Antônio Camargo

Not sure if this is related (if not, I can create a different issue), but it looks like gradients in embedded PDFs are not appearing in iOS's PDF reader: **iOS:**...

Hi @Kir283, You can identify these regions by looking for chains of multiple plasmid markers (`GENOMAD.*.P*`) uninterrupted by chromosome-specific markers (`GENOMAD.*.C*`) in the `_annotate/_genes.tsv` file. However, since conjugative elements can...

Hi @gweeenis, Yes, that makes sense. When you use `--enable-score-calibration`, the values represent approximate probabilities. For instance, a sequence with a plasmid score of 0.4 and a virus score of...

Thank you, @EricDeveaud! Just a few small changes: - Please move `get_available_cpus` to [`utils.py`](https://github.com/apcamargo/genomad/blob/main/genomad/utils.py) - Rename the `CPUS` variable to `n_cpus` Once that's done, I’ll be happy to merge :)

@EricDeveaud do you plan to continue working on this PR?

Can you download from [this](https://portal.nersc.gov/genomad/__data__/genomad_db_v1.9.tar.gz) link? This is the current latest version.

This could be because you don't have enough available memory. Can you try setting `--splits 8` or even `--splits 12`? This will make the execution a bit slower, but memory...

Hi @roo-weed, I've tested the new version of MMseqs2 and had no issue. Can you try running your data with both version 16 and 15 and tell me if it...

@WUD2018 can you try to run with `--splits 12`? Just to make sure the issue is not insufficient memory.

Hi @zzzfire Here are some resources with the mathematical formulation of SPM: https://apcamargo.github.io/tspex/metrics/#specificity-measure-spm https://academic.oup.com/bioinformatics/article/26/9/1273/199782