/assets/nf-core/vipr/nextflow.config
Jun-16 20:42:35.669 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jun-16 20:42:35.949 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, gis, conda, singularity, awsbatch, none, docker]
Jun-16 20:42:36.149 [main] DEBUG nextflow.Session - Session uuid: c67ae226-6e74-46bf-b256-057a172bbeaa
Jun-16 20:42:36.149 [main] DEBUG nextflow.Session - Run name: sick_morse
Jun-16 20:42:36.150 [main] DEBUG nextflow.Session - Executor pool size: 32
Jun-16 20:42:36.254 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 19.04.1 build 5072
  Modified: 03-05-2019 12:29 UTC (14:29 EEST)
  System: Linux 3.13.0-95-generic
  Runtime: Groovy 2.5.6 on OpenJDK 64-Bit Server VM 1.8.0_191-8u191-b12-2ubuntu0.16.04.1-b12
  Encoding: UTF-8 (UTF-8)
  Process: 27467@metagenomics-bio [127.0.1.1]
  CPUs: 32 - Mem: 125.9 GB (405.3 MB) - Swap: 122.1 GB (121.1 GB)
Jun-16 20:42:36.303 [main] DEBUG nextflow.Session - Work-dir: /work [ext2/ext3]
Jun-16 20:42:36.304 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /root/.nextflow/assets/nf-core/vipr/bin
Jun-16 20:42:36.648 [main] WARN  nextflow.config.Manifest - Invalid config manifest attribute `pipelineVersion`
Jun-16 20:42:36.678 [main] DEBUG nextflow.Session - Session start invoked
Jun-16 20:42:36.687 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Jun-16 20:42:36.689 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /results/pipeline_info/pipeline_info/nfcore-vipr_trace.txt
Jun-16 20:42:36.700 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Jun-16 20:42:37.541 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-16 20:42:37.545 [main] WARN  nextflow.script.ScriptBinding - Access to undefined parameter `nf_required_version` -- Initialise it to a default value eg. `params.nf_required_version = some_value`
Jun-16 20:42:37.560 [main] ERROR nextflow.Nextflow - ====================================================
  Nextflow version null required! You are running v19.04.1.
  Pipeline execution will continue, but things may break.
  Please run `nextflow self-update` to update Nextflow.
============================================================
Jun-16 20:42:37.579 [main] INFO  nextflow.Nextflow - ==================================================
Jun-16 20:42:37.579 [main] INFO  nextflow.Nextflow -  nf-core/vipr : Viral amplicon/enrichment analysis and intrahost variant calling: v1.0dev
Jun-16 20:42:37.580 [main] INFO  nextflow.Nextflow - ==================================================
Jun-16 20:42:37.914 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:37.914 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:37.927 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:37.930 [main] INFO  nextflow.executor.Executor - [warm up] executor > local
Jun-16 20:42:37.935 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=125.9 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Jun-16 20:42:37.948 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
Jun-16 20:42:37.949 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jun-16 20:42:37.953 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
Jun-16 20:42:38.011 [main] DEBUG nextflow.Session - >>> barrier register (process: trim_and_combine)
Jun-16 20:42:38.015 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_and_combine -- maxForks: 32
Jun-16 20:42:38.080 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.080 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.081 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.085 [main] DEBUG nextflow.Session - >>> barrier register (process: decont)
Jun-16 20:42:38.086 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > decont -- maxForks: 32
Jun-16 20:42:38.111 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.112 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.113 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.115 [main] DEBUG nextflow.Session - >>> barrier register (process: kraken)
Jun-16 20:42:38.115 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > kraken -- maxForks: 32
Jun-16 20:42:38.136 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.136 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.136 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.138 [main] DEBUG nextflow.Session - >>> barrier register (process: tadpole)
Jun-16 20:42:38.138 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > tadpole -- maxForks: 32
Jun-16 20:42:38.160 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.161 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.161 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.163 [main] DEBUG nextflow.Session - >>> barrier register (process: gap_fill_assembly)
Jun-16 20:42:38.167 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > gap_fill_assembly -- maxForks: 32
Jun-16 20:42:38.200 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.201 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.201 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.202 [main] DEBUG nextflow.Session - >>> barrier register (process: polish_assembly)
Jun-16 20:42:38.202 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > polish_assembly -- maxForks: 32
Jun-16 20:42:38.220 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.221 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.221 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.223 [main] DEBUG nextflow.Session - >>> barrier register (process: final_mapping)
Jun-16 20:42:38.224 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > final_mapping -- maxForks: 32
Jun-16 20:42:38.238 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.238 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.238 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.239 [main] DEBUG nextflow.Session - >>> barrier register (process: var_calling)
Jun-16 20:42:38.240 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > var_calling -- maxForks: 32
Jun-16 20:42:38.249 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.249 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.249 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.250 [main] DEBUG nextflow.Session - >>> barrier register (process: genomecov)
Jun-16 20:42:38.250 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > genomecov -- maxForks: 32
Jun-16 20:42:38.258 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jun-16 20:42:38.258 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-16 20:42:38.258 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-16 20:42:38.259 [main] DEBUG nextflow.Session - >>> barrier register (process: vipr_tools)
Jun-16 20:42:38.259 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > vipr_tools -- maxForks: 32
Jun-16 20:42:38.262 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
Jun-16 20:42:38.262 [main] DEBUG nextflow.Session - Session await
