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epi2me-labs / wf-bacterial-genomes

Small variant calling for haploid samples
https://labs.epi2me.io/
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failing to run test_data #22

Closed splaisan closed 1 year ago

splaisan commented 1 year ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v0.4.0-g70714be

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-bacterial-genomes --fastq ./test_data/fastq --isolates --reference_based_assembly --reference ./test_data/ref/reference.subseq.fa.gz --sample_sheet ./test_data/isolates_sample_sheet.csv --out_dir test_run

Workflow Execution - CLI Execution Profile

None

What happened?

N E X T F L O W  ~  version 23.04.3
Launching `https://github.com/epi2me-labs/wf-bacterial-genomes` [loving_pasteur] DSL2 - revision: 70714be9ef [master]

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-bacterial-genomes v0.4.0-g70714be
--------------------------------------------------------------------------------
Core Nextflow options
  revision                : master
  runName                 : loving_pasteur
  containerEngine         : docker
  launchDir               : /opt/biotools/wf-bacterial-genomes
  workDir                 : /opt/biotools/wf-bacterial-genomes/work
  projectDir              : /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes
  userName                : u0002316
  profile                 : standard
  configFiles             : /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/nextflow.config, /opt/biotools/wf-bacterial-genomes/nextflow.config

Input Options
  fastq                   : ./test_data/fastq
  reference_based_assembly: true
  reference               : ./test_data/ref/reference.subseq.fa.gz

Sample Options
  sample_sheet            : ./test_data/isolates_sample_sheet.csv

Output Options
  out_dir                 : test_run

Isolate options
  isolates                : true

Advanced Options
  threads                 : 3

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-bacterial-genomes for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

--------------------------------------------------------------------------------
This is epi2me-labs/wf-bacterial-genomes v0.4.0-g70714be.
--------------------------------------------------------------------------------
Checking fastq input.
executor >  local (12)
executor >  local (12)
[5d/540bd7] process > validate_sample_sheet                                [100%] 1 of 1 ✔
[2c/b38300] process > fastcat (2)                                          [100%] 2 of 2 ✔
[15/a5e619] process > calling_pipeline:alignReads (1)                      [  0%] 0 of 1
[-        ] process > calling_pipeline:readStats                           -
[-        ] process > calling_pipeline:coverStats                          -
[-        ] process > calling_pipeline:splitRegions                        -
[31/2f8008] process > calling_pipeline:lookup_medaka_consensus_model (1)   [100%] 1 of 1 ✔
[a2/68e1ce] process > calling_pipeline:lookup_medaka_variant_model (1)     [100%] 1 of 1 ✔
[-        ] process > calling_pipeline:medakaNetwork                       -
[-        ] process > calling_pipeline:medakaConsensus                     -
[-        ] process > calling_pipeline:medakaVariantHdf                    -
[-        ] process > calling_pipeline:medakaVariant                       -
[-        ] process > calling_pipeline:runProkka                           -
[-        ] process > calling_pipeline:run_isolates:mlstSearch             -
[-        ] process > calling_pipeline:run_isolates:getPointfinderSpecies  -
[-        ] process > calling_pipeline:run_isolates:resfinder              -
[-        ] process > calling_pipeline:run_isolates:processResfinder       -
[0a/1f72d5] process > calling_pipeline:prokkaVersion                       [100%] 1 of 1 ✔
[0e/870bc7] process > calling_pipeline:medakaVersion                       [100%] 1 of 1 ✔
[6d/253928] process > calling_pipeline:mlstVersion                         [100%] 1 of 1 ✔
[23/bd2054] process > calling_pipeline:getVersions                         [100%] 1 of 1 ✔
[ab/321412] process > calling_pipeline:getParams                           [100%] 1 of 1 ✔
[-        ] process > calling_pipeline:makeReport                          -
[-        ] process > calling_pipeline:makePerSampleReports                -
[92/60cdb1] process > calling_pipeline:collectFastqIngressResultsInDir (1) [  0%] 0 of 3
[-        ] process > output                                               -
Reference based assembly selected.
ERROR ~ Cannot invoke method resolve() on null object

