artic assembly - Command failed:muscle -in & -out

[AnyaKovalenko]

Hello Everyone. Please could you help with the strange issue. After running the artic assembly (nanopolish) command in the end I see the following:

Running: muscle -in NB09_9.muscle.in.fasta -out NB09_9.muscle.out.fasta

Invalid command line
Unknown option in

Command failed:muscle -in NB09_9.muscle.in.fasta -out NB09_9.muscle.out.fasta

Can not find any answer regarding this muscle issue and what it means. I removed and installed the artic pipeline again but the same still exist. Please could somebody help. Many thanks.

[iferres]

Hi, I had the same issue. The problem is that muscle has been updated in conda to version 5.+ which is not backward compatible as it accept different arguments. The solution is to add the old version of muscle to the artic's environment.yml file and to rebuild the conda environment:

name: artic-ncov2019
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - artic=1.2.1
  - artic-network::rampart=1.2.0
  - snakemake-minimal=5.8.1
  - muscle=3.8.1551

[AnyaKovalenko]

Thank @iferres so much. It is very helpful.