atlas: Snakemake stuck at 'Downloading and installing remote packages.'
Hello
I’ve been trying to run Atlas on two different systems, one cluster and one linux server. In both cases, it gets stuck at ‘Downloading and installing remote packages.’ I’ve tried removing and reinstalling the atlas environment. I’ve tried installing each package in the dRep.yaml list independently with no issues. I’ve tried with both Conda and Mamba. None of these seems to prevent it from hanging. This is the command (linux) and stdout that it produces:
(atlasenv) sh-4.3$ atlas run genomes --keep-going -j 70 --resources mem=700 --conda-frontend mamba --verbose [2021-05-11 13:20 INFO] Executing: snakemake --snakefile /home/anita/.conda/envs/atlasenv/lib/python3.6/site-packages/atlas/Snakefile --directory /Datadrives/bulk1/anita/microbial/2008_30 --jobs 70 --rerun-incomplete --configfile '/Datadrives/bulk1/anita/microbial/2008_30/config.yaml' --nolock --use-conda --conda-prefix /Datadrives/bulk1/anita/microbial/2008_30/databases/conda_envs genomes --keep-going --resources mem=700 --conda-frontend mamba --verbose Building DAG of jobs... Removing incomplete Conda environment /home/anita/.conda/envs/atlasenv/lib/python3.6/site-packages/atlas/rules/../envs/dRep.yaml... Creating conda environment /home/anita/.conda/envs/atlasenv/lib/python3.6/site-packages/atlas/rules/../envs/dRep.yaml... Downloading and installing remote packages.
Any help or suggestions would be very much appreciated.
About this issue
- Original URL
- State: closed
- Created 3 years ago
- Comments: 16 (7 by maintainers)
Commits related to this issue
- tested drep env #390 — committed to metagenome-atlas/atlas by SilasK 3 years ago
- dereplicate only once #390 — committed to metagenome-atlas/atlas by SilasK 3 years ago
I tried that solution, but had to edit dRep.yaml a little more to get it running without an error while solving the environment. It’s running now, although I’m having a new issue (see #395)