init ATLAS from contigs or MAGs as well

[Mechah]

Hi,
as it is possible to skip the qc step in ATLAS if you already have quality filtered reads, I think it would be great to allow ATLAS to initiate a run also from contigs or MAGs and just execute downstream steps of the entire ATLAS pipeline.
What do you think? Or is this already possible?

[SilasK]

You can add an argument genome_dir with the path to a folder with fast a files (genomes).
Take care to name them with simple names.

[Mechah]

I do not really understand which command could accept the genome_dir as an additional argument. I tried with atlas run genomes and atlas run all but it does not accept this argument. Do I need to specify the genome_dir in the config.yaml file or where can I start the analysis from my genome bins?

[SilasK]

Yes you need to add it in the config file.

[Mechah]

Hm, but then I get the following error:
AttributeError in line 188 of /home/apps/metagenome-atlas/2.9.1/lib/python3.8/site-packages/atlas/workflow/rules/genomes.smk:
'Logger' object has no attribute 'critical'
File "/home/apps/metagenome-atlas/2.9.1/lib/python3.8/site-packages/atlas/workflow/Snakefile", line 222, in
File "/home/apps/metagenome-atlas/2.9.1/lib/python3.8/site-packages/atlas/workflow/rules/genomes.smk", line 197, in
File "/home/apps/metagenome-atlas/2.9.1/lib/python3.8/site-packages/atlas/workflow/rules/genomes.smk", line 188, in get_genome_dir

Is there something else I need to consider e.g. already with atlas init or the place to the genome_dir in my config file?

[SilasK]

For now the limitation is that the genomes should have a .fasta extension.

[Mechah]

Cool. ATLAS is getting more and more fun! :-)

[SilasK]

How to use atlas with external genomes

Put all your genomes in a folder. The genomes should be unziped and contain a .fasta extension.
specify the path to this folder in the config file.

genome_dir: path/to/genome_dir

run atlas qc if you don't have quality controlled reads

run

atlas run None quant --dryrun

And check that no assembly would be performed.
Activate or deactivate annotations according to your needs.
(genes are predicted anyway)

[trickovicmatija]

The command

atlas run None quant --dryrun

should be changed to :

atlas run None quantify_genomes --dryrun