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need help with 'pipeline:assembleCore' #60

Open
Suchi-alt opened this issue Dec 5, 2024 · 4 comments
Open

need help with 'pipeline:assembleCore' #60

Suchi-alt opened this issue Dec 5, 2024 · 4 comments

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@Suchi-alt
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Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.5.0-g1196320

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-clone-validation --fastq combined_reads.fastq.gz --full_reference CSWA.fasta --out_dir output --assembly_tool flye --threads 8 -w work --process.memory '16 GB' --process.cpus 8

Workflow Execution - CLI Execution Profile

None

What happened?

I'm currently trying to run the wf-clone-validation workflow from the epi2me-labs repository using my FASTQ files. I have configured the workflow to use Flye as the assembly tool, but I'm encountering an error during the assembleCore process."[fc/61b5be] NOTE: Process pipeline:assembleCore (1) terminated with an error exit status (1) -- Execution is retried (1)"

Relevant log output

$ nextflow run epi2me-labs/wf-clone-validation \
  --fastq combined_reads.fastq.gz \
  --full_reference CSWA.fasta \
  --out_dir output \
  --assembly_tool flye \
  --threads 8 \
  -w work \
  --process.memory '16 GB' \
  --process.cpus 8

 N E X T F L O W   ~  version 24.10.2

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [e2543f0351]
Launching `https://github.com/epi2me-labs/wf-clone-validation` [confident_swirles] DSL2 - revision: 11963203a3 [master]


WARN: Found unexpected parameters:
* --process: [memory:16 GB, cpus:8]
- Ignore this warning: params.schema_ignore_params = "process"


||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-clone-validation v1.5.0-g1196320
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : confident_swirles
  containerEngine: docker
  container      : [withLabel:wfplasmid:ontresearch/wf-clone-validation:sha55e97540ca3ca4f06310269c2ebd3175e1e9352a, withLabel:canu:ontresearch/canu:shabbdea3813f6fb436ea0cbaa19958ad772db9154c, withLabel:medaka:ontresearch/medaka:sha447c70a639b8bcf17dc49b51e74dfcde6474837b, withLabel:wf_common:ontresearch/wf-common:shad28e55140f75a68f59bbecc74e880aeab16ab158, withLabel:plannotate:ontresearch/plannotate:shaf7f37f751dd0bc529121b765fb63322502288a03]
  launchDir      : /mnt/d/Email CSWA/Email CSWA
  workDir        : /mnt/d/Email CSWA/Email CSWA/work
  projectDir     : /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation
  userName       : epi2mewsl
  profile        : standard
  configFiles    : /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config

Input Options
  fastq          : combined_reads.fastq.gz

Reference Genome Options
  full_reference : CSWA.fasta

Miscellaneous Options
  threads        : 8

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

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


--------------------------------------------------------------------------------
This is epi2me-labs/wf-clone-validation v1.5.0-g1196320.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
executor >  local (21)
[72/699c75] fastcat (1)                     [100%] 1 of 1 ✔
[-        ] cutsite_qc                      -
[73/5afb2e] pipeline:checkIfEnoughReads (1) [100%] 1 of 1 ✔
[1b/c907ec] pipeline:assembleCore (1)       [100%] 5 of 5, failed: 4, retries: 4 ✔
[-        ] pipeline:medakaPolishAssembly   -
[2d/1c5870] pipeline:downsampledStats (1)   [100%] 1 of 1 ✔
[-        ] pipeline:findPrimers            -
[11/c9a479] pipeline:medakaVersion          [100%] 1 of 1 ✔
[42/530317] pipeline:flyeVersion            [100%] 1 of 1 ✔
[82/80409a] pipeline:getVersions            [100%] 1 of 1 ✔
[ff/0bfdef] pipeline:getParams              [100%] 1 of 1 ✔
[-        ] pipeline:assembly_qc            -
[1b/97c382] pipeline:inserts (1)            [100%] 1 of 1 ✔
[-        ] pipeline:insert_qc              -
[-        ] pipeline:align_assembly         -
[-        ] pipeline:assembly_comparison    -
[1a/1d2d15] pipeline:runPlannotate (1)      [100%] 1 of 1 ✔
[-        ] pipeline:assemblyMafs           -
[90/f37700] pipeline:report (1)             [100%] 1 of 1 ✔
[7f/407acc] output (3)                      [100%] 6 of 6 ✔
[fc/61b5be] NOTE: Process `pipeline:assembleCore (1)` terminated with an error exit status (1) -- Execution is retried (1)
[4a/956905] NOTE: Process `pipeline:assembleCore (1)` terminated with an error exit status (1) -- Execution is retried (2)
[2a/73da7c] NOTE: Process `pipeline:assembleCore (1)` terminated with an error exit status (1) -- Execution is retried (3)
[04/55d635] NOTE: Process `pipeline:assembleCore (1)` terminated with an error exit status (1) -- Execution is retried (4)

