Antônio Camargo

Wouldn't it possible to use an EM algorithm to "distribute" the read among its multiple hits?

I don't know. It would depend on the total amount of proteins and reads. I imagine it would be much slower than a typical RNA-Seq quantification, but not unfeasible. But...

I'm having the same issue. I'm now using [@maginapp/vuepress-plugin-katex](https://classic.yarnpkg.com/en/package/@maginapp/vuepress-plugin-katex).

Thanks @SMillerDev! Do I need to do something to get this PR merged?

Thanks!

Done https://github.com/Homebrew/homebrew-core/pull/106770 Thanks a lot for solving this quickly :)

@BurntSushi Any chance this will be fixed in the master branch sometime in the future?

Can you provide the contents of the log file inside `_annotate/mmseqs2`?

It seems the prefilter step of the mmseqs2 search died. Likely to lack of memory. Can you try setting `--splits 12`? See [here](https://portal.nersc.gov/genomad/quickstart.html#notes-about-parameters) an explanation.

How large is your input? Can you try to split it in multiple parts an run geNomad on each? You can use [seqkit](https://bioinf.shenwei.me/seqkit/usage/#split2) for that. How much memory your machine...