nf-core / vipr Goto Github PK

Assembly and intrahost / low-frequency variant calling for viral samples

License: MIT License

Nextflow 84.06% Python 14.02% Dockerfile 1.92%

nf-core nextflow workflow viral viral-genomics variant-calling metagenomics genome-assembly viral-ngs viral-metagenomics

vipr's Introduction

Introduction

nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Pipeline Steps

Step	Main program/s
Trimming, combining of read-pairs per sample and QC	Skewer, FastQC
Decontamination	decont
Metagenomics classification / Sample purity	Kraken
Assembly to contigs	BBtools' Tadpole
Assembly polishing	ViPR Tools
Mapping to assembly	BWA, LoFreq
Low frequency variant calling	LoFreq
Coverage and variant AF plots (two processes)	Bedtools, ViPR Tools

Documentation

Documentation about the pipeline can be found in the docs/ directory:

Credits

This pipeline was originally developed by Andreas Wilm (andreas-wilm) at Genome Institute of Singapore. It started out as an ecosystem around LoFreq and went through a couple of iterations. The current version had three predecessors ViPR 1, ViPR 2 and ViPR 3

An incomplete list of publications using (previous versions of) ViPR:

Plenty of people provided essential feedback, including:

October SESSIONS
Paola Florez DE SESSIONS
ZHU Yuan
Shuzhen SIM
CHU Wenhan Collins

vipr's People

Contributors

Stargazers

Watchers

Forkers

andreas-wilm hpcbio alneberg apeltzer ewels esteinig dockstoretestuser2 tuj-aerish nilesh-tawari biofriends latchbio-nfcore

vipr's Issues

Add aws, docker and singularity profiles

Add docs/configuration

Allow other means of read input besides params.yaml

Error when run pipeline with docker file

Hi, when I ran this command :

nextflow run nf-core/vipr -params-file vi.yaml -profile docker

I met this error:

N E X T F L O W  ~  version 0.31.1
Launching `nf-core/vipr` [gloomy_almeida] - revision: 1ca3412b9d [master]
==================================================
 nf-core/vipr : Viral amplicon/enrichment analysis and intrahost variant calling: v1.0-dev
==================================================
List of samples: PDH203_GTGGCC
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$trim_and_combine = <value>` with a process selector
[warm up] executor > local
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$decont = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$kraken = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$tadpole = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$gap_fill_assembly = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$polish_assembly = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$final_mapping = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$var_calling = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$genomecov = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$vipr_tools = <value>` with a process selector
[c6/04f746] Submitted process > trim_and_combine (Preprocessing of 1  read pairs for PDH203_GTGGCC)
ERROR ~ Error executing process > 'trim_and_combine (Preprocessing of 1  read pairs for PDH203_GTGGCC)'

Caused by:
  Process `trim_and_combine (Preprocessing of 1  read pairs for PDH203_GTGGCC)` terminated with an error exit status (125)

Command executed:

  # loop over readunits in pairs per sample
  pairno=0
  echo 425-N706-S517_S6_L001_R1_001.fastq 425-N706-S517_S6_L001_R2_001.fastq | xargs -n2 | while read fq1 fq2; do
      let pairno=pairno+1
      # note: don't make reads smaller than assembler kmer length
      skewer --quiet -t 4 -m pe -q 3 -n -l 31 -z -o pair${pairno}-skewer-out $fq1 $fq2;
      cat *-trimmed-pair1.fastq.gz >> PDH203_GTGGCC_R1-trimmed.fastq.gz;
      cat *-trimmed-pair2.fastq.gz >> PDH203_GTGGCC_R2-trimmed.fastq.gz;
      rm *-trimmed-pair[12].fastq.gz;
  done
  fastqc -t {task.cpus} PDH203_GTGGCC_R1-trimmed.fastq.gz PDH203_GTGGCC_R2-trimmed.fastq.gz;

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'nfcore/vipr:1.0-dev' locally
  docker: Error response from daemon: manifest for nfcore/vipr:1.0-dev not found.
  See 'docker run --help'.

Work dir:
  /home/vi/work/c6/04f746274f2e2baec8dcb1b457ba47

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option `-resume`

 -- Check '.nextflow.log' file for details
Oops... Pipeline execution stopped with the following message: Unable to find image 'nfcore/vipr:1.0-dev' locally
docker: Error response from daemon: manifest for nfcore/vipr:1.0-dev not found.
See 'docker run --help'.
Pipeline execution summary
    ---------------------------
    Completed at : Mon Sep 24 03:55:39 UTC 2018
    Duration     : 5.6s
    Success      : false
    Work Dir     : /home/vi/work
    Exit status  : 125
    Error report : Error executing process > 'trim_and_combine (Preprocessing of 1  read pairs for PDH203_GTGGCC)'