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response
@cjw85
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cjw85 commented Dec 5, 2024

Please provide a full log after the workflow has failed to complete successfully. The log above shows that the workflow is still running.

@Suchi-alt
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Author

its completed, attached a picture
Screenshot 2024-12-05 094320

@Suchi-alt
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Dec-05 07:28:38.964 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-clone-validation --fastq combined_reads.fastq.gz --full_reference CSWA.fasta --out_dir output --assembly_tool flye --threads 8 -w work --process.memory '16 GB' --process.cpus 8
Dec-05 07:28:39.050 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.2
Dec-05 07:28:39.067 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/epi2mewsl/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Dec-05 07:28:39.083 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Dec-05 07:28:39.086 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Dec-05 07:28:39.088 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Dec-05 07:28:39.103 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Dec-05 07:28:39.112 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/epi2mewsl/.nextflow/scm
Dec-05 07:28:39.593 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/.git/config; branch: null; remote: origin; url: https://github.com/epi2me-labs/wf-clone-validation.git
Dec-05 07:28:39.616 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Dec-05 07:28:39.624 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/.git/config; branch: null; remote: origin; url: https://github.com/epi2me-labs/wf-clone-validation.git
Dec-05 07:28:40.443 [main] INFO nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [e2543f0]
Dec-05 07:28:40.453 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config
Dec-05 07:28:40.456 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config
Dec-05 07:28:40.461 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/epi2mewsl/.nextflow/secrets/store.json
Dec-05 07:28:40.464 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@7b53b1ad] - activable => nextflow.secret.LocalSecretsProvider@7b53b1ad
Dec-05 07:28:40.472 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Dec-05 07:28:40.578 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Dec-05 07:28:40.579 [main] DEBUG nextflow.cli.CmdRun - Launching https://github.com/epi2me-labs/wf-clone-validation [confident_swirles] DSL2 - revision: 1196320 [master]
Dec-05 07:28:40.581 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Dec-05 07:28:40.581 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Dec-05 07:28:40.617 [main] DEBUG nextflow.Session - Session UUID: 20d0aad0-d2f6-484a-9578-38613e6bd91f
Dec-05 07:28:40.618 [main] DEBUG nextflow.Session - Run name: confident_swirles
Dec-05 07:28:40.619 [main] DEBUG nextflow.Session - Executor pool size: 14
Dec-05 07:28:40.627 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Dec-05 07:28:40.631 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=42; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Dec-05 07:28:40.647 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.10.2 build 5932
Created: 27-11-2024 21:23 UTC (21:23 GMT)
System: Linux 5.15.167.4-microsoft-standard-WSL2
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 11.0.21+9-post-Ubuntu-0ubuntu122.04
Encoding: UTF-8 (UTF-8)
Process: 25464@LAPTOP-GB3OBPGT [127.0.1.1]
CPUs: 14 - Mem: 13.7 GB (11.9 GB) - Swap: 4 GB (4 GB)
Dec-05 07:28:40.670 [main] DEBUG nextflow.file.FileHelper - Can't check if specified path is NFS (1): /mnt/d/Email CSWA/Email CSWA/work