Jun-16 20:42:38.295 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-16 20:42:38.300 [Task submitter] INFO  nextflow.Session - [b0/1ada91] Submitted process > trim_and_combine (Preprocessing of 11  read pairs for Relapsed)
Jun-16 20:42:38.324 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-16 20:42:38.325 [Task submitter] INFO  nextflow.Session - [cb/89764f] Submitted process > trim_and_combine (Preprocessing of 8  read pairs for Naive)
Jun-16 20:47:38.108 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 1; name: trim_and_combine (Preprocessing of 11  read pairs for Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/b0/1ada91bfb7e06ffc2ec531660dfe7a]
~> TaskHandler[id: 2; name: trim_and_combine (Preprocessing of 8  read pairs for Naive); status: RUNNING; exit: -; error: -; workDir: /work/cb/89764f6650d83b3cf971cf5191cfe6]
Jun-16 20:52:38.193 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 1; name: trim_and_combine (Preprocessing of 11  read pairs for Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/b0/1ada91bfb7e06ffc2ec531660dfe7a]
~> TaskHandler[id: 2; name: trim_and_combine (Preprocessing of 8  read pairs for Naive); status: RUNNING; exit: -; error: -; workDir: /work/cb/89764f6650d83b3cf971cf5191cfe6]
Jun-16 20:53:48.600 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: trim_and_combine (Preprocessing of 8  read pairs for Naive); status: COMPLETED; exit: 0; error: -; workDir: /work/cb/89764f6650d83b3cf971cf5191cfe6]
Jun-16 20:53:48.636 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-16 20:53:48.636 [Task submitter] INFO  nextflow.Session - [09/950d69] Submitted process > decont (Decontaminating Naive)
Jun-16 20:57:38.292 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 1; name: trim_and_combine (Preprocessing of 11  read pairs for Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/b0/1ada91bfb7e06ffc2ec531660dfe7a]
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
Jun-16 21:02:38.320 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 1; name: trim_and_combine (Preprocessing of 11  read pairs for Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/b0/1ada91bfb7e06ffc2ec531660dfe7a]
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
Jun-16 21:07:38.403 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 1; name: trim_and_combine (Preprocessing of 11  read pairs for Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/b0/1ada91bfb7e06ffc2ec531660dfe7a]
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
Jun-16 21:08:23.287 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: trim_and_combine (Preprocessing of 11  read pairs for Relapsed); status: COMPLETED; exit: 0; error: -; workDir: /work/b0/1ada91bfb7e06ffc2ec531660dfe7a]
Jun-16 21:08:23.297 [Actor Thread 6] DEBUG nextflow.Session - <<< barrier arrive (process: trim_and_combine)
Jun-16 21:08:23.341 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-16 21:08:23.341 [Task submitter] INFO  nextflow.Session - [ea/8173e3] Submitted process > decont (Decontaminating Relapsed)
Jun-16 21:12:38.462 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:17:38.514 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:22:38.564 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:27:38.637 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:32:38.679 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:37:38.709 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:42:38.782 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:47:38.797 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:52:38.831 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 21:57:38.896 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:02:38.904 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:07:38.916 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:12:38.947 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:17:38.982 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:22:39.065 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:27:39.076 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:32:39.082 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:37:39.171 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:42:39.271 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:47:39.371 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:52:39.454 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 22:57:39.461 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 23:02:39.554 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 23:07:39.619 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 23:12:39.663 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 23:17:39.758 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 23:22:39.831 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below
~> TaskHandler[id: 3; name: decont (Decontaminating Naive); status: RUNNING; exit: -; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
Jun-16 23:26:30.413 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: decont (Decontaminating Naive); status: COMPLETED; exit: 0; error: -; workDir: /work/09/950d69e231126703658bc59b246997]
Jun-16 23:26:30.616 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-16 23:26:30.617 [Task submitter] INFO  nextflow.Session - [48/8eac4d] Submitted process > tadpole (Tadpole assembly of Naive)
Jun-16 23:26:30.630 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-16 23:26:30.630 [Task submitter] INFO  nextflow.Session - [3c/bd7fb4] Submitted process > kraken (Running Kraken on Naive)
Jun-16 23:27:39.925 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- pending tasks are shown below
~> TaskHandler[id: 4; name: decont (Decontaminating Relapsed); status: RUNNING; exit: -; error: -; workDir: /work/ea/8173e3c09ca1cb6d5bde40f2aa70f2]
~> TaskHandler[id: 5; name: tadpole (Tadpole assembly of Naive); status: RUNNING; exit: -; error: -; workDir: /work/48/8eac4dd36282d7fea21aa65e82c31a]
~> TaskHandler[id: 6; name: kraken (Running Kraken on Naive); status: RUNNING; exit: -; error: -; workDir: /work/3c/bd7fb4849d814eebd3ce6003c9827f]
Jun-16 23:28:20.513 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: tadpole (Tadpole assembly of Naive); status: COMPLETED; exit: 0; error: -; workDir: /work/48/8eac4dd36282d7fea21aa65e82c31a]
Jun-16 23:28:20.583 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-16 23:28:20.644 [Task submitter] INFO  nextflow.Session - [e2/9e0cb1] Submitted process > gap_fill_assembly (Orienting and gap filling contigs for Naive)
Jun-16 23:28:30.810 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: gap_fill_assembly (Orienting and gap filling contigs for Naive); status: COMPLETED; exit: 127; error: -; workDir: /work/e2/9e0cb12560db3fbf7d3ad56f9a653b]
Jun-16 23:28:31.092 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'gap_fill_assembly (Orienting and gap filling contigs for Naive)'