Caused by:
  Process `trim_and_combine (Preprocessing of 1  read pairs for PDH203_GTGGCC)` terminated with an error exit status (125)

Command executed:

  # loop over readunits in pairs per sample
  pairno=0
  echo 425-N706-S517_S6_L001_R1_001.fastq 425-N706-S517_S6_L001_R2_001.fastq | xargs -n2 | while read fq1 fq2; do
      let pairno=pairno+1
      # note: don't make reads smaller than assembler kmer length
      skewer --quiet -t 4 -m pe -q 3 -n -l 31 -z -o pair${pairno}-skewer-out $fq1 $fq2;
      cat *-trimmed-pair1.fastq.gz >> PDH203_GTGGCC_R1-trimmed.fastq.gz;
      cat *-trimmed-pair2.fastq.gz >> PDH203_GTGGCC_R2-trimmed.fastq.gz;
      rm *-trimmed-pair[12].fastq.gz;
  done
  fastqc -t {task.cpus} PDH203_GTGGCC_R1-trimmed.fastq.gz PDH203_GTGGCC_R2-trimmed.fastq.gz;

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'nfcore/vipr:1.0-dev' locally
  docker: Error response from daemon: manifest for nfcore/vipr:1.0-dev not found.
  See 'docker run --help'.

Work dir:
  /home/vi/work/c6/04f746274f2e2baec8dcb1b457ba47

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option `-resume`

WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

After that, I think I have prolem with the url of docker, So I edited the nextflow.config from
container = "nfcore/vipr:${version}" // for GIS translated into conda env name!
to
container = "nfcore/vipr
So the pipeline worked on first process. But it error on the second process

>N E X T F L O W  ~  version 0.31.1
Launching `nf-core/vipr` [ridiculous_boyd] - revision: 1ca3412b9d [master]
==================================================
 nf-core/vipr : Viral amplicon/enrichment analysis and intrahost variant calling: v1.0-dev
==================================================
List of samples: PDH203_GTGGCC
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$trim_and_combine = <value>` with a process selector
[warm up] executor > local
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$decont = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$kraken = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$tadpole = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$gap_fill_assembly = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$polish_assembly = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$final_mapping = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$var_calling = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$genomecov = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$vipr_tools = <value>` with a process selector
[f8/88c7c1] Submitted process > trim_and_combine (Preprocessing of 1  read pairs for PDH203_GTGGCC)
[42/27852b] Submitted process > decont (Decontaminating PDH203_GTGGCC)
ERROR ~ Error executing process > 'decont (Decontaminating PDH203_GTGGCC)'

Caused by:
  Process `decont (Decontaminating PDH203_GTGGCC)` terminated with an error exit status (1)

Command executed:

  decont.py -i PDH203_GTGGCC_R1-trimmed.fastq.gz PDH203_GTGGCC_R2-trimmed.fastq.gz -t 4 -c 0.5 -r human_g1k_v37.fasta -o PDH203_GTGGCC_trimmed_decont;
  # since this is the last fastqc processing step, let's run fastqc here
  fastqc -t {task.cpus} PDH203_GTGGCC_trimmed_decont_1.fastq.gz PDH203_GTGGCC_trimmed_decont_2.fastq.gz;

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  Traceback (most recent call last):
    File "/opt/conda/bin/decont.py", line 449, in <module>
      assert shutil.which('bwa') and shutil.which('samtools')
  AttributeError: 'module' object has no attribute 'which'

Work dir:
  /home/vi/.nextflow/assets/nf-core/vipr/work/42/27852be75b8444b072ea29c2bbaa61

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
Oops... Pipeline execution stopped with the following message: WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
  File "/opt/conda/bin/decont.py", line 449, in <module>
    assert shutil.which('bwa') and shutil.which('samtools')
AttributeError: 'module' object has no attribute 'which'
Pipeline execution summary
    ---------------------------
    Completed at : Mon Sep 24 04:09:36 UTC 2018
    Duration     : 24.8s
    Success      : false
    Work Dir     : /home/vi/.nextflow/assets/nf-core/vipr/work
    Exit status  : 1
    Error report : Error executing process > 'decont (Decontaminating PDH203_GTGGCC)'

Caused by:
  Process `decont (Decontaminating PDH203_GTGGCC)` terminated with an error exit status (1)

Command executed:

  decont.py -i PDH203_GTGGCC_R1-trimmed.fastq.gz PDH203_GTGGCC_R2-trimmed.fastq.gz -t 4 -c 0.5 -r human_g1k_v37.fasta -o PDH203_GTGGCC_trimmed_decont;
  # since this is the last fastqc processing step, let's run fastqc here
  fastqc -t {task.cpus} PDH203_GTGGCC_trimmed_decont_1.fastq.gz PDH203_GTGGCC_trimmed_decont_2.fastq.gz;

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  Traceback (most recent call last):
    File "/opt/conda/bin/decont.py", line 449, in <module>
      assert shutil.which('bwa') and shutil.which('samtools')
  AttributeError: 'module' object has no attribute 'which'

Work dir:
  /home/vi/.nextflow/assets/nf-core/vipr/work/42/27852be75b8444b072ea29c2bbaa61

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

I think, i had problem with the docker file. Do you recommend I will use docker or using conda for software dependencies ?.