Dec-05 07:28:40.671 [main] DEBUG nextflow.Session - Work-dir: /mnt/d/Email CSWA/Email CSWA/work [null]
Dec-05 07:28:40.694 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Dec-05 07:28:40.703 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Dec-05 07:28:40.742 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Dec-05 07:28:40.750 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 15; maxThreads: 1000
Dec-05 07:28:40.834 [main] DEBUG nextflow.Session - Session start
Dec-05 07:28:40.836 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/d/Email CSWA/Email CSWA/output/execution/trace.txt
Dec-05 07:28:40.845 [main] DEBUG nextflow.Session - Using default localLib path: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/lib
Dec-05 07:28:40.849 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/lib
Dec-05 07:28:40.850 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/lib/nfcore_external_java_deps.jar
Dec-05 07:28:42.577 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Dec-05 07:28:43.650 [main] WARN nextflow.Nextflow - Found unexpected parameters:

  • --process: [memory:16 GB, cpus:8]
    Dec-05 07:28:43.651 [main] INFO nextflow.Nextflow - �[2m- Ignore this warning: params.schema_ignore_params = "process" �[0m
    Dec-05 07:28:43.665 [main] INFO nextflow.Nextflow -
    �[0;92m|||||||||| �[0m�[2m_____ ____ ___ ____ __ __ _____ _ _
    �[0;92m|||||||||| �[0m�[2m| | _ _ | | / | | | | __ | | ___
    �[0;33m||||| �[0m�[2m| | | |) | | __) | |/| | | _| |/ ` | ' / |
    �[0;33m||||| �[0m�[2m| |    | /| | / /| | | | ||    | | (    | | |    ) _
    �[0;94m|||||||||| �[0m�[2m|_____|    | |    ||| ||| ||_,|./|__/
    �[0;94m|||||||||| �[0m�[1mwf-clone-validation v1.5.0-g1196320�[0m
    �[2m--------------------------------------------------------------------------------�[0m
    �[1mCore Nextflow options�[0m
    �[0;34mrevision : �[0;32mmaster�[0m
    �[0;34mrunName : �[0;32mconfident_swirles�[0m
    �[0;34mcontainerEngine: �[0;32mdocker�[0m
    �[0;34mcontainer : �[0;32m[withLabel:wfplasmid:ontresearch/wf-clone-validation:sha55e97540ca3ca4f06310269c2ebd3175e1e9352a, withLabel:canu:ontresearch/canu:shabbdea3813f6fb436ea0cbaa19958ad772db9154c, withLabel:medaka:ontresearch/medaka:sha447c70a639b8bcf17dc49b51e74dfcde6474837b, withLabel:wf_common:ontresearch/wf-common:shad28e55140f75a68f59bbecc74e880aeab16ab158, withLabel:plannotate:ontresearch/plannotate:shaf7f37f751dd0bc529121b765fb63322502288a03]�[0m
    �[0;34mlaunchDir : �[0;32m/mnt/d/Email CSWA/Email CSWA�[0m
    �[0;34mworkDir : �[0;32m/mnt/d/Email CSWA/Email CSWA/work�[0m
    �[0;34mprojectDir : �[0;32m/home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation�[0m
    �[0;34muserName : �[0;32mepi2mewsl�[0m
    �[0;34mprofile : �[0;32mstandard�[0m
    �[0;34mconfigFiles : �[0;32m/home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config�[0m

�[1mInput Options�[0m
�[0;34mfastq : �[0;32mcombined_reads.fastq.gz�[0m

�[1mReference Genome Options�[0m
�[0;34mfull_reference : �[0;32mCSWA.fasta�[0m

�[1mMiscellaneous Options�[0m
�[0;34mthreads : �[0;32m8�[0m

!! Only displaying parameters that differ from the pipeline defaults !!
�[2m--------------------------------------------------------------------------------�[0m
If you use epi2me-labs/wf-clone-validation for your analysis please cite:

