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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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gtdbtk classify: error: one of the arguments --skip_ani_screen --mash_db is required #612

Closed JustinGibbons closed 1 year ago

JustinGibbons commented 1 year ago

Hi,

I hope you're having a good week.

I'm running atlas, version 2.14.0 Snakemake 7.18.2 on the provided test data and I get the following error:

gtdbtk classify: error: one of the arguments --skip_ani_screen --mash_db is required

I'm running on slurm, but I didn't use Snakemake to submit the job I just submitted "atlas run genomes" to sbatch.

I've attached the log file with the error and the standard output from the cluster.

Is this something you can help me with?

Thank you,

Justin G

classify.txt atlas.txt

SilasK commented 1 year ago

Related to https://github.com/Ecogenomics/GTDBTk/issues/472

SilasK commented 1 year ago

It should be fixed with the latest commit on the master branch.

@JustinGibbons Could you please try.

JustinGibbons commented 1 year ago

Hi @SilasK,

I installed the latest conda environment (2.14.2) and it is now working.

Thank you for your help