Antônio Camargo

Thank you for the response, @Alecaddd Is there any file I can edit/delete to reset my bookmarks?

Thanks, Milot! The new mode is `--pseudo-cnt-mode 1` (context-specific)? And what are the new `--pca` and `--pcb` default values? They are not showing up in the help dialogue. ``` --pca...

Thanks! So, if I create a profile database in `13-45111` with a command like this: ``` mmseqs msa2profile msa_db/msa_db profile_db_pseudo/profile_db --match-mode 1 --match-ratio 0.5 --threads 64 --pca 1.1 --pcb 4.1...

Do you have sequences longer than 100,000 bp? I had a similar problem (https://github.com/soedinglab/hh-suite/issues/262) and I could fix it by modifying the sequence length limit in `ffindex_from_fasta`.

Hey @zhaoxvwahaha You'll have to clone the repository, change [this line](https://github.com/soedinglab/ffindex_soedinglab/blob/master/src/ffindex_from_fasta.c#L31), and then compile HH-Suite anew. Otherwise you could try Milot's suggestion above.

Thanks! I got it now! I managed to get the download links for the [HHPred databases](http://ftp.tuebingen.mpg.de/pub/protevo/toolkit/databases/hhsuite_dbs/), so I can use SCOPe and ECOD now. Regardless, my only concern is that...

I changed the source and did some quick tests. Found no problems so far (this doesn't mean that I encourage people to do this). @milot-mirdita This is sort of related...

Thanks for the suggestion, @milot-mirdita!

Hey @willmcgugan. Is this a feature that could be considered? If so, do I need to add anything to the PR?

In my case, I wanted to be able to grep a log and be able to check the time it was recorded. But my motivation to write this PR was...