�[2m--------------------------------------------------------------------------------�[0m
This is epi2me-labs/wf-clone-validation v1.5.0-g1196320.
�[2m--------------------------------------------------------------------------------�[0m
Dec-05 07:28:44.380 [main] INFO nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Dec-05 07:28:44.470 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_common matches labels ingress,wf_common for process with name fastcat
Dec-05 07:28:44.479 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.479 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.485 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Dec-05 07:28:44.490 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=14; memory=13.7 GB; capacity=14; pollInterval=100ms; dumpInterval=5m
Dec-05 07:28:44.492 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Dec-05 07:28:44.576 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name cutsite_qc
Dec-05 07:28:44.578 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.578 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.611 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:checkIfEnoughReads
Dec-05 07:28:44.613 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.613 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.622 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:assembleCore
Dec-05 07:28:44.624 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.624 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.656 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:medaka matches labels medaka for process with name pipeline:medakaPolishAssembly
Dec-05 07:28:44.660 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.660 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.669 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:downsampledStats
Dec-05 07:28:44.670 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.671 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.677 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:findPrimers
Dec-05 07:28:44.678 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.679 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.684 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:medaka matches labels medaka for process with name pipeline:medakaVersion
Dec-05 07:28:44.685 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.685 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.689 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:flyeVersion
Dec-05 07:28:44.690 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.691 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.694 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:getVersions
Dec-05 07:28:44.695 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.695 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.698 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:getParams
Dec-05 07:28:44.699 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.700 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.708 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:assembly_qc
Dec-05 07:28:44.710 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.710 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.715 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:inserts
Dec-05 07:28:44.716 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.716 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.733 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:insert_qc
Dec-05 07:28:44.734 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.735 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.744 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:align_assembly
Dec-05 07:28:44.745 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.746 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.751 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:assembly_comparison
Dec-05 07:28:44.753 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.753 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:plannotate matches labels plannotate for process with name pipeline:runPlannotate
Dec-05 07:28:44.781 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.781 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.787 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:assemblyMafs
Dec-05 07:28:44.789 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.789 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.817 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name pipeline:report
Dec-05 07:28:44.819 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.820 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.840 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfplasmid matches labels wfplasmid for process with name output