 -- Check script '/home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/main.nf' at line: 586 or see '.nextflow.log' file for more details
ERROR ~ Error executing process > 'calling_pipeline:alignReads (3)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

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

Relevant log output

Oct-27 15:51:09.716 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-bacterial-genomes --fastq ./test_data/fastq --isolates --reference_based_assembly --reference ./test_data/ref/reference.subseq.fa.gz --sample_sheet ./test_data/isolates_sample_sheet.csv --out_dir test_run
Oct-27 15:51:09.782 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.04.3
Oct-27 15:51:09.807 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/luna.kuleuven.be/u0002316/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.4
Oct-27 15:51:09.817 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-27 15:51:09.818 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-27 15:51:09.821 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-27 15:51:09.831 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Oct-27 15:51:09.845 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/luna.kuleuven.be/u0002316/.nextflow/scm
Oct-27 15:51:10.824 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-bacterial-genomes.git
Oct-27 15:51:10.850 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Oct-27 15:51:10.859 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-bacterial-genomes.git
Oct-27 15:51:11.654 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/nextflow.config
Oct-27 15:51:11.654 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /opt/biotools/wf-bacterial-genomes/nextflow.config
Oct-27 15:51:11.655 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/nextflow.config
Oct-27 15:51:11.655 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /opt/biotools/wf-bacterial-genomes/nextflow.config
Oct-27 15:51:11.666 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Oct-27 15:51:11.833 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Oct-27 15:51:11.867 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Oct-27 15:51:11.867 [main] INFO  nextflow.cli.CmdRun - Launching `https://github.com/epi2me-labs/wf-bacterial-genomes` [loving_pasteur] DSL2 - revision: 70714be9ef [master]
Oct-27 15:51:11.867 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-27 15:51:11.868 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-27 15:51:11.870 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/luna.kuleuven.be/u0002316/.nextflow/secrets/store.json
Oct-27 15:51:11.874 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6df4af5] - activable => nextflow.secret.LocalSecretsProvider@6df4af5
Oct-27 15:51:11.934 [main] DEBUG nextflow.Session - Session UUID: c5808332-0855-466a-aced-f2c7f191bfab
Oct-27 15:51:11.934 [main] DEBUG nextflow.Session - Run name: loving_pasteur
Oct-27 15:51:11.934 [main] DEBUG nextflow.Session - Executor pool size: 88
Oct-27 15:51:11.946 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=264; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct-27 15:51:11.971 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.04.3 build 5875
  Created: 11-08-2023 18:37 UTC (20:37 CEST)
  System: Linux 5.4.0-165-generic
  Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.8.1+1-Ubuntu-0ubuntu120.04
  Encoding: UTF-8 (UTF-8)
  Process: 343660@gbw-s-pacbio01 [10.118.132.7]
  CPUs: 88 - Mem: 503.8 GB (3.6 GB) - Swap: 0 (0)
Oct-27 15:51:11.990 [main] DEBUG nextflow.Session - Work-dir: /opt/biotools/wf-bacterial-genomes/work [ext2/ext3]
Oct-27 15:51:12.004 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-27 15:51:12.014 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-27 15:51:12.116 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-27 15:51:12.131 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 89; maxThreads: 1000
Oct-27 15:51:12.201 [main] DEBUG nextflow.Session - Session start
Oct-27 15:51:12.206 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /opt/biotools/wf-bacterial-genomes/test_run/execution/trace.txt
Oct-27 15:51:12.214 [main] DEBUG nextflow.Session - Using default localLib path: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/lib
Oct-27 15:51:12.217 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/lib
Oct-27 15:51:12.218 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/lib/nfcore_external_java_deps.jar
Oct-27 15:51:14.386 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-27 15:51:14.970 [main] INFO  nextflow.Nextflow - 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-bacterial-genomes v0.4.0-g70714be
--------------------------------------------------------------------------------
Core Nextflow options
  revision                : master
  runName                 : loving_pasteur
  containerEngine         : docker
  launchDir               : /opt/biotools/wf-bacterial-genomes
  workDir                 : /opt/biotools/wf-bacterial-genomes/work
  projectDir              : /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes
  userName                : u0002316
  profile                 : standard
  configFiles             : /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/nextflow.config, /opt/biotools/wf-bacterial-genomes/nextflow.config

