Hi all,

I'm trying to run HHblits but running into an error. I have several multiple sequence alignments that I have trimmed and concatenated and then converted the resulting .phy file to a .fasta (so HHblits can accept it).

Downloaded the database using:

    wget http://www.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08_hhsuite.tar.gz
    tar xzvf uniclust30_2018_08_hhsuite.tar.gz

When I run HHblits though, I keep getting this error message:

    $ hhblits -i sample.fasta -o hhblits_results.hhr -d ./databases/uniclust30_2018_08

    - 13:51:18.331 ERROR: In /dev/shm/ebuser/avx2/HHsuite/3.0-beta.3/iccifort-2018.3/hh-suite-3.0-beta.3/src/hhdatabase.cpp:35: FFindexDatabase:
    - 13:51:18.331 ERROR: 	could not open file './databases/uniclust30_2018_08_cs219.ffdata'

my ./databases/uniclust30_2018_08 contains the following files:

uniclust30_2018_08_a3m_db	   uniclust30_2018_08.cs219	   uniclust30_2018_08_hhm_db	    uniclust30_2018_08_md5sum
uniclust30_2018_08_a3m_db.index  uniclust30_2018_08_cs219.ffdata   uniclust30_2018_08_hhm_db.index
uniclust30_2018_08_a3m.ffdata	 uniclust30_2018_08_cs219.ffindex  uniclust30_2018_08_hhm.ffdata
uniclust30_2018_08_a3m.ffindex	 uniclust30_2018_08.cs219.sizes    uniclust30_2018_08_hhm.ffindex

Thank you
In the older versions at least, you had to provide the base name of the file itself, not just the directory.

With `hhsearch` its sufficient to use the `/path/to/databasename/databasename.ffdata`. With `hhblits` I believe it needs more than a single file, so you provide the basename of the files.

In your case it may look something like `./databases/uniclust30_2018_08/uniclust30_2018_08`.

This is also assuming you’re in the correct directory, since you’re using relative filepaths.