Caused by:
  Process `gap_fill_assembly (Orienting and gap filling contigs for Naive)` terminated with an error exit status (127)

Command executed:

  set +e;
  log=Naive-gap-filled-assembly.log;
  simple_contig_joiner.py -c Naive_contigs.fa -r HBV.fa           -s "Naive-gap-filled-assembly" -o Naive-gap-filled-assembly.fa           -b "Naive-gap-filled-assembly.gaps.bed" >& $log;

  rc=$?
  if [ $rc -ne 0 ]; then
      # nothing to join, means we cannot continue. so stop here.
      grep 'Nothing to join' $log && exit 3;
      exit $rc;
  fi

Command exit status:
  127

Command output:
  (empty)

Work dir:
  /work/e2/9e0cb12560db3fbf7d3ad56f9a653b

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Jun-16 23:28:31.165 [Task monitor] DEBUG nextflow.trace.TraceRecord - Not a valid trace `realtime` value: '2'
Jun-16 23:28:31.167 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `gap_fill_assembly (Orienting and gap filling contigs for Naive)` terminated with an error exit status (127)
Jun-16 23:28:31.392 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] kraken
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] tadpole
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] gap_fill_assembly
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: input_ref_fasta
  port 2: (cntrl) -     ; channel: $

[process] polish_assembly
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] final_mapping
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] var_calling
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] genomecov
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] vipr_tools
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