Input Options
  fastq                   : ./test_data/fastq
  reference_based_assembly: true
  reference               : ./test_data/ref/reference.subseq.fa.gz

Sample Options
  sample_sheet            : ./test_data/isolates_sample_sheet.csv

Output Options
  out_dir                 : test_run

Isolate options
  isolates                : true

Advanced Options
  threads                 : 3

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-bacterial-genomes for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

--------------------------------------------------------------------------------
This is epi2me-labs/wf-bacterial-genomes v0.4.0-g70714be.
--------------------------------------------------------------------------------
Oct-27 15:51:15.219 [main] INFO  nextflow.Nextflow - Checking fastq input.
Oct-27 15:51:15.274 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `fastq_ingress,wf_common` for process with name validate_sample_sheet
Oct-27 15:51:15.292 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.292 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.299 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-27 15:51:15.305 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=8 GB; capacity=88; pollInterval=100ms; dumpInterval=5m
Oct-27 15:51:15.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `fastq_ingress,wf_common` for process with name fastcat
Oct-27 15:51:15.483 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.483 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.517 [main] INFO  nextflow.Nextflow - Reference based assembly selected.
Oct-27 15:51:15.534 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:alignReads
Oct-27 15:51:15.535 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.535 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.541 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:readStats
Oct-27 15:51:15.542 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.542 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.548 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:coverStats
Oct-27 15:51:15.549 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.550 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.554 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name calling_pipeline:splitRegions
Oct-27 15:51:15.554 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.554 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.563 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:lookup_medaka_consensus_model
Oct-27 15:51:15.564 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.565 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.570 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:lookup_medaka_variant_model
Oct-27 15:51:15.571 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.571 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.583 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name calling_pipeline:medakaNetwork
Oct-27 15:51:15.584 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.584 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.596 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name calling_pipeline:medakaConsensus
Oct-27 15:51:15.597 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.597 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.602 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name calling_pipeline:medakaVariantHdf
Oct-27 15:51:15.602 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.602 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.611 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name calling_pipeline:medakaVariant
Oct-27 15:51:15.611 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.611 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.617 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:prokka` matches labels `prokka` for process with name calling_pipeline:runProkka
Oct-27 15:51:15.618 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.618 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.622 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mlst` matches labels `mlst` for process with name calling_pipeline:run_isolates:mlstSearch
Oct-27 15:51:15.623 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.623 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.629 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:run_isolates:getPointfinderSpecies
Oct-27 15:51:15.630 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.630 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:amr` matches labels `amr` for process with name calling_pipeline:run_isolates:resfinder
Oct-27 15:51:15.641 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.641 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.648 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:run_isolates:processResfinder
Oct-27 15:51:15.649 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.649 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.654 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:prokka` matches labels `prokka` for process with name calling_pipeline:prokkaVersion
Oct-27 15:51:15.655 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.655 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.657 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name calling_pipeline:medakaVersion
Oct-27 15:51:15.658 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.658 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.660 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mlst` matches labels `mlst` for process with name calling_pipeline:mlstVersion
Oct-27 15:51:15.661 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.661 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.663 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:getVersions
Oct-27 15:51:15.664 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.664 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.666 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:getParams
