I am alway stuck at 3% done about atlas HOT 2 CLOSED

metagenomic assembly uses a lot of resources and a lot of steps need to be executed.. The percentage might not increase rapidly, but check the number of steps done.

You can try:

• If you encounter errors. do grep Error -a5 <snakemake log file> and see the error files.
• In the beginning, many databases need to be downloaded which can take time.
  • You can run atlas run qc and download the dbs later
  • You can deactivate some annotations in the config file.
• You can try a test run (see example data in the docs).

Do you have a cluster to work with? Otherwise, you might be limited to doing 1 or 2 steps at a time which will drastically increase the time compared to parallelizing it on a cluster system

from atlas.

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Thank you for your contributions.

from atlas.