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genomicsITER / NanoCLUST

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
MIT License
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SOLVED: how to solve "ERROR ~ No such variable: barcode" ? #21

Closed Robvh-git closed 3 years ago

Robvh-git commented 3 years ago

Hello,

I'm trying to run the NanoCLUST test using following command:

nextflow run main.nf -profile test,conda

However, when I run this, I receive error "No such variable: barcode".

I also tried to analyse my own dataset using following command:

nextflow run ../main.nf -profile conda --reads 'HAC_run_all.fastq' --db "./../db/16S_ribosomal_RNA" --tax "./../db/taxdb/"

However, I recieve the same error. The full output is given below.

Could you advise me on how to solve this problem?

OUTPUT:

~/Documents/Software/NanoCLUST/NanoCLUST$
nextflow run main.nf -profile test,conda
N E X T F L O W  ~  version 19.01.0
Launching `main.nf` [nauseous_ptolemy] - revision: c3b5ee2f3d

----------------------------------------------------
      _   __                     ________    __  _____________
     / | / /___ _____  ____     / ____/ /   / / / / ___/_  __/
    /  |/ / __ `/ __ \/ __ \   / /   / /   / / / /\__ \ / /   
   / /|  / /_/ / / / / /_/ /  / /___/ /___/ /_/ /___/ // /    
  /_/ |_/\__,_/_/ /_/\____/   \____/_____/\____//____//_/     

  NanoCLUST v1.0dev
----------------------------------------------------

Run Name          : nauseous_ptolemy
Reads             : /home/datura-workstation/Documents/Software/NanoCLUST/NanoCLUST/test_datasets/mock4_run3bc08_5000.fastq
Max Resources     : 128 GB memory, 16 cpus, 10d time per job
Output dir        : ./results
Launch dir        : /home/datura-workstation/Documents/Software/NanoCLUST/NanoCLUST
Working dir       : /home/datura-workstation/Documents/Software/NanoCLUST/NanoCLUST/work
Script dir        : /home/datura-workstation/Documents/Software/NanoCLUST/NanoCLUST
User              : datura-workstation
Config Profile    : test,conda
Config Description: Minimal test dataset to check pipeline function
----------------------------------------------------
ERROR ~ No such variable: barcode

 -- Check script 'main.nf' at line: 200 or see '.nextflow.log' file for more details
Robvh-git commented 3 years ago

I found the problem: I was using an older version of nextflow and after installation of the latest nextflow version, the problem was solved.