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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Regarding groovyx.gpar error: #951

Closed BADMANSachin closed 1 year ago

BADMANSachin commented 1 year ago

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:

System

Nextflow Installation

Container engine

Additional context

BADMANSachin commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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:

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: bb32ae3b01 [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:

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

jfy133 commented 1 year ago

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 commented 1 year ago

Thanks for your suggestion. I will do the same and get back to you.

Thank

On Mon, Mar 6, 2023 at 1:16 PM James A. Fellows Yates < @.***> wrote:

hi @BADMANSachin https://github.com/BADMANSachin

  1. I would recommend reading the documention https://nf-co.re/eager (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.

— Reply to this email directly, view it on GitHub https://github.com/nf-core/eager/issues/951#issuecomment-1455625867, or unsubscribe https://github.com/notifications/unsubscribe-auth/AYAU4WSJISVJ7HLWI6MVX5DW2WI6LANCNFSM6AAAAAAVOQ6Y2Y . You are receiving this because you were mentioned.Message ID: @.***>

-- Sachin Kumar Srivastava Ph.D Scholar (Junior Research Fellow)

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jfy133 commented 1 year ago

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