Open esha-joshi opened 3 years ago
Has this been solved? I am facing the same problem
Hi @csawye01,
This artic pipeline version this wrapper uses is relatively old. What ended up working for me with the V4 primer scheme was using the artic-networks' 1.3.0-dev pipeline version from this branch, in addition to using the latest version of artic-tools to avoid errors at the vcf-check step for control sequences with no SNVs. I replaced the artic-tools binary in the conda environment with that of the compiled 0.3.1 version since there is no conda release for this version of artic-tools yet (issue here).
Hope that helps.
Hi @esha-joshi , thanks so much for responding and letting me know what to do to troubleshoot this. Much appreciated!
Hi @esha-joshi I think I have confused myself a bit. Am I using 1.3.0-dev/environment.yml to recreate the artic-ncov2019 conda env or adding this into the connorlab pipeline somewhere? Do you have this on you github?
Hi @csawye01, I would recommend downloading via source and building the conda env using the 1.3.0-dev/environment.yml. Within this conda env, I replaced the artic-tools binary with the most recent version (v0.3.1) to run the pipeline. Hope that helps.
Hello, I am trying to run the ARTIC pipeline on the Singularity profile with the new ARTIC V4 primer scheme set (https://github.com/artic-network/primer-schemes).
I am running the Nextflow pipeline on Nanopore data with the minimum required arguments and my
conf/base.config
is set up as such with parameters for the primer scheme:The pipeline fails when getting to the alignment step using
minimap2
.Versions (on a CentOS 7 VM):
nextflow version 21.04.1.5556
singularity version 3.5.3
Python 3.6.13
Full error log:
Is there a workaround or potential solution to this?
Thank you so much.