Kiên

Add a report (MultiQC) summarizing analysis

Run nf-core lint

Speed up consensus iteration

Use plain consensus rules for variant calling in consensus update. This will be much faster and we can live with a few FP / FN, since a final LoFreq call is done eventually anyway

Push containers to nf-core

add Singularity file

cf #10

Error executing process > gap_fill_assembly

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

Naming conventions

Please follow our naming conventions too :-)
cf qbic-pipelines/icgc-featurecounts#8

Add your name to copyright in licence.md

Add the copyright holder to Licence file again.

Get rid of Groovy flag in GitHub

==> create a file ".gitattributes" that assumes the configs are nextflow ;-)

https://github.com/nf-core/rnaseq/blob/master/.gitattributes

Missing TEMPLATE branch

Hi,
I'm looking at all pipelines, and I noticed that this one is missing a branch.
All pipelines should have a TEMPLATE branch.

Add support for single-end read data

Error on VIPR4

Dear
I met this error when running VIPR4 pipeline, please help me. This is the log file

root@vi-dengue:~# cat .nextflow.log
Sep-20 10:00:08.987 [main] DEBUG nextflow.cli.Launcher - $> /usr/local/bin/nextflow run vipr/ -params-file vi.yaml -profile docker
Sep-20 10:00:09.097 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.31.1
Sep-20 10:00:09.591 [main] INFO  nextflow.cli.CmdRun - Launching `vipr/main.nf` [nice_hoover] - revision: 26fe4451e5
Sep-20 10:00:09.605 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/vi/vipr/nextflow.config
Sep-20 10:00:09.606 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/vi/vipr/nextflow.config
Sep-20 10:00:09.613 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Sep-20 10:00:09.687 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, gis, conda, awsbatch, singularity, docker]
Sep-20 10:00:09.755 [main] DEBUG nextflow.Session - Session uuid: 40df97f6-a0ea-4127-a041-2b75d8ffbe9c
Sep-20 10:00:09.755 [main] DEBUG nextflow.Session - Run name: nice_hoover
Sep-20 10:00:09.756 [main] DEBUG nextflow.Session - Executor pool size: 5
Sep-20 10:00:09.939 [main] DEBUG nextflow.cli.CmdRun -
  Version: 0.31.1 build 4886
  Modified: 07-08-2018 15:53 UTC
  System: Linux 4.4.0-133-generic
  Runtime: Groovy 2.4.15 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_181-b13
  Encoding: UTF-8 (UTF-8)
  Process: 1620@localhost null
  CPUs: 5 - Mem: 15.3 GB (383.4 MB) - Swap: 31.2 GB (31.2 GB)
Sep-20 10:00:09.964 [main] DEBUG nextflow.Session - Work-dir: /home/vi/work [ext2/ext3]
Sep-20 10:00:09.964 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/vi/vipr/bin
Sep-20 10:00:10.229 [main] DEBUG nextflow.Session - Session start invoked
Sep-20 10:00:10.233 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Sep-20 10:00:10.233 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/vi/results/pipeline_info/nfcore-vipr_trace.txt
Sep-20 10:00:10.238 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Sep-20 10:00:10.283 [main] DEBUG nextflow.Session - Session aborted -- Cause: startup failed:
_nf_script_1396a082: 94: unexpected token: } @ line 94, column 1.
}
^

1 error

Sep-20 10:00:10.296 [main] ERROR nextflow.cli.Launcher - startup failed:
_nf_script_1396a082: 94: unexpected token: } @ line 94, column 1.
}
^

1 error

Pipeline development

Is this pipeline being developed?

add CHANGELOG

cf #10

Add a DOI on first release

params.tracedir in nextflow.config

When I run the pipeline, I found the error :
${params.tracedir} is not found
I don't find any record which has related to tracedir. So I added the value of tracedir like outdir

params {
    // defaults. best not changed
    version = '1.0-dev' // Pipeline version
    container = "nfcore/vipr:${version}" // for GIS translated into conda env name!
    nf_required_version = '0.30.2' // Minimum version of nextflow required
    outdir = 'results'
    tracedir = 'results'
    // Pipeline options
    skip_kraken = false
}

It worked but is it wrong ?.

Thanks,
Kien

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