scop70_1.75_cs219.ffdata missing? about hh-suite HOT 7 CLOSED

Hi. You are using the wrong database. Take the hhsuite database. Since
hhsuite 3.0 hhsearch requires the same database as hhblits. Hope that helps
you.

Am 11.11.2016 14:02 schrieb "sowani" [email protected]:

Hi,

I am testing the hh-suite on ppc64le. I downloaded following databases
before I begun testing.
From http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
:
pdb70_14Sep16.tgz
pfamA_29.0.tgz
uniprot20_2016_02.tgz
From http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsearch_dbs/
:
scop70_1.75.a3m.tar.gz
scop70_1.75.hhm.tar.gz

I extracted these databases to their appropriate locations, so that I
could just copy-paste test commands from User Guide and execute them. Also
I have set all the recommended environment variables and paths as per User
Guide. However, the very first command "hhsearch -cpu 4 -i data/query.a3m
-d dbs/scop70_1.75 -o data/query.hhr" gives me following error:

• 18:22:32.998 ERROR: In /root/hh-suite/src/hhdatabase.cpp:35:
  FFindexDatabase:
• 18:22:32.998 ERROR: could not open file
  'dbs/scop70_1.75_cs219.ffdata'

I checked for the presence of scop70_1.75_cs219.ffdata file everywhere,
but it is missing. User Guide section 2.4 on page 8 mentions that
_cs219.ffdata is one of the eight files a database consists of. However
this file seems to be missing.

Am I working with correct databases? Do I have to install something
additional? Or do I have to "condition" existing database files to generate
these kinds of files?

Thanks,
Atul.

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from hh-suite.

Hi Atul,

Sorry for the confusion. We were not providing the SCOP70 database in a format that could be used by HH-suite version 3. I just uploaded an archive with a complete SCOP70 database (including cs219). Do note however that this cs219 is not compatible to old HH-suite versions, that would need a bit more work. (Write me if you need it, I could generate it.)

You can find the database here.

Best regards,
Milot

from hh-suite.

Thanks for updating the database! I am downloading the new DB file and I will update soon once I complete the download and extract the DB files.

from hh-suite.

Update on the new scop70_1.75 database: I could successfully run the first hhsearch command given in the User Guide with this database. Many thanks to @milot-mirdita ! :)

I am closing this issue as the original problem got resolved. Here is the output I received (whether this is accurate or not is another topic).
root@pts00433-vm12:~/hh-suite# hhsearch -cpu 4 -i data/query.a3m -d dbs/scop70_1.75 -o data/query.hhr

• 17:25:30.890 INFO: data/query.a3m is in A2M, A3M or FASTA format
• 17:25:30.951 INFO: Searching 13730 database HHMs without prefiltering
• 17:25:30.959 INFO: Iteration 1
• 17:25:31.306 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 13730
• 17:25:31.307 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 13730
• 17:25:31.307 INFO: Scoring 13730 HMMs using HMM-HMM Viterbi alignment
• 17:25:31.411 INFO: Alternative alignment: 0
• 17:26:59.299 INFO: 13730 alignments done
• 17:26:59.310 INFO: Alternative alignment: 1
• 17:26:59.310 INFO: Alternative alignment: 2
• 17:26:59.310 INFO: Alternative alignment: 3
• 17:26:59.450 INFO: Realigning 10 HMM-HMM alignments using Maximum Accuracy algorithm
• 17:26:59.770 INFO: 0 sequences belonging to 0 database HMMs found with an E-value < 0.001

Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 59 out of 59
Neff 4.27431
Searched_HMMs 13730
Date Mon Nov 14 17:26:59 2016
Command hhsearch -cpu 4 -i data/query.a3m -d dbs/scop70_1.75 -o data/query.hhr

No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 d1muka_ e.8.1.4 (A:) Reovirus 0.0 1.4E+04 1 -127.0 0.0 14 188-201 746-759 (1264)
2 d1u6gc_ a.118.1.2 (C:) Cullin- 0.0 1.4E+04 1 -127.0 0.0 1 1-1 1-1 (1207)
3 d1jrob2 d.133.1.1 (B:124-777) 0.0 1.4E+04 1 -127.0 0.0 12 154-165 231-242 (654)
4 d1ffvb2 d.133.1.1 (B:147-803) 0.0 1.4E+04 1 -127.0 0.0 15 154-168 251-265 (657)
5 d1bjta_ e.11.1.1 (A:) DNA topo 0.0 1.4E+04 1 -127.0 0.0 32 192-230 284-315 (760)
6 d1twfa_ e.29.1.2 (A:) RBP1 {Ba 0.0 1.4E+04 1 -127.0 0.0 4 35-38 570-573 (1449)
7 d1w7ca1 b.30.2.1 (A:316-775) L 0.0 1.4E+04 1 -127.0 0.0 14 105-118 144-157 (460)
8 d1by5a_ f.4.3.3 (A:) Ferric hy 0.0 1.4E+04 1 -127.0 0.0 1 25-25 57-57 (697)
9 d1dmta_ d.92.1.4 (A:) Neutral 0.0 1.4E+04 1 -127.0 0.0 3 92-94 87-89 (696)
10 d2i3oa1 d.153.1.6 (A:1-516) Hy 0.0 1.4E+04 1 -127.0 0.0 1 279-279 264-264 (516)

from hh-suite.

I have downloaded uniprot20_2016_02.tgz. While running miprun to build a3m format database, I get the same error: 'could not open file '/dir/_cs219.ffdata. Also in my usr/bin folder, ffindex_apply_mpi is not found. I can see only ffinidex_apply_mpi.c in hh-suite/lib/ffindex/src/ folder. Is ffindex_apply and ffindex_apply_mpi is same?. I don't know whether export path problem or installation problem in ffinder_apply_mpi.
Please help me to resolve this.

from hh-suite.

@yazhinia, can you please open a new issue and add a link to the discussion here? That way it is much easier for us keeping track and handling of your issue.

from hh-suite.

Here is the link: #65

from hh-suite.