Michael Roach

I think there are a couple of things I need to fix. I'll see if I can get it done this week.

Hi, what version of conda are you running? EDIT: I think the issue is that the prefix filepath is just too long. Can you please try and run the following?...

Thanks Kailun, can you please try with the custom conda prefix? `hecatomb test build_envs --conda-prefix hecatomb.out/conda/` or if you haven't installed the databases yet: `hecatomb install --conda-prefix hecatomb.out/conda/`

It looks like it pretty much finished. I can't see which jobs failed. Can you let me know if this is an issue in the main branch? you can install...

Hi, You shouldn't need to perform host removal as this step is performed by Hecatomb, but there will be a difference due to the way Hecatomb prepares the references for...

Yes, I agree 100%. This misclassification of host DNA as RNA viruses is very typical. I like the idea of switching off searching for RNA viruses; I'll have to think...

Hi, The target is `ctg_annotate`. Try this: `hecatomb run --reads reads/ ctg_annotate --threads 16`

Yes, it's dumb. The issue is that there are both direct annotations of the contigs and read-based annotations of the contigs in the targets for ctg_annotate, so it's essentially just...

I've reworked these rules and it seems to be working. I've dropped BBTools for minimap and BEDtools, and just using the normal refseq viral db rather than the shredded version....

Yes you can substitute your own databases. Check out the MMSeqs documentation on downloading or creating your own databases: https://mmseqs.com/latest/userguide.pdf At the moment, you would need primary and secondary aa...