Dec-05 07:28:44.841 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Dec-05 07:28:44.841 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-05 07:28:44.844 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: pipeline:medakaPolishAssembly, pipeline:inserts, move_or_compress_fq_file, pipeline:getParams, align_assembly, pipeline:assembleCore, downsampledStats, pipeline:flyeVersion, checkBamHeaders, medakaVersion, mergeBams, assembly_comparison, output, pipeline:align_assembly, findPrimers, assembleCore, getVersions, validateIndex, pipeline:report, bamstats, assembly_qc, canuVersion, fastcat, filterHostReads, pipeline:runPlannotate, samtools_index, getParams, pipeline:assembly_qc, pipeline:assemblyMafs, sortBam, assemblyMafs, validate_sample_sheet, checkIfEnoughReads, pipeline:medakaVersion, assembleCore_flye, insert_qc, flyeVersion, runPlannotate, cutsite_qc, pipeline:getVersions, pipeline:checkIfEnoughReads, pipeline:downsampledStats, split_fq_file, pipeline:findPrimers, medakaPolishAssembly, pipeline:assembly_comparison, report, pipeline:insert_qc, inserts, catSortBams
Dec-05 07:28:44.845 [main] DEBUG nextflow.Session - Igniting dataflow network (22)
Dec-05 07:28:44.853 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastcat
Dec-05 07:28:44.854 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > cutsite_qc
Dec-05 07:28:44.855 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:checkIfEnoughReads
Dec-05 07:28:44.857 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:assembleCore
Dec-05 07:28:44.859 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:medakaPolishAssembly
Dec-05 07:28:44.859 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:downsampledStats
Dec-05 07:28:44.860 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:findPrimers
Dec-05 07:28:44.861 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:medakaVersion
Dec-05 07:28:44.862 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:flyeVersion
Dec-05 07:28:44.862 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getVersions
Dec-05 07:28:44.863 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getParams
Dec-05 07:28:44.863 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:assembly_qc
Dec-05 07:28:44.865 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:inserts
Dec-05 07:28:44.865 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:insert_qc
Dec-05 07:28:44.865 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:align_assembly
Dec-05 07:28:44.866 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:assembly_comparison
Dec-05 07:28:44.867 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:runPlannotate
Dec-05 07:28:44.867 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:assemblyMafs
Dec-05 07:28:44.867 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:report
Dec-05 07:28:44.869 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output
Dec-05 07:28:44.871 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_18a09640d1f864d9: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/./lib/ingress.nf
Script_596de616803176eb: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/./modules/local/flye_assembly.nf
Script_6624ee78039f48dd: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/main.nf
Dec-05 07:28:44.871 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Dec-05 07:28:44.872 [main] DEBUG nextflow.Session - Session await
Dec-05 07:28:45.049 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:45.052 [Task submitter] INFO nextflow.Session - [72/699c75] Submitted process > fastcat (1)
Dec-05 07:28:45.063 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:45.064 [Task submitter] INFO nextflow.Session - [ff/0bfdef] Submitted process > pipeline:getParams
Dec-05 07:28:45.077 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:45.078 [Task submitter] INFO nextflow.Session - [11/c9a479] Submitted process > pipeline:medakaVersion
Dec-05 07:28:46.579 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: fastcat (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/72/699c7551f20eb2eec384ff8e7be312]
Dec-05 07:28:46.579 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=42; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Dec-05 07:28:46.640 [Actor Thread 8] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Dec-05 07:28:46.677 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:46.679 [Task submitter] INFO nextflow.Session - [73/5afb2e] Submitted process > pipeline:checkIfEnoughReads (1)
Dec-05 07:28:46.728 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: pipeline:getParams; status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/ff/0bfdef8fcae00b98851aac73aaaf54]
Dec-05 07:28:47.763 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: pipeline:checkIfEnoughReads (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/73/5afb2e1c215fd081fd6506a2f29c65]
Dec-05 07:28:47.809 [Actor Thread 13] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/deconcatenate.py
Dec-05 07:28:47.827 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:47.828 [Task submitter] INFO nextflow.Session - [fc/61b5be] Submitted process > pipeline:assembleCore (1)
Dec-05 07:28:48.110 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: pipeline:medakaVersion; status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/11/c9a479c228d98e136ba082dee33a59]
Dec-05 07:28:48.127 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:48.128 [Task submitter] INFO nextflow.Session - [42/530317] Submitted process > pipeline:flyeVersion
Dec-05 07:28:49.477 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: pipeline:flyeVersion; status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/42/530317e19e9d1f14825a6292c30ed6]
Dec-05 07:28:49.495 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:49.495 [Task submitter] INFO nextflow.Session - [82/80409a] Submitted process > pipeline:getVersions
