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soedinglab / hh-suite

Remote protein homology detection suite.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
GNU General Public License v3.0
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hhpred is looking for a file that is not in the database #235

Open Barak19 opened 3 years ago

Barak19 commented 3 years ago

Hello

I'm working on ConSurf in Nir Ben-Tal's laboratory. The ConSurf website uses a local installation of hhsuite. It has worked for many years but lately it stopped working. In order to see where the problem, I decided to install it on my account, and failed. I hope that you can help me with this local installation.

The problem is as follows: I downloaded the database pdb70_from_mmcif_latest.tar.gz When I run hhpred, the program seems to be looking for the file pdb.hhm_cs219.ffdata but this file is missing from the pdb70_from_mmcif_latest.tar.gz dataset.

The command I use is:

!/bin/bash

HHLIB=/data/hh-suite3/build export HHLIB perl /data/hh-suite3/scripts/hhpred/hhpred.pl -i /a/home/cc/lifesci/barakyariv/work1/protein_seq.fas -o /a/home/cc/lifesci/barakyariv/pdb_seq_hhpred

The error I get is:

I run it on a queue with the following five nodes:

compute-0-293 28 Cores support avx/2 sse/2/3/4_1/4_2 125G Mem CentOS Linux release 7.3.1611

compute-0-309 36 Cores support avx/2 sse/2/3/4_1/4_2 188G Mem CentOS Linux release 7.6.1810

compute-0-305 28 Cores support avx/2 sse/2/3/4_1/4_2 125G Mem CentOS Linux release 7.6.1810

compute-0-304 28 Cores support avx/2 sse/2/3/4_1/4_2 125G Mem CentOS Linux release 7.6.1810

compute-0-308 36 Cores support avx/2 sse/2/3/4_1/4_2 188G Mem CentOS Linux release 7.6.1810

yours truly

Barak

barakyariv@gmail.com

milot-mirdita commented 3 years ago

The hhpred perl script are currently unsupported due to the lack of resources/funding. They also don't work with HHsuite3. I think you have to downgrade and keep using an old PDB database or build your own.

Barak19 commented 3 years ago

Thank you for your quick response.

I don't necessarily need the hhpred in perl, is there another version, say python, which does work?

On Mon, Dec 14, 2020 at 9:22 PM Milot Mirdita notifications@github.com wrote:

The hhpred perl script are currently unsupported due to the lack of resources/funding. They also don't work with HHsuite3. I think you have to downgrade and keep using an old PDB database or build your own.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/soedinglab/hh-suite/issues/235#issuecomment-744656030, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASDKQ6C5Q5AHBMWU4OMBBZLSUZQX7ANCNFSM4UZQL37A .

milot-mirdita commented 3 years ago

No other versions exist and all funding applications for continued development of HHpred were denied. We are currently only providing best effort bug fixes to HHblits/HHsearch. HHpred is completely unmaintained. However, we would be very happy to give feedback and merge any PR from outside contributors to get HHpred running again.

Barak19 commented 3 years ago

Which version of HHsuite would you recommend?

On Tue, Dec 15, 2020 at 3:13 PM Milot Mirdita notifications@github.com wrote:

No other versions exist and all funding applications for continued development of HHpred were denied. We are currently only providing best effort bug fixes to HHblits/HHsearch. HHpred is completely unmaintained. However, we would be very happy to give feedback and merge any PR from outside contributors to get HHpred running again.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/soedinglab/hh-suite/issues/235#issuecomment-745278487, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASDKQ6BT3RQS6RXWNOY6AATSU5OGDANCNFSM4UZQL37A .

Barak19 commented 3 years ago

The problem is in hhsearch. Is there support for that? see below the command and the error messages.

HHLIB=/data/hh-suite3/build /data/hh-suite3/build/bin/hhsearch -i /tmp/29928/protein_seq/protein_seqEyultCz.hhm -d /bioseq/hhpred-databases/db/pdb.hhm -mact 0.05 -cpu 4 -atab /tmp/29928/protein_seq/protein_seqEyultCz.start.tab

On Tue, Dec 15, 2020 at 3:25 PM Barak Yariv barakyariv@gmail.com wrote:

Which version of HHsuite would you recommend?

On Tue, Dec 15, 2020 at 3:13 PM Milot Mirdita notifications@github.com wrote:

No other versions exist and all funding applications for continued development of HHpred were denied. We are currently only providing best effort bug fixes to HHblits/HHsearch. HHpred is completely unmaintained. However, we would be very happy to give feedback and merge any PR from outside contributors to get HHpred running again.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/soedinglab/hh-suite/issues/235#issuecomment-745278487, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASDKQ6BT3RQS6RXWNOY6AATSU5OGDANCNFSM4UZQL37A .