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hhpred is looking for a file that is not in the database #235
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The hhpred perl script are currently unsupported due to the lack of resources/funding. They also don't work with HHsuite3. |
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.
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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. |
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.
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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>
> .
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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
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