jdwinkler-lanzatech

Thanks for the suggestions! I may just throw some EC2 instances at the problem until it is solved essentially, but I'll do some experimentation to figure out how much faster...

Yeah, I'm using prodigal + the emapper wrapper around diamond in protein mode I believe. Looks like the blastp mode is running.

Ah, I'll take a look. I couldn't find any options besides genome_dir in the online documentation, but I see it in the CLI. Thanks for the tip.

Thanks! That is about what I figured; I've implemented a similar estimate for a primary clustering approach in another tool that suffers from the same time/sequence complexity. I'll keep an...

Column 8 would be the target, I think. I believe right now the -F option is an exact match though, so I am thinking of another flag that basically uses...

Great, thanks! I figure it is a logical addition to the custom filtering offered by -F already.

Yep! I'm set up to run instances in parallel, but was just I thought I had watching the initial testing.

I also just ran into this problem as well.

Sure: ``` emapper.py -i {protein_fasta filepath} --cpu {number of cores/threads to use} -m diamond --output {output name} --output_dir {output folder} ``` Anything in {} you'll need to replace with your...