Jun-16 23:28:31.423 [main] DEBUG nextflow.Session - Session await > all process finished
Jun-16 23:28:31.423 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-16 23:28:31.430 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
Jun-16 23:28:31.507 [main] WARN  n.processor.TaskPollingMonitor - Killing pending tasks (2)
Jun-16 23:28:33.646 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=4; failedCount=3; ignoredCount=0; cachedCount=0; succeedDuration=3h 11m 26s; failedDuration=10.1s; cachedDuration=0ms]
Jun-16 23:28:33.646 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Jun-16 23:28:33.713 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Jun-16 23:28:34.053 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  {"kraken":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"decont":{"cpu":{"mean":123.6,"min":123.6,"q1":123.6,"q2":123.6,"q3":123.6,"max":123.6,"minLabel":"decont (Decontaminating Naive)","maxLabel":"decont (Decontaminating Naive)","q1Label":"decont (Decontaminating Naive)","q2Label":"decont (Decontaminating Naive)","q3Label":"decont (Decontaminating Naive)"},"mem":{"mean":5612908544,"min":5612908544,"q1":5612908544,"q2":5612908544,"q3":5612908544,"max":5612908544,"minLabel":"decont (Decontaminating Naive)","maxLabel":"decont (Decontaminating Naive)","q1Label":"decont (Decontaminating Naive)","q2Label":"decont (Decontaminating Naive)","q3Label":"decont (Decontaminating Naive)"},"vmem":{"mean":5895512064,"min":5895512064,"q1":5895512064,"q2":5895512064,"q3":5895512064,"max":5895512064,"minLabel":"decont (Decontaminating Naive)","maxLabel":"decont (Decontaminating Naive)","q1Label":"decont (Decontaminating Naive)","q2Label":"decont (Decontaminating Naive)","q3Label":"decont (Decontaminating Naive)"},"time":{"mean":9161559,"min":9161559,"q1":9161559,"q2":9161559,"q3":9161559,"max":9161559,"minLabel":"decont (Decontaminating Naive)","maxLabel":"decont (Decontaminating Naive)","q1Label":"decont (Decontaminating Naive)","q2Label":"decont (Decontaminating Naive)","q3Label":"decont (Decontaminating Naive)"},"reads":{"mean":24030255178,"min":24030255178,"q1":24030255178,"q2":24030255178,"q3":24030255178,"max":24030255178,"minLabel":"decont (Decontaminating Naive)","maxLabel":"decont (Decontaminating Naive)","q1Label":"decont (Decontaminating Naive)","q2Label":"decont (Decontaminating Naive)","q3Label":"decont (Decontaminating Naive)"},"writes":{"mean":18594019020,"min":18594019020,"q1":18594019020,"q2":18594019020,"q3":18594019020,"max":18594019020,"minLabel":"decont (Decontaminating Naive)","maxLabel":"decont (Decontaminating Naive)","q1Label":"decont (Decontaminating Naive)","q2Label":"decont (Decontaminating Naive)","q3Label":"decont (Decontaminating Naive)"},"cpuUsage":{"mean":123.6,"min":123.6,"q1":123.6,"q2":123.6,"q3":123.6,"max":123.6,"minLabel":"decont (Decontaminating Naive)","maxLabel":"decont (Decontaminating Naive)","q1Label":"decont (Decontaminating Naive)","q2Label":"decont (Decontaminating Naive)","q3Label":"decont (Decontaminating Naive)"},"memUsage":null,"timeUsage":null},"tadpole":{"cpu":{"mean":246.5,"min":246.5,"q1":246.5,"q2":246.5,"q3":246.5,"max":246.5,"minLabel":"tadpole (Tadpole assembly of Naive)","maxLabel":"tadpole (Tadpole assembly of Naive)","q1Label":"tadpole (Tadpole assembly of Naive)","q2Label":"tadpole (Tadpole assembly of Naive)","q3Label":"tadpole (Tadpole assembly of Naive)"},"mem":{"mean":9461837824,"min":9461837824,"q1":9461837824,"q2":9461837824,"q3":9461837824,"max":9461837824,"minLabel":"tadpole (Tadpole assembly of Naive)","maxLabel":"tadpole (Tadpole assembly of Naive)","q1Label":"tadpole (Tadpole assembly of Naive)","q2Label":"tadpole (Tadpole assembly of Naive)","q3Label":"tadpole (Tadpole assembly of Naive)"},"vmem":{"mean":18225332224,"min":18225332224,"q1":18225332224,"q2":18225332224,"q3":18225332224,"max":18225332224,"minLabel":"tadpole (Tadpole assembly of Naive)","maxLabel":"tadpole (Tadpole assembly of Naive)","q1Label":"tadpole (Tadpole assembly of Naive)","q2Label":"tadpole (Tadpole assembly of Naive)","q3Label":"tadpole (Tadpole assembly of Naive)"},"time":{"mean":109624,"min":109624,"q1":109624,"q2":109624,"q3":109624,"max":109624,"minLabel":"tadpole (Tadpole assembly of Naive)","maxLabel":"tadpole (Tadpole assembly of Naive)","q1Label":"tadpole (Tadpole assembly of Naive)","q2Label":"tadpole (Tadpole assembly of Naive)","q3Label":"tadpole (Tadpole assembly of Naive)"},"reads":{"mean":349938217,"min":349938217,"q1":349938217,"q2":349938217,"q3":349938217,"max":349938217,"minLabel":"tadpole (Tadpole assembly of Naive)","maxLabel":"tadpole (Tadpole assembly of Naive)","q1Label":"tadpole (Tadpole assembly of Naive)","q2Label":"tadpole (Tadpole assembly of Naive)","q3Label":"tadpole (Tadpole assembly of Naive)"},"writes":{"mean":41655608,"min":41655608,"q1":41655608,"q2":41655608,"q3":41655608,"max":41655608,"minLabel":"tadpole (Tadpole assembly of Naive)","maxLabel":"tadpole (Tadpole assembly of Naive)","q1Label":"tadpole (Tadpole assembly of Naive)","q2Label":"tadpole (Tadpole assembly of Naive)","q3Label":"tadpole (Tadpole assembly of Naive)"},"cpuUsage":{"mean":246.5,"min":246.5,"q1":246.5,"q2":246.5,"q3":246.5,"max":246.5,"minLabel":"tadpole (Tadpole assembly of Naive)","maxLabel":"tadpole (Tadpole assembly of Naive)","q1Label":"tadpole (Tadpole assembly of Naive)","q2Label":"tadpole (Tadpole assembly of Naive)","q3Label":"tadpole (Tadpole assembly of Naive)"},"memUsage":null,"timeUsage":null},"trim_and_combine":{"cpu":{"mean":216.25,"min":211.6,"q1":213.93,"q2":216.25,"q3":218.58,"max":220.9,"minLabel":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","maxLabel":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q1Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q2Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q3Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)"},"mem":{"mean":367212544,"min":365715456,"q1":366464000,"q2":367212544,"q3":367961088,"max":368709632,"minLabel":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","maxLabel":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q1Label":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q2Label":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q3Label":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)"},"vmem":{"mean":3564378112,"min":3538059264,"q1":3551218688,"q2":3564378112,"q3":3577537536,"max":3590696960,"minLabel":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","maxLabel":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q1Label":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q2Label":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q3Label":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)"},"time":{"mean":1107417.5,"min":670077,"q1":888747.25,"q2":1107417.5,"q3":1326087.75,"max":1544758,"minLabel":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","maxLabel":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q1Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q2Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q3Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)"},"reads":{"mean":35232222368,"min":20647943676,"q1":27940083022,"q2":35232222368,"q3":42524361714,"max":49816501060,"minLabel":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","maxLabel":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q1Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q2Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q3Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)"},"writes":{"mean":30821984038,"min":18147152151,"q1":24484568094.5,"q2":30821984038,"q3":37159399981.5,"max":43496815925,"minLabel":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","maxLabel":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q1Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q2Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q3Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)"},"cpuUsage":{"mean":216.25,"min":211.6,"q1":213.93,"q2":216.25,"q3":218.58,"max":220.9,"minLabel":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","maxLabel":"trim_and_combine (Preprocessing of 11  read pairs for Relapsed)","q1Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q2Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)","q3Label":"trim_and_combine (Preprocessing of 8  read pairs for Naive)"},"memUsage":null,"timeUsage":null},"gap_fill_assembly":{"cpu":null,"mem":null,"vmem":null,"time":{"mean":10096,"min":10096,"q1":10096,"q2":10096,"q3":10096,"max":10096,"minLabel":"gap_fill_assembly (Orienting and gap filling contigs for Naive)","maxLabel":"gap_fill_assembly (Orienting and gap filling contigs for Naive)","q1Label":"gap_fill_assembly (Orienting and gap filling contigs for Naive)","q2Label":"gap_fill_assembly (Orienting and gap filling contigs for Naive)","q3Label":"gap_fill_assembly (Orienting and gap filling contigs for Naive)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null}}
Jun-16 23:28:35.357 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Jun-16 23:28:39.071 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jun-16 23:28:39.275 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye