errors in building customized databases about hh-suite HOT 4 CLOSED

Hello,

I assume you start with a fasta file.
Could you share this fasta file and all commands you used?

Probable commands:

• ffindex_from_fasta
• hhblits_omp or ffindex_apply_mpi with hhblits

Can you also share your files:

• bdd_a3m_wo_ss.ff{data,index}
• the original fasta-file

Cheers,
Markus

from hh-suite.

Hi,

Not sure if this has already been solved already but I came across this same issue just before going on holiday a couple of weeks ago. I think there might be a couple of typos/errors in the documentation for building custom databases. When building the a3m_wo_ss.ff{index,data} files, I had to deliberately specify the a3m output:

hhblits_omp -d <path_to/uniprot> -i <db>_fas -oa3m <db>_a3m_wo_ss -n <num_iterations> -cpu <num_threads>

note the use of -oa3m; for me at least, the default -o option produces a .hhr style file, rather than an a3m format file.

Also, I think there's a typo in the documenation detailing the commands for adding the psipred predictions and building hhms? Using LichAmnesia's command as an example:

mpirun -np 16 ffindex_apply_mpi bdd_a3m_wo_ss.ff{data,index} -i bdd_hhm.ffindex -d bdd_hhm.ffindex -- hhmake -i stdin -o stdout -v 0

shouldn't the -d argument be for the .ffdata file? I was able to build a working custom database with these fixes. Just looking at the scripts I used, I see that I also suppressed the output (using -v 0 again) when adding secondary structure. Can't remember if this was necessary though or not, sorry.

Cheers,
Jon

from hh-suite.

Thanks for your report. Your suggested bugfixes in the userguide should be included now.

from hh-suite.

When I enter the following command: I get an error:
"ffindex_apply cluster1091_msa.ff{data,index} -i cluster1091_a3m_wo_ss.ffindex -d cluster1091_a3m_wo_ss.ffdata -- hhconsensus -i stdin -M first -maxres 100000 -oa3m stdout"
ERROR:"
Error inhhsuite/hh-suite/src/hhfunc.cpp:84: ReadQueryFile:
unrecognized input file format in 'stdin'
line = 1U09_A.IDs.mfa"

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