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kzeglinski / nabseq_nf

Nextflow pipeline for NAb-seq (analyses nanopore sequencing data from hybridomas and single B cells)
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Hi, how to solve this issue. #5

Open wangsiling123 opened 1 year ago

wangsiling123 commented 1 year ago

ERROR ~ Error executing process > 'parse_sample_sheet:concat_reads (28-21-4E10-2-1)'

Caused by: java.io.IOException: Cannot run program "sbatch" (in directory "/home/data/ssy11/work/f8/9be911196892548b6c6e5dc016237e"): error=2, No such file or directory

Command executed:

sbatch .command.run

Command exit status:

Command output: (empty)

Work dir: /home/data/ssy11/work/f8/9be911196892548b6c6e5dc016237e

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details

kzeglinski commented 1 year ago

Hi, so this issue is coming up because the nextflow.config file shipped with nabseq is set up to use slurm as the executor, and it seems like you don't have slurm installed on your system ('sbatch' is a slurm command).

You'll need to edit the config file to suit your computer system. There are some pre-written config files available for different institutes/HPCs in the nf-core repository (https://github.com/nf-core/configs) or you can read the nextflow documentation about different executors and how to enable them here (https://www.nextflow.io/docs/latest/executor.html)

Hope this helps! :)