Erorr running HHblits
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1
Entering edit mode
3.7 years ago
max_19 ▴ 170

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 • 3.7k views
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I have a similar question as the author of this post at - https://github.com/soedinglab/hh-suite/issues/167

Which link did you download your hhblits database from, and how are they different for the hhblits runs / results? uniclust30_2018_08_hhsuite.tar.gz = 25G, @ http://gwdu111.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08_hhsuite.tar.gz OR uniclust30_2018_08.tar.gz = 6.6G, @ http://gwdu111.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08.tar.gz

Since you are running hhblits successfully, I thought you might know :) Could you help please? Thanks!

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3
Entering edit mode
3.7 years ago
Joe 20k

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.

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

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No problem. Learned from bitter experience :P

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0
Entering edit mode
3.5 years ago

try to give the full path of the query sequence as well as database

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0
Entering edit mode

I have a similar question as the author of this post at - https://github.com/soedinglab/hh-suite/issues/167

Which link did you download your hhblits database from, and how are they different for the hhblits runs / results? uniclust30_2018_08_hhsuite.tar.gz = 25G, @ http://gwdu111.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08_hhsuite.tar.gz OR uniclust30_2018_08.tar.gz = 6.6G, @ http://gwdu111.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08.tar.gz

Since you are running hhblits successfully, I thought you might know :) Could you help please? Thanks!

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