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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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Erreur on: nextflow run epi2me-labs/wf-artic --scheme_name SARS-CoV-2 -- scheme_version Midnight-ONT/V1 --min_len 200 --max_len 1100 --out_dir #114

Open Yacsaw81 opened 2 weeks ago

Yacsaw81 commented 2 weeks ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v0.3.21-g0175e81

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

We have run the script on a computer after changing the version of Minknow to version 24.06.8.

EPI2ME Version

v0.3.21-g0175e81

CLI command run

nextflow run epi2me-labs/wf-artic --scheme_name SARS-CoV-2 -- scheme_version Midnight-ONT/V1 --min_len 200 --max_len 1100 --out_dir

Workflow Execution - CLI Execution Profile

None

What happened?

I got this :Checking fastq input. [- ] process > pipeline:getVersions - [- ] process > pipeline:getParams - [- ] process > pipeline:copySchemeDir - [- ] process > pipeline:getVersions - [- ] process > pipeline:getParams - [- ] process > pipeline:copySchemeDir -

Whereas I usually get Fasta with this command

Relevant log output

(base) seq-chuss@Seq-CHUSS:~$ nextflow run epi2me-labs/wf-artic --scheme_name SARS-CoV-2 --scheme_version Midnight-ONT/V1 --min_len 200 --max_len 1100 --out_dir MidnightResults_Run7_1 --fastq Run7_1_fastq_pass/ -work-dir /tmp/
N E X T F L O W  ~  version 22.10.6
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [21a482fb48]
Launching `https://github.com/epi2me-labs/wf-artic` [furious_poisson] DSL2 - revision: 0175e81492 [master]

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-artic v0.3.21-g0175e81
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : furious_poisson
  containerEngine: docker
  launchDir      : /home/seq-chuss
  workDir        : /tmp
  projectDir     : /home/seq-chuss/.nextflow/assets/epi2me-labs/wf-artic
  userName       : seq-chuss
  profile        : standard
  configFiles    : /home/seq-chuss/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config

Input Options
  fastq          : Run7_1_fastq_pass/

Primer Scheme Selection
  scheme_version : Midnight-ONT/V1

Output Options
  out_dir        : MidnightResults_Run7_1

Advanced Options
  min_len        : 200
  max_len        : 1100

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

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

--------------------------------------------------------------------------------
This is epi2me-labs/wf-artic v0.3.21-g0175e81.
--------------------------------------------------------------------------------

      ------------------------------------
      Available Primer Schemes:
      ------------------------------------

  Name      Version
  SARS-CoV-2    Midnight-IDT/V1 
  SARS-CoV-2    ARTIC/V1    
  SARS-CoV-2    ARTIC/V2    
  SARS-CoV-2    ARTIC/V4    
  SARS-CoV-2    ARTIC/V4.1  
  SARS-CoV-2    ARTIC/V3    
  SARS-CoV-2    NEB-VarSkip/v1a-long    
  SARS-CoV-2    NEB-VarSkip/v2b 
  SARS-CoV-2    NEB-VarSkip/v1a 
  SARS-CoV-2    NEB-VarSkip/v2  
  SARS-CoV-2    Midnight-ONT/V1 
  SARS-CoV-2    Midnight-ONT/V2 
  SARS-CoV-2    Midnight-ONT/V3 
  spike-seq ONT/V1  
  spike-seq ONT/V4.1    

      ------------------------------------

Checking fastq input.
[-        ] process > pipeline:getVersions   -
[-        ] process > pipeline:getParams     -
[-        ] process > pipeline:copySchemeDir -
[-        ] process > pipeline:getVersions   -
[-        ] process > pipeline:getParams     -
[-        ] process > pipeline:copySchemeDir -

Application activity log entry

(base) seq-chuss@Seq-CHUSS:~$ nextflow run epi2me-labs/wf-artic --scheme_name SARS-CoV-2 --scheme_version Midnight-ONT/V1 --min_len 200 --max_len 1100 --out_dir MidnightResults_Run7_1 --fastq Run7_1_fastq_pass/ -work-dir /tmp/
N E X T F L O W  ~  version 22.10.6
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [21a482fb48]
Launching `https://github.com/epi2me-labs/wf-artic` [furious_poisson] DSL2 - revision: 0175e81492 [master]

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-artic v0.3.21-g0175e81
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : furious_poisson
  containerEngine: docker
  launchDir      : /home/seq-chuss
  workDir        : /tmp
  projectDir     : /home/seq-chuss/.nextflow/assets/epi2me-labs/wf-artic
  userName       : seq-chuss
  profile        : standard
  configFiles    : /home/seq-chuss/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config

Input Options
  fastq          : Run7_1_fastq_pass/

Primer Scheme Selection
  scheme_version : Midnight-ONT/V1

Output Options
  out_dir        : MidnightResults_Run7_1

Advanced Options
  min_len        : 200
  max_len        : 1100

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

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

--------------------------------------------------------------------------------
This is epi2me-labs/wf-artic v0.3.21-g0175e81.
--------------------------------------------------------------------------------

      ------------------------------------
      Available Primer Schemes:
      ------------------------------------

  Name      Version
  SARS-CoV-2    Midnight-IDT/V1 
  SARS-CoV-2    ARTIC/V1    
  SARS-CoV-2    ARTIC/V2    
  SARS-CoV-2    ARTIC/V4    
  SARS-CoV-2    ARTIC/V4.1  
  SARS-CoV-2    ARTIC/V3    
  SARS-CoV-2    NEB-VarSkip/v1a-long    
  SARS-CoV-2    NEB-VarSkip/v2b 
  SARS-CoV-2    NEB-VarSkip/v1a 
  SARS-CoV-2    NEB-VarSkip/v2  
  SARS-CoV-2    Midnight-ONT/V1 
  SARS-CoV-2    Midnight-ONT/V2 
  SARS-CoV-2    Midnight-ONT/V3 
  spike-seq ONT/V1  
  spike-seq ONT/V4.1    

      ------------------------------------

Checking fastq input.
[-        ] process > pipeline:getVersions   -
[-        ] process > pipeline:getParams     -
[-        ] process > pipeline:copySchemeDir -
[-        ] process > pipeline:getVersions   -
[-        ] process > pipeline:getParams     -
[-        ] process > pipeline:copySchemeDir -

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

no

Other demo data information

No response