Oct-27 15:51:15.667 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.667 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.696 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:makeReport
Oct-27 15:51:15.697 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.697 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.717 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:makePerSampleReports
Oct-27 15:51:15.718 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.718 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.722 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name calling_pipeline:collectFastqIngressResultsInDir
Oct-27 15:51:15.723 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.723 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.732 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfbacterialgenomes` matches labels `wfbacterialgenomes` for process with name output
Oct-27 15:51:15.733 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-27 15:51:15.733 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-27 15:51:15.735 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: resfinder, deNovo, calling_pipeline:getParams, calling_pipeline:mlstVersion, medakaVersion, alignReads, output, medakaVariant, medakaNetwork, collectFastqIngressResultsInDir, makeReport, calling_pipeline:collectFastqIngressResultsInDir, getVersions, calling_pipeline:coverStats, calling_pipeline:readStats, calling_pipeline:run_isolates:processResfinder, calling_pipeline:medakaConsensus, getPointfinderSpecies, calling_pipeline:getVersions, coverStats, calling_pipeline:runProkka, fastcat, mlstVersion, calling_pipeline:medakaVariantHdf, getParams, calling_pipeline:prokkaVersion, calling_pipeline:alignReads, medakaConsensus, validate_sample_sheet, medakaVariantHdf, calling_pipeline:run_isolates:resfinder, calling_pipeline:lookup_medaka_variant_model, calling_pipeline:medakaVersion, calling_pipeline:run_isolates:mlstSearch, readStats, runProkka, calling_pipeline:run_isolates:getPointfinderSpecies, lookup_medaka_variant_model, prokkaVersion, calling_pipeline:makePerSampleReports, lookup_medaka_consensus_model, calling_pipeline:medakaNetwork, splitRegions, calling_pipeline:makeReport, calling_pipeline:splitRegions, calling_pipeline:lookup_medaka_consensus_model, move_or_compress, processResfinder, mlstSearch, calling_pipeline:medakaVariant, makePerSampleReports
Oct-27 15:51:15.738 [main] DEBUG nextflow.Session - Igniting dataflow network (32)
Oct-27 15:51:15.738 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > validate_sample_sheet
Oct-27 15:51:15.744 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastcat
Oct-27 15:51:15.745 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:alignReads
Oct-27 15:51:15.745 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:readStats
Oct-27 15:51:15.746 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:coverStats
Oct-27 15:51:15.746 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:splitRegions
Oct-27 15:51:15.746 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:lookup_medaka_consensus_model
Oct-27 15:51:15.747 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:lookup_medaka_variant_model
Oct-27 15:51:15.747 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:medakaNetwork
Oct-27 15:51:15.747 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:medakaConsensus
Oct-27 15:51:15.747 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:medakaVariantHdf
Oct-27 15:51:15.747 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:medakaVariant
Oct-27 15:51:15.747 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:runProkka
Oct-27 15:51:15.747 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:run_isolates:mlstSearch
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:run_isolates:getPointfinderSpecies
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:run_isolates:resfinder
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:run_isolates:processResfinder
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:prokkaVersion
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:medakaVersion
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:mlstVersion
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:getVersions
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:getParams
Oct-27 15:51:15.748 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:makeReport
Oct-27 15:51:15.749 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:makePerSampleReports
Oct-27 15:51:15.749 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > calling_pipeline:collectFastqIngressResultsInDir
Oct-27 15:51:15.749 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output
Oct-27 15:51:15.749 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Oct-27 15:51:15.749 [main] DEBUG nextflow.Session - Session await
Oct-27 15:51:15.819 [Actor Thread 79] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/bin/workflow-glue
Oct-27 15:51:15.842 [Actor Thread 83] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/data/medaka_models.tsv
Oct-27 15:51:15.888 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:15.890 [Task submitter] INFO  nextflow.Session - [ab/321412] Submitted process > calling_pipeline:getParams
Oct-27 15:51:15.897 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:15.897 [Task submitter] INFO  nextflow.Session - [0a/1f72d5] Submitted process > calling_pipeline:prokkaVersion
Oct-27 15:51:15.903 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:15.903 [Task submitter] INFO  nextflow.Session - [5d/540bd7] Submitted process > validate_sample_sheet
Oct-27 15:51:15.908 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:15.909 [Task submitter] INFO  nextflow.Session - [a2/68e1ce] Submitted process > calling_pipeline:lookup_medaka_variant_model (1)
Oct-27 15:51:17.007 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: calling_pipeline:getParams; status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/ab/321412e265e6dfb37d01304470c290]
Oct-27 15:51:17.024 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:17.025 [Task submitter] INFO  nextflow.Session - [31/2f8008] Submitted process > calling_pipeline:lookup_medaka_consensus_model (1)