Dec-05 07:28:50.566 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: pipeline:assembleCore (1); status: COMPLETED; exit: 1; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/fc/61b5be608e51e678115057c0918300]
Dec-05 07:28:50.574 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:assembleCore (1); work-dir=/mnt/d/Email CSWA/Email CSWA/work/fc/61b5be608e51e678115057c0918300
error [nextflow.exception.ProcessFailedException]: Process pipeline:assembleCore (1) terminated with an error exit status (1)
Dec-05 07:28:50.584 [TaskFinalizer-6] INFO nextflow.processor.TaskProcessor - [fc/61b5be] NOTE: Process pipeline:assembleCore (1) terminated with an error exit status (1) -- Execution is retried (1)
Dec-05 07:28:50.600 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:50.601 [Task submitter] INFO nextflow.Session - [4a/956905] Re-submitted process > pipeline:assembleCore (1)
Dec-05 07:28:52.302 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: pipeline:getVersions; status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/82/80409abc6d72a165dbdf14d82159c0]
Dec-05 07:28:53.148 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: pipeline:assembleCore (1); status: COMPLETED; exit: 1; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/4a/956905f325872fdb1cac8a2a725d4f]
Dec-05 07:28:53.152 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:assembleCore (1); work-dir=/mnt/d/Email CSWA/Email CSWA/work/4a/956905f325872fdb1cac8a2a725d4f
error [nextflow.exception.ProcessFailedException]: Process pipeline:assembleCore (1) terminated with an error exit status (1)
Dec-05 07:28:53.153 [TaskFinalizer-8] INFO nextflow.processor.TaskProcessor - [4a/956905] NOTE: Process pipeline:assembleCore (1) terminated with an error exit status (1) -- Execution is retried (2)
Dec-05 07:28:53.167 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:53.168 [Task submitter] INFO nextflow.Session - [2a/73da7c] Re-submitted process > pipeline:assembleCore (1)
Dec-05 07:28:55.629 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: pipeline:assembleCore (1); status: COMPLETED; exit: 1; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/2a/73da7c741fcc3ab31e5a8ddd31a4ad]
Dec-05 07:28:55.632 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:assembleCore (1); work-dir=/mnt/d/Email CSWA/Email CSWA/work/2a/73da7c741fcc3ab31e5a8ddd31a4ad
error [nextflow.exception.ProcessFailedException]: Process pipeline:assembleCore (1) terminated with an error exit status (1)
Dec-05 07:28:55.633 [TaskFinalizer-9] INFO nextflow.processor.TaskProcessor - [2a/73da7c] NOTE: Process pipeline:assembleCore (1) terminated with an error exit status (1) -- Execution is retried (3)
Dec-05 07:28:55.647 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:55.648 [Task submitter] INFO nextflow.Session - [04/55d635] Re-submitted process > pipeline:assembleCore (1)
Dec-05 07:28:58.118 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: pipeline:assembleCore (1); status: COMPLETED; exit: 1; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/04/55d6355d633f7bc22451365bdf8655]
Dec-05 07:28:58.123 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:assembleCore (1); work-dir=/mnt/d/Email CSWA/Email CSWA/work/04/55d6355d633f7bc22451365bdf8655
error [nextflow.exception.ProcessFailedException]: Process pipeline:assembleCore (1) terminated with an error exit status (1)
Dec-05 07:28:58.124 [TaskFinalizer-10] INFO nextflow.processor.TaskProcessor - [04/55d635] NOTE: Process pipeline:assembleCore (1) terminated with an error exit status (1) -- Execution is retried (4)
Dec-05 07:28:58.140 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:28:58.141 [Task submitter] INFO nextflow.Session - [1b/c907ec] Re-submitted process > pipeline:assembleCore (1)
Dec-05 07:29:00.542 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: pipeline:assembleCore (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/1b/c907ece2ccaa199d38803d44b60102]
Dec-05 07:29:00.545 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process pipeline:assembleCore (1) is unable to find [UnixPath]: /mnt/d/Email CSWA/Email CSWA/work/1b/c907ece2ccaa199d38803d44b60102/combined_reads.reconciled.fasta (pattern: combined_reads.reconciled.fasta)
Dec-05 07:29:00.599 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process pipeline:assembleCore > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Dec-05 07:29:00.618 [Actor Thread 11] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/data/OPTIONAL_FILE
Dec-05 07:29:00.619 [Actor Thread 11] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/workflow-glue
Dec-05 07:29:00.632 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:00.633 [Task submitter] INFO nextflow.Session - [2d/1c5870] Submitted process > pipeline:downsampledStats (1)
Dec-05 07:29:00.643 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:00.643 [Task submitter] INFO nextflow.Session - [1b/97c382] Submitted process > pipeline:inserts (1)
Dec-05 07:29:01.694 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: pipeline:downsampledStats (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/2d/1c58707ff010f2e2707e52366b269f]
Dec-05 07:29:02.733 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: pipeline:inserts (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/1b/97c3820e187d8b3d6e29ff22024c85]
