failed to run demo data

[xiranli007]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.4.0

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

it look like the sample sheet is invalid nextflow.log

Relevant log output

}                                                                                                                                                                  
  }' > params.json                                                                                                                                                       

Command exit status:                                                                                                                                                     
executor >  local (3)                                                                                                                                                    
[7f/f1c12d] validate_sample_sheet                               [100%] 1 of 1, failed: 1 ✘                                                                               
[-        ] fastcat                                             [  0%] 0 of 2                                                                                            
[-        ] calling_pipeline:ingressCheckpoint                  -                                                                                                        
[-        ] calling_pipeline:deNovo                             -                                                                                                        
[-        ] calling_pipeline:alignReads                         -                                                                                                        
[-        ] calling_pipeline:alignmentCheckpoint                -                                                                                                        
[-        ] calling_pipeline:readStats                          -                                                                                                        
[-        ] calling_pipeline:coverStats                         -                                                                                                        
[-        ] calling_pipeline:splitRegions                       -                                                                                                        
[-        ] calling_pipeline:medakaInference_consensus          -                                                                                                        
[-        ] calling_pipeline:medakaConsensus                    -                                                                                                        
[-        ] calling_pipeline:assemblyCheckpoint                 -                                                                                                        
[93/c80017] calling_pipeline:prokkaVersion                      [100%] 1 of 1, failed: 1 ✘                                                                               
[ab/893074] calling_pipeline:getParams                          [100%] 1 of 1, failed: 1 ✘                                                                               
Plus 21 more processes waiting for tasks…                                                                                                                                
Running Denovo assembly.                                                                                                                                                 
ERROR ~ Error executing process > 'calling_pipeline:getParams'                                                                                                           

Caused by:                                                                                                                                                               
  Process `calling_pipeline:getParams` terminated with an error exit status (127)                                                                                        

Command executed:                                                                                                                                                        

  # Output nextflow params object to JSON                                                                                                                                
      echo '{                                                                                                                                                            
      "fastq": "wf-bacterial-genomes-demo/isolates_fastq",                                                                                                               
      "isolates": true,                                                                                                                                                  
      "sample_sheet": "wf-bacterial-genomes-demo/isolates_sample_sheet.csv",                                                                                             
[1] 0:[tmux]*                                                                                                                                      "farm" 08:36 26-Oct-24

Application activity log entry

No response

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

no

Other demo data information

No response

[cjalder]

Hi @xiranli007 - from the log it looks like nextflow can’t find docker .command.run: line 296: docker: command not found. Can you check whether it is on your system?

[xiranli007]

Hello @cjalder thanks for your reply. I am trying to run this pipeline on a remote cluster with ubuntu. do you have any suggestions on how can i run docker in this case?

[xiranli007]

never mind I figured that I could use singularity instead. Thank you