HHblits with FFindexDatabase error

[Lsz-20]

After conda install hhsuite=3.3.0, i try to run the hhblits command: hhblits -i query.seq -o query.hhr -d ./uniclust30 ,but got these errors:

• ERROR: In /opt/conda/conda-bld/hhsuite_1594935877759/work/src/ffindexdatabase.cpp:11: FFindexDatabase:
• ERROR: could not open file './uniclust30_cs219.ffdata' There seems to be a similar problem in issues, but it can't work well on my machine： Here is my database: ls -la ./uniclust30

drwxrwxrwx 2 jovyan users 4.0K Jul 25 07:37 drwxrwxrwx 3 jovyan users 4.0K Jul 25 07:33 -rwxrwxrwx 1 jovyan users 65G Jul 25 07:37 uniclust30_2018_08_a3m_db ................................... -rwxrwxrwx 1 jovyan users 7.8M Jul 25 07:34 uniclust30_2018_08_hhm.ffindex -rwxrwxrwx 1 jovyan users 767 Jul 25 07:34 uniclust30_2018_08_md5sum what can i do now?

[milot-mirdita]

It looks like you haven’t specified the full database base name (missing the version)

the command line should look something like … -d path-to-db/uniclust30_2018_08

i would also recommend to download a newer Uniclust/uniref version. 2018_08 is really old.

[Lsz-20]

Thanks for your apply, but i have tried the full database base name and it show me the same question?

[milot-mirdita]

Can you please post the command line you used

[Lsz-20]

Can you please post the command line you used

Here it my command: hhblits -i query.seq -o query.hhr -d ./uniclust30/uniclust30_2018_08 and i don't think these database have anything wrong caused by download, it can work well in others

[milot-mirdita]

Here is my database: ls -la ./uniclust30

drwxrwxrwx 2 jovyan users 4.0K Jul 25 07:37 drwxrwxrwx 3 jovyan users 4.0K Jul 25 07:33 -rwxrwxrwx 1 jovyan users 65G Jul 25 07:37 uniclust30_2018_08_a3m_db ................................... -rwxrwxrwx 1 jovyan users 7.8M Jul 25 07:34 uniclust30_2018_08_hhm.ffindex -rwxrwxrwx 1 jovyan users 767 Jul 25 07:34 uniclust30_2018_08_md5sum

Can you repeat this, I am not sure this looks right. I don’t see a couple files that should be there

[Lsz-20]

Here they are: command : ls -la ./uniclust30/uniclust30_2018_08 total 172280328 drwxr-xr-x 2 jovyan users 4096 Jul 25 09:06 . drwxr-xr-x 3 jovyan users 4096 Jul 25 09:02 .. -rwxrwxrwx 1 jovyan users 69490273138 Jul 25 09:06 uniclust30_2018_08_a3m_db -rwxrwxrwx 1 jovyan users 436453157 Jul 25 09:04 uniclust30_2018_08_a3m_db.index -rwxrwxrwx 1 jovyan users 69490273138 Jul 25 09:03 uniclust30_2018_08_a3m.ffdata -rwxrwxrwx 1 jovyan users 375805833 Jul 25 09:04 uniclust30_2018_08_a3m.ffindex -rwxrwxrwx 1 jovyan users 4044015407 Jul 25 09:04 uniclust30_2018_08.cs219 -rwxrwxrwx 1 jovyan users 3860466139 Jul 25 09:04 uniclust30_2018_08_cs219.ffdata -rwxrwxrwx 1 jovyan users 356545673 Jul 25 09:04 uniclust30_2018_08_cs219.ffindex -rwxrwxrwx 1 jovyan users 19 Jul 25 09:04 uniclust30_2018_08.cs219.sizes -rwxrwxrwx 1 jovyan users 14171782777 Jul 25 09:04 uniclust30_2018_08_hhm_db -rwxrwxrwx 1 jovyan users 9427452 Jul 25 09:06 uniclust30_2018_08_hhm_db.index -rwxrwxrwx 1 jovyan users 14171782777 Jul 25 09:04 uniclust30_2018_08_hhm.ffdata -rwxrwxrwx 1 jovyan users 8167108 Jul 25 09:04 uniclust30_2018_08_hhm.ffindex -rwxrwxrwx 1 jovyan users 767 Jul 25 09:04 uniclust30_2018_08_md5sum

[s-j-99]

Hi, did you resolve this issue? I am also getting the same error