Oct-27 15:51:17.202 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: calling_pipeline:prokkaVersion; status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/0a/1f72d5cc3ca0a225bf2f31177070a2]
Oct-27 15:51:17.215 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:17.216 [Task submitter] INFO  nextflow.Session - [0e/870bc7] Submitted process > calling_pipeline:medakaVersion
Oct-27 15:51:18.675 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: calling_pipeline:medakaVersion; status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/0e/870bc758a3f3d7274743e8c5b0b5b6]
Oct-27 15:51:18.696 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:18.697 [Task submitter] INFO  nextflow.Session - [6d/253928] Submitted process > calling_pipeline:mlstVersion
Oct-27 15:51:28.452 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: calling_pipeline:mlstVersion; status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/6d/253928b88a84420488faf94a90eb04]
Oct-27 15:51:28.467 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:28.468 [Task submitter] INFO  nextflow.Session - [23/bd2054] Submitted process > calling_pipeline:getVersions
Oct-27 15:51:29.872 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: calling_pipeline:getVersions; status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/23/bd20541e8f1e6cd8dc2b2692f735fb]
Oct-27 15:51:37.325 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: calling_pipeline:lookup_medaka_variant_model (1); status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/a2/68e1ce0dce4d13116f48a9767b7922]
Oct-27 15:51:37.414 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: validate_sample_sheet; status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/5d/540bd7d4b8ae2fcbbe11d0ba96e070]
Oct-27 15:51:37.449 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:37.450 [Task submitter] INFO  nextflow.Session - [20/335c74] Submitted process > fastcat (1)
Oct-27 15:51:38.045 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: calling_pipeline:lookup_medaka_consensus_model (1); status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/31/2f80086f6d1e7368581b0ce3c0450b]
Oct-27 15:51:38.584 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: fastcat (1); status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/20/335c74a6db68e30f7fb05dc84d8bbd]
Oct-27 15:51:38.592 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:38.593 [Task submitter] INFO  nextflow.Session - [2c/b38300] Submitted process > fastcat (2)
Oct-27 15:51:39.553 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: fastcat (2); status: COMPLETED; exit: 0; error: -; workDir: /opt/biotools/wf-bacterial-genomes/work/2c/b38300b76f95b72dd8b5351ace4841]
Oct-27 15:51:39.561 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:39.562 [Task submitter] INFO  nextflow.Session - [15/a5e619] Submitted process > calling_pipeline:alignReads (1)
Oct-27 15:51:39.561 [Actor Thread 84] ERROR nextflow.extension.OperatorImpl - @unknown
java.lang.NullPointerException: Cannot invoke method resolve() on null object
    at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:44)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:34)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:49)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
    at Script_96e8d947$_runScript_closure22$_closure54$_closure74.doCall(Script_96e8d947:586)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at org.codehaus.groovy.runtime.metaclass.TransformMetaMethod.invoke(TransformMetaMethod.java:55)
    at groovy.lang.MetaClassImpl$2.invoke(MetaClassImpl.java:1298)
    at org.codehaus.groovy.runtime.metaclass.TransformMetaMethod.doMethodInvoke(TransformMetaMethod.java:62)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
    at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56)
    at jdk.internal.reflect.GeneratedMethodAccessor226.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
    at groovy.lang.Closure.call(Closure.java:412)
    at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
    at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108)
    at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
    at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
    at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
    at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
    at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:833)
Oct-27 15:51:39.565 [Actor Thread 81] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=calling_pipeline:alignReads (3); work-dir=null
  error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)
Oct-27 15:51:39.566 [Actor Thread 85] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/luna.kuleuven.be/u0002316/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/data/OPTIONAL_FILE
Oct-27 15:51:39.567 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-27 15:51:39.571 [Task submitter] INFO  nextflow.Session - [92/60cdb1] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (1)
Oct-27 15:51:39.572 [Actor Thread 84] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke method resolve() on null object
Oct-27 15:51:39.576 [Actor Thread 81] ERROR nextflow.processor.TaskProcessor - Error executing process > 'calling_pipeline:alignReads (3)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Oct-27 15:51:39.578 [Actor Thread 87] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=calling_pipeline:alignReads (4); work-dir=null
  error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)
Oct-27 15:51:39.580 [Actor Thread 79] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=calling_pipeline:alignReads; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Oct-27 15:51:39.588 [Actor Thread 89] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.021 s; external sort time: 0.001 s; total time: 0.022 s
Oct-27 15:51:39.600 [Actor Thread 84] DEBUG nextflow.Session - The following nodes are still active:
[process] calling_pipeline:readStats
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

