hhpred is looking for a file that is not in the database

[Barak19]

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:

• 13:19:49.685 ERROR: In /data/hh-suite3/src/ffindexdatabase.cpp:11: FFindexDatabase:

• 13:19:49.685 ERROR: could not open file '/bioseq/hhpred-databases/db/pdb.hhm_cs219.ffdata'

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]

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]

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 ***@***.***> 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 <#235 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASDKQ6C5Q5AHBMWU4OMBBZLSUZQX7ANCNFSM4UZQL37A> .

[milot-mirdita]

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]

Which version of HHsuite would you recommend?

…

On Tue, Dec 15, 2020 at 3:13 PM Milot Mirdita ***@***.***> 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 <#235 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASDKQ6BT3RQS6RXWNOY6AATSU5OGDANCNFSM4UZQL37A> .

[Barak19]

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 - 12:20:38.078 INFO: Search results will be written to /tmp/29928/protein_seq/protein_seqEyultCz.hhr - 12:20:38.079 ERROR: In /data/hh-suite3/src/ffindexdatabase.cpp:11: FFindexDatabase: - 12:20:38.079 ERROR: could not open file '/bioseq/hhpred-databases/db/pdb.hhm_cs219.ffdata'

…

On Tue, Dec 15, 2020 at 3:25 PM Barak Yariv ***@***.***> wrote: Which version of HHsuite would you recommend? On Tue, Dec 15, 2020 at 3:13 PM Milot Mirdita ***@***.***> 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 > <#235 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ASDKQ6BT3RQS6RXWNOY6AATSU5OGDANCNFSM4UZQL37A> > . >