Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Regarding groovyx.gpar error: #951

Closed
5 tasks done
BADMANSachin opened this issue Mar 3, 2023 · 6 comments
Closed
5 tasks done

Regarding groovyx.gpar error: #951

BADMANSachin opened this issue Mar 3, 2023 · 6 comments
Labels
bug Something isn't working

Comments

@BADMANSachin
Copy link

BADMANSachin commented Mar 3, 2023 •
edited
Loading

Check Documentation

I have checked the following places for your error:

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line: nextflow run ...
  2. See error: Please provide your error message

Expected behaviour

Log files

Have you provided the following extra information/files:

  • The command used to run the pipeline
  • The .nextflow.log file
  • The exact error:

System

  • Hardware:
  • Executor:
  • OS:
  • Version

Nextflow Installation

  • Version:

Container engine

  • Engine:
  • version:
  • Image tag:

Additional context
@BADMANSachin BADMANSachin added the bug Something isn't working label Mar 3, 2023
@BADMANSachin
Copy link
Author

When I an running the nextflow I encountered something that was not there earlier:

No signature of method: groovyx.gpars.dataflow.DataflowBroadcast.into() is applicable for argument types: (Script_78514563$_runScript_closure23) values: [Script_78514563$_runScript_closure23@3842317]
Possible solutions: find(), any(), bind(java.lang.Object), any(groovy.lang.Closure), print(java.lang.Object), find(groovy.lang.Closure)

-- Check script '/home/adna-niraj/.nextflow/assets/nf-core/eager/main.nf' at line: 199 or see '.nextflow.log' file for more details

Kindly help in this regard

@jfy133
Copy link
Member

jfy133 commented Mar 3, 2023 •
edited
Loading

Hi @BADMANSachin

You've ticked you've supplied th following but I don't see them posted... can you send them again? We unable to evaluate your issue without them as you've provided no context to what is giving your error above.

image

@BADMANSachin
Copy link
Author

Oh Sorry, my Bad

Here are they
Command:
nextflow run nf-core/eager -profile conda --input '*_R{1,2}.fastq.gz' --paired_end --fasta chrM.fasta

Error:
WARN: Found unexpected parameters:

  • --paired_end: true
  • Ignore this warning: params.schema_ignore_params = "paired_end"

No signature of method: groovyx.gpars.dataflow.DataflowBroadcast.into() is applicable for argument types: (Script_78514563$_runScript_closure23) values: [Script_78514563$_runScript_closure23@4d6ad67b]
Possible solutions: find(), any(), bind(java.lang.Object), any(groovy.lang.Closure), print(java.lang.Object), find(groovy.lang.Closure)

-- Check script '/home/adna-niraj/.nextflow/assets/nf-core/eager/main.nf' at line: 199 or see '.nextflow.log' file for more details

Log:
Mar-03 17:12:00.569 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/eager -profile conda --input '*_R{1,2}.fastq.gz' --paired_end --fasta chrM.fasta
Mar-03 17:12:00.653 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.02.1-edge
Mar-03 17:12:00.679 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/adna-niraj/.nextflow/plugins; core-plugins: nf-amazon@1.15.0,nf-azure@0.15.1,nf-codecommit@0.1.3,nf-console@1.0.5,nf-ga4gh@1.0.4,nf-google@1.7.0,nf-tower@1.5.10,nf-wave@0.7.2
Mar-03 17:12:00.693 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-03 17:12:00.694 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-03 17:12:00.698 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Mar-03 17:12:00.711 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Mar-03 17:12:00.728 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/adna-niraj/.nextflow/scm
Mar-03 17:12:01.962 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/adna-niraj/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git
Mar-03 17:12:01.986 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Mar-03 17:12:01.995 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/adna-niraj/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git
Mar-03 17:12:06.445 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/adna-niraj/.nextflow/assets/nf-core/eager/nextflow.config
Mar-03 17:12:06.447 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/adna-niraj/.nextflow/assets/nf-core/eager/nextflow.config
Mar-03 17:12:06.459 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: conda
Mar-03 17:12:07.551 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [test_tsv_fna, cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, lugh, unibe_ibu, vai, test_tsv_kraken, czbiohub_aws, jax, ccga_med, scw, tigem, google, ipop_up, eddie, medair, test_direct, bi, bigpurple, sbc_sharc, adcra, test_bam, cedars, ucl_myriad, utd_ganymede, charliecloud, icr_davros, test_tsv_humanbam, ceres, test_kraken, munin, rosalind, hasta, cfc, uzh, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, wehi, awsbatch, imperial, maestro, test_tsv_bam, genotoul, abims, nihbiowulf, nu_genomics, oist, sahmri, benchmarking_human, mpcdf, test_stresstest_human, leicester, vsc_ugent, sage, cambridge, podman, cheaha, test, computerome, seg_globe, sanger, dkfz, pasteur, test_full, test_fna, azurebatch, hki, test_pretrim, crukmi, docker, engaging, gis, psmn, eva, benchmarking_vikingfish, test_humanbam, fgcz, conda, crg, singularity, prince, utd_sysbio, debug, genouest, cbe, test_tsv_pretrim, test_tsv_complex, phoenix, uct_hpc, aws_tower, binac]
Mar-03 17:12:07.589 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Mar-03 17:12:07.589 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/nf-core/eager [crazy_panini] DSL2 - revision: bb32ae3 [master]
Mar-03 17:12:07.590 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Mar-03 17:12:07.590 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Mar-03 17:12:07.594 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/adna-niraj/.nextflow/secrets/store.json
Mar-03 17:12:07.597 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@7c453c34] - activable => nextflow.secret.LocalSecretsProvider@7c453c34
Mar-03 17:12:07.694 [main] DEBUG nextflow.Session - Session UUID: 5fb5c7cb-c9c3-4d72-96cb-33ae700c87ef
Mar-03 17:12:07.694 [main] DEBUG nextflow.Session - Run name: crazy_panini
Mar-03 17:12:07.705 [main] DEBUG nextflow.Session - Executor pool size: 40
Mar-03 17:12:07.719 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=120; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Mar-03 17:12:07.743 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.02.1-edge build 5845
Created: 26-02-2023 18:43 UTC (27-02-2023 00:13 IDT)
System: Linux 5.15.0-60-generic
Runtime: Groovy 3.0.15 on OpenJDK 64-Bit Server VM 11.0.18+10-post-Ubuntu-0ubuntu120.04.1
Encoding: UTF-8 (UTF-8)
Process: 391788@aDNA-workstation [127.0.1.1]
CPUs: 40 - Mem: 251.6 GB (112.4 GB) - Swap: 2 GB (2 GB)
Mar-03 17:12:07.761 [main] DEBUG nextflow.file.FileHelper - Can't check if specified path is NFS (1): /media/adna-niraj/One Touch/Project_9_Kottapuram_29032022/Kottapurram/New_Analysis_03032023/EAGER_Kotta/work

