cactus-minigraph: error: unrecognized arguments: --mgCores 13

[mictadlo]

Hi, I got this error

> nextflow run WarrenLab/minigraph-cactus-nf -profile lorencm --seqFile ../seqFile.txt --reference AU --binariesMode singularit
cactus-minigraph: error: unrecognized arguments: --mgCores 13

Thank you in advance,

Michal

[esrice]

Hi Michal,

First, I should note that I'm not really supporting this pipeline anymore: you can now run the full minigraph-cactus pipeline with a single command, so a nextflow pipeline is no longer necessary or helpful.

As for the error, I can't know for sure without seeing your config file, but my guess is that the option --mgCores doesn't exist in the version of cactus you are using, whereas it does in 2.4.2, the version I wrote this nextflow pipeline for.

I'd recommend using the latest version of cactus, and not my out-of-date pipeline.

Ed

[mictadlo]

> less nextflow.config 
profiles {
    lorencm {
        process {
            executor = 'pbspro'
            queue = 'lyra'
            time = '2d'
            memory = '125 GB'
            clusterOptions = ''
            cpus = 13
            container = 'docker://quay.io/comparative-genomics-toolkit/cactus:v2.4.2'

            withName: 'CACTUS_GRAPHMAP_JOIN|VG_REFERENCE' {
                publishDir = [ path: 'out/', mode: 'copy' ]
            }
        }

        singularity {
            enabled = true
            runOptions = "--bind /work,/scratch"
        }

        params {
            scratch = '/scratch/waterhouse_team/cactus'
        }
    }
}

How else would you recommend to cactus without nextflow?

[esrice]

Weird, no idea. But again, I'm not supporting this pipeline anymore and it shouldn't be necessary to use it. You can find out how to run minigraph-cactus in the docs for that software.