I finally got around to testing this on a clean Ubuntu server.
I did the following:
1. Install via
$ sudo apt-get install hhsuite
This installed the binary
hhsearch in to
/usr/local/bin/hhsearch as one would expect. It also left the main hhsuite directory in my home directory, with the path
/home/username/hhsuite-2.0.16-linux-x86-64/. This is important.
Note also how the version in
apt is not version 3.x - for that, I believe you will need to compile from source.
2. Set environment variables:
This step is absolutely required, so ensure that this variable is set, and is pointing at the right base directory. In my case:
$ export HHLIB=/home/username/hhsuite-2.0.16-linux-x86-64/
To make this change permanent, also copy the command in to your
.bashrc or similar dotfile (or run the following command):
$ echo 'export HHLIB=/home/username/hhsuite-2.0.16-linux-x86-64/' >> ~/.bashrc
If you are unsure which versions you have (since you may have confused things by compiling from source and installing from
which hhsearch, and then run the whole path as a command, to get the version; e.g. in my case:
(This will correspond to the first binary found in your PATH, and therefore the one you're invoking when you issue the
hhsearch command alone)
Gives the output (header only).
HHsearch version 2.0.15 (June 2012)
Search a database of HMMs with a query alignment or query HMM
(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser
Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960 (2005).
I think its important we clarify what binaries and directories are at play here since it seems there may be a bit of confusion.
3. Download and extract the databases
I made a databases folder inside the HHSuite folder discussed in Step 1, however you can put it anywhere, change to that directory, download and extract.
$ mkdir /home/username/hhsuite-2.0.16-linux-x86-64/databases ; cd !$
$ wget http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_from_mmcif_181114.tar.gz
$ tar xvzf pdb70_from_mmcif_181114.tar.gz
If you want to be certain there are no files missing/your database download was correct, the
md5sum for the
tar.gz for me was :
So, I have the following
$ ls /home/username/hhsuite-2.0.16-linux-x86_64/databases
md5sum pdb70_a3m.ffindex pdb70_cs219.ffindex pdb70_hhm_db.index
pdb70_a3m_db pdb70_clu.tsv pdb70.cs219.sizes pdb70_hhm.ffdata
pdb70_a3m_db.index pdb70.cs219 pdb70_from_mmcif_181114.tar.gz pdb70_hhm.ffindex
pdb70_a3m.ffdata pdb70_cs219.ffdata pdb70_hhm_db pdb_filter.dat
Then the command:
$ hhsearch -d /home/username/hhsuite-2.0.16-linux-x86_64/databases/pdb70_hhm.ffdata -i protein.faa -cpu 32
Worked without error:
Search results will be written to protein.hhr
protein.faa is in A2M, A3M or FASTA format
Read protein.faa with 1 sequences
Alignment in protein.faa contains 508 match states
1 out of 1 sequences passed filter (90% max pairwise sequence identity)
Effective number of sequences exp(entropy) = 1.0
.................................................. 1000 HMMs searched
.................................................. 61000 HMMs searched
Realigning 40 database HMMs using HMM-HMM Maximum Accuracy algorithm
Query hypothetical protein 3919442:3920968 reverse MW:51681
No_of_seqs 1 out of 1
Date Tue Nov 20 06:47:31 2018
Command hhsearch -d /home/ubuntu/hhsuite-2.0.16-linux-x86_64/databases/pdb70_hhm.ffdata -i PAU_03380.faa -cpu 32
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1PDI_R Short tail fiber protei 93.7 0.012 2E-07 55.7 0.0 26 323-348 90-116 (278)
40 6GAP_A Outer capsid protein si 32.0 30 0.00049 32.3 0.0 60 130-191 182-241 (261)
I haven't tested HHSuite 3.x but I can give it a go if you desperately want 3.