Dec-05 07:29:02.745 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process pipeline:inserts > Skipping output binding because one or more optional files are missing: fileoutparam<0>
Dec-05 07:29:02.796 [Actor Thread 16] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.008 s; total time: 0.009 s
Dec-05 07:29:02.811 [Actor Thread 16] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mnt/d/Email CSWA/Email CSWA/work/collect-file/8f87707a2af9d8c58ac0c5bae2556923
Dec-05 07:29:02.817 [Actor Thread 16] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-8410525957829904177
Dec-05 07:29:02.836 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:02.837 [Task submitter] INFO nextflow.Session - [1a/1d2d15] Submitted process > pipeline:runPlannotate (1)
Dec-05 07:29:06.119 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: pipeline:runPlannotate (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/1a/1d2d15e6683d6393a10f03bcfe7d47]
Dec-05 07:29:06.142 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process pipeline:runPlannotate > Skipping output binding because one or more optional files are missing: fileoutparam<2>
Dec-05 07:29:06.142 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process pipeline:runPlannotate > Skipping output binding because one or more optional files are missing: fileoutparam<4>
Dec-05 07:29:06.213 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:06.214 [Task submitter] INFO nextflow.Session - [90/f37700] Submitted process > pipeline:report (1)
Dec-05 07:29:19.122 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: pipeline:report (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/90/f3770041114e29560ec3974c659180]
Dec-05 07:29:19.181 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process pipeline:report > Skipping output binding because one or more optional files are missing: fileoutparam<2>
Dec-05 07:29:19.201 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:19.202 [Task submitter] INFO nextflow.Session - [04/b0ed3c] Submitted process > output (6)
Dec-05 07:29:19.209 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:19.210 [Task submitter] INFO nextflow.Session - [b8/572548] Submitted process > output (2)
Dec-05 07:29:19.219 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:19.219 [Task submitter] INFO nextflow.Session - [f3/14ac1e] Submitted process > output (4)
Dec-05 07:29:19.229 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:19.229 [Task submitter] INFO nextflow.Session - [7c/d51a13] Submitted process > output (1)
Dec-05 07:29:19.241 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:19.241 [Task submitter] INFO nextflow.Session - [7f/407acc] Submitted process > output (3)
Dec-05 07:29:19.252 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Dec-05 07:29:19.253 [Task submitter] INFO nextflow.Session - [69/826078] Submitted process > output (5)
Dec-05 07:29:20.588 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: output (6); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/04/b0ed3cb487232bc0ff7450dd39d953]
Dec-05 07:29:20.599 [TaskFinalizer-6] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=42; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Dec-05 07:29:21.013 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: output (2); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/b8/5725486c43fca2e88accf14436e130]
Dec-05 07:29:21.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: output (4); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/f3/14ac1efdc2fdedb63edd22c14a157b]
Dec-05 07:29:21.899 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: output (5); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/69/8260786ac29b790e97e7f2bd4c7515]
Dec-05 07:29:22.094 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: output (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/7c/d51a134b5cc624d6b4e3560e8e293e]
Dec-05 07:29:22.294 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: output (3); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/Email CSWA/Email CSWA/work/7f/407accb1e0b080fac6b977753fa21f]
Dec-05 07:29:22.298 [main] DEBUG nextflow.Session - Session await > all processes finished
Dec-05 07:29:22.394 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Dec-05 07:29:22.395 [main] DEBUG nextflow.Session - Session await > all barriers passed
Dec-05 07:29:22.399 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Dec-05 07:29:22.400 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Dec-05 07:29:22.865 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=17; failedCount=4; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=4; abortedCount=0; succeedDuration=36s; failedDuration=1m 20s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=6; peakCpus=10; peakMemory=6 GB; ]
Dec-05 07:29:22.866 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Dec-05 07:29:22.868 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Dec-05 07:29:23.258 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Dec-05 07:29:23.414 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Dec-05 07:29:23.432 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Dec-05 07:29:23.434 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