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

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

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

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

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

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

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

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

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

[process] calling_pipeline:run_isolates:resfinder
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: resfinder_threshold
  port 2: (value) bound ; channel: resfinder_coverage
  port 3: (cntrl) -     ; channel: $

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

[process] calling_pipeline:makeReport
  status=ACTIVE
  port 0: (value) bound ; channel: versions/*
  port 1: (value) bound ; channel: params.json
  port 2: (value) OPEN  ; channel: variants/*
  port 3: (value) bound ; channel: sample_ids
  port 4: (value) OPEN  ; channel: prokka/*
  port 5: (queue) OPEN  ; channel: per_read_stats
  port 6: (value) OPEN  ; channel: fwd/*
  port 7: (value) OPEN  ; channel: rev/*
  port 8: (value) OPEN  ; channel: total_depth/*
  port 9: (value) bound ; channel: flye_stats/*
  port 10: (value) OPEN  ; channel: resfinder/*
  port 11: (value) OPEN  ; channel: mlst/*
  port 12: (cntrl) -     ; channel: $

[process] calling_pipeline:makePerSampleReports
  status=ACTIVE
  port 0: (value) bound ; channel: versions.txt
  port 1: (value) bound ; channel: params.json
  port 2: (queue) OPEN  ; channel: -
  port 3: (cntrl) -     ; channel: $

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

Oct-27 15:51:39.609 [Actor Thread 89] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /opt/biotools/wf-bacterial-genomes/work/collect-file/d35a16d66436dbbd20902f201ee6075d
Oct-27 15:51:39.617 [Actor Thread 89] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-662444189237774055
Oct-27 15:51:39.686 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-27 15:51:39.686 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-27 15:51:39.727 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (2)
Oct-27 15:51:39.744 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=10; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=4; submittedCount=2; runningCount=-2; retriesCount=0; abortedCount=2; succeedDuration=1m 4s; failedDuration=0ms; cachedDuration=0ms;loadCpus=-4; loadMemory=0; peakRunning=4; peakCpus=4; peakMemory=0; ]
Oct-27 15:51:39.745 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Oct-27 15:51:39.747 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Oct-27 15:51:39.825 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  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Oct-27 15:51:40.370 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Oct-27 15:51:40.432 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-27 15:51:40.452 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Application activity log entry

No response

splaisan commented 1 year ago

HI again Sam, Apparently the samplesheet I used wongtains more barcodes than there are barcodes in the fastq which lead to crash I re-ran with ./test_data/sample_sheet.csv and it now finished

I was misled by the example command included in the --help output

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-bacterial-genomes v0.4.0-g70714be
--------------------------------------------------------------------------------
Typical pipeline command:

  nextflow run epi2me-labs/wf-bacterial-genomes \ 
    --fastq 'wf-bacterial-genomes-demo/isolates_fastq' \ 
    --isolates \ 
    --reference_based_assembly \ 
    --reference 'wf-bacterial-genomes-demo/ref/ref.fasta.gz' \ 
    --sample_sheet 'wf-bacterial-genomes-demo/isolates_sample_sheet.csv'

maybe just edit this in the next version to use the right sample_sheet.csv

cheers,

SamStudio8 commented 1 year ago

@splaisan Thanks for pointing that out, I'll raise a ticket!

splaisan commented 1 year ago

nice report, looking forward to see my own data there!