Closed Robvh-git closed 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
I found the problem: I was using an older version of nextflow and after installation of the latest nextflow version, the problem was solved.
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: