Question: Erorr running HHblits
1
gravatar for max_19
7 days ago by
max_19100
max_19100 wrote:

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

protein homology hmm • 64 views
ADD COMMENTlink modified 7 days ago by jrj.healey12k • written 7 days ago by max_19100
3
gravatar for jrj.healey
7 days ago by
jrj.healey12k
United Kingdom
jrj.healey12k wrote:

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.

ADD COMMENTlink written 7 days ago by jrj.healey12k
1

That fixed it! I just needed to provide the basename of the files. Thanks very much!

ADD REPLYlink written 7 days ago by max_19100
1

No problem. Learned from bitter experience :P

ADD REPLYlink written 7 days ago by jrj.healey12k
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