Mar-03 17:12:07.761 [main] DEBUG nextflow.Session - Work-dir: /media/adna-niraj/One Touch/Project_9_Kottapuram_29032022/Kottapurram/New_Analysis_03032023/EAGER_Kotta/work [null]
Mar-03 17:12:07.779 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Mar-03 17:12:07.790 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Mar-03 17:12:08.010 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Mar-03 17:12:08.022 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 41; maxThreads: 1000
Mar-03 17:12:08.320 [main] DEBUG nextflow.Session - Session start
Mar-03 17:12:08.333 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /media/adna-niraj/One Touch/Project_9_Kottapuram_29032022/Kottapurram/New_Analysis_03032023/EAGER_Kotta/results/pipeline_info/execution_trace_2023-03-03_17-12-07.txt
Mar-03 17:12:08.352 [main] DEBUG nextflow.Session - Using default localLib path: /home/adna-niraj/.nextflow/assets/nf-core/eager/lib
Mar-03 17:12:08.357 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/adna-niraj/.nextflow/assets/nf-core/eager/lib
Mar-03 17:12:08.358 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/adna-niraj/.nextflow/assets/nf-core/eager/lib/nfcore_external_java_deps.jar
Mar-03 17:12:14.329 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-03 17:12:14.357 [main] INFO nextflow.Nextflow -

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
nf-core/eager v2.4.6

Mar-03 17:12:14.755 [main] WARN nextflow.Nextflow - Found unexpected parameters:

  • --paired_end: true
    Mar-03 17:12:14.756 [main] INFO nextflow.Nextflow - - Ignore this warning: params.schema_ignore_params = "paired_end"
    Mar-03 17:12:14.804 [main] DEBUG nextflow.Session - Session aborted -- Cause: No signature of method: groovyx.gpars.dataflow.DataflowBroadcast.into() is applicable for argument types: (Script_78514563$_runScript_closure23) values: [Script_78514563$_runScript_closure23@60950f4b]
    Possible solutions: any(), find(), bind(java.lang.Object), with(groovy.lang.Closure), print(java.io.PrintWriter), print(java.lang.Object)
    Mar-03 17:12:14.826 [main] ERROR nextflow.cli.Launcher - @unknown
    groovy.lang.MissingMethodException: No signature of method: groovyx.gpars.dataflow.DataflowBroadcast.into() is applicable for argument types: (Script_78514563$_runScript_closure23) values: [Script_78514563$_runScript_closure23@60950f4b]
    Possible solutions: any(), find(), bind(java.lang.Object), with(groovy.lang.Closure), print(java.io.PrintWriter), print(java.lang.Object)
    at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:70)
    at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:46)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
    at Script_78514563.runScript(Script_78514563:199)
    at nextflow.script.BaseScript.run0(BaseScript.groovy:146)
    at nextflow.script.BaseScript.run(BaseScript.groovy:193)
    at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:230)
    at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:225)
    at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:131)
    at nextflow.cli.CmdRun.run(CmdRun.groovy:369)
    at nextflow.cli.Launcher.run(Launcher.groovy:495)

Please have a look....................

@jfy133
Copy link
Member

jfy133 commented Mar 6, 2023

hi @BADMANSachin

  1. I would recommend reading the documention (usage, parameters pages), before you run the pipeline - you are providing a non-existing parameter (--paired-end)
  2. If you are trying the pipeline out for the first time, I would also recommend running with the latest stable release of the pipeline not an edge release (this is equivalent to a beta release, where things may be 'broken') - you should be trying with 22.10.* not 23.02.1-edge
  3. However if you really want to run with the edge version, you could try running by adding the following to your command -dsl1 -dsl2 false, this may fix your issue. This should be set in the pipeline, but I suspect something has been removed in the edge release of nextflow...

Please let me know if either reverting back to an earlier version (recommended), or adding the -dsl* flags work.

@BADMANSachin
Copy link
Author

BADMANSachin commented Mar 6, 2023 via email

@jfy133
Copy link
Member

jfy133 commented Mar 22, 2023

Hi @BADMANSachin , I 'm going to assume this is solved so closing now. Feel free to reopen if necessayr.

@jfy133 jfy133 closed this as completed Mar 22, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@jfy133 @BADMANSachin