@Suchi-alt
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okay, it worked i guess.
$ nextflow run epi2me-labs/wf-clone-validation --fastq combined_reads.fastq/ --out_dir output --assembly_tool flye --threads 4 --approx_size 10000 --assm_coverage 60 --trim_length 150 --flye_quality nano-hq --large_construct True --cutsite_mismatch 1 --primer_mismatch 2 --canu_fast False

N E X T F L O W ~ version 24.10.2

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [e2543f0]
Launching https://github.com/epi2me-labs/wf-clone-validation [admiring_hawking] DSL2 - revision: 1196320 [master]

|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | | _ _ | | / | | | | __ | | ___
||||| | | | |) | | __) | |/| | | _| |/ ` | ' / |
||||| | || /| | / /| | | | ||| | (| | |) _
|||||||||| |_____|| |||| ||| ||_,|./|__/
|||||||||| wf-clone-validation v1.5.0-g1196320

Core Nextflow options
revision : master
runName : admiring_hawking
containerEngine: docker
container : [withLabel:wfplasmid:ontresearch/wf-clone-validation:sha55e97540ca3ca4f06310269c2ebd3175e1e9352a, withLabel:canu:ontresearch/canu:shabbdea3813f6fb436ea0cbaa19958ad772db9154c, withLabel:medaka:ontresearch/medaka:sha447c70a639b8bcf17dc49b51e74dfcde6474837b, withLabel:wf_common:ontresearch/wf-common:shad28e55140f75a68f59bbecc74e880aeab16ab158, withLabel:plannotate:ontresearch/plannotate:shaf7f37f751dd0bc529121b765fb63322502288a03]
launchDir : /mnt/d/Email_CSWA/Email_cSWA
workDir : /mnt/d/Email_CSWA/Email_cSWA/work
projectDir : /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation
userName : epi2mewsl
profile : standard
configFiles : /home/epi2mewsl/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config

Input Options
fastq : combined_reads.fastq/
approx_size : 10000

Advanced Options
large_construct: true

!! Only displaying parameters that differ from the pipeline defaults !!

If you use epi2me-labs/wf-clone-validation for your analysis please cite:

This is epi2me-labs/wf-clone-validation v1.5.0-g1196320.

Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
executor > local (25)
[c3/55d8d7] fastcat (1) | 1 of 1 ✔
[- ] cutsite_qc -
[48/24bc81] pipeline:checkIfEnoughReads (1) | 1 of 1 ✔
[77/6fcd21] pipeline:assembleCore (1) | 1 of 1 ✔
[84/6725ce] pipeline:medakaPolishAssembly (1) | 1 of 1 ✔
[5b/e30511] pipeline:downsampledStats (1) | 1 of 1 ✔
[18/527d4b] pipeline:findPrimers (1) | 1 of 1 ✔
[1b/128f33] pipeline:medakaVersion | 1 of 1 ✔
[2c/6983c8] pipeline:flyeVersion | 1 of 1 ✔
[bb/2d336f] pipeline:getVersions | 1 of 1 ✔
[b6/5baab7] pipeline:getParams | 1 of 1 ✔
[7e/9f0f41] pipeline:assembly_qc (1) | 1 of 1 ✔
[91/42c20d] pipeline:inserts (1) | 1 of 1 ✔
[- ] pipeline:insert_qc -
[- ] pipeline:align_assembly -
[- ] pipeline:assembly_comparison -
[58/ca6b9c] pipeline:runPlannotate (1) | 1 of 1 ✔
[21/9ed26d] pipeline:assemblyMafs (1) | 1 of 1 ✔
[dc/55290a] pipeline:report (1) | 1 of 1 ✔
[fc/16f2b5] output (10) | 10 of 10 ✔
Completed at: 05-Dec-2024 09:37:04
Duration : 1m 8s
CPU hours : (a few seconds)
Succeeded : 25

the read length changes everytime I combine the fastq files or use just the .fastq.gz

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@cjw85 @Suchi-alt