A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
I have a quick question regarding the articGuppyPlex module. I'm (trying) to run the pipeline on nanopore data, however I do not have access to the actual Guppy output, instead I'm just providing a directory with a bunch of fastq files.
When running with --medaka, I was hoping that's enough. However for some reason the articGuppyPlex step runs forever and eventually times out, without doing anything. The articDownloadScheme step seems to work.
I'm running on a slurm cluster with singularity.
Do you have any idea what could be the issue? Maybe you have observed this before.
Hi,
I have a quick question regarding the
articGuppyPlexmodule. I'm (trying) to run the pipeline on nanopore data, however I do not have access to the actual Guppy output, instead I'm just providing a directory with a bunch of fastq files.When running with
--medaka, I was hoping that's enough. However for some reason thearticGuppyPlexstep runs forever and eventually times out, without doing anything. ThearticDownloadSchemestep seems to work.I'm running on a slurm cluster with singularity.
Do you have any idea what could be the issue? Maybe you have observed this before.
Thanks!
Cheers, Kevin