usage of HMMer format profiles about hh-suite HOT 9 OPEN

Hi Margo,

Sorry for the delay. We do not support the HH-suite version 2 anymore.

I am not too sure, if anything changed between 2 and 3 in this case however.
Our profiles do not contain pseudocount information, they are added later. HMMer profiles do contain them, which will result in a conflict.

Please rerun the original alignments with hhmake to produce profiles in our format.

Best regards,
Milot

from hh-suite.

Hi Milot,

Thank you for your reply, but what I really want to know if it is possible at all to use HMMer profiles if you do not have the original alignments?

I also tested hhsuite version-3.0-beta.3-Linux, and that also did not work.

Best regards,

Margo

from hh-suite.

Could you post the log please? Does it crash or say anything unusual? It should be working, just not extremly well.

from hh-suite.

Hi yes, this is all I have,

I tried running hhmake on a HMMER3 and HMMER2 formatted file, I attached the HMMER3 file and the output of the hhmake.
I got this error message and an "empty" output (see attached files)

• 11:08:01.706 ERROR: Use of HMMER format as input will result in severe loss of sensitivity!

Done

VOG0001.hhm.txt
VOG0001.hmm.txt

from hh-suite.

Hi all,
I still have a same error when I use hhmake for HMMER 3 format!

from hh-suite.

You need to create new profiles from the original MSAs. Using hmmer profiles isn't supported anymore.

from hh-suite.

@milot-mirdita
Ah, alright. Thank you for the clarification!

from hh-suite.

You need to create new profiles from the original MSAs. Using hmmer profiles isn't supported anymore.

These hmm relevant operations are still in HH-suite's documentation. How about remove them to avoid future complain?

from hh-suite.

You need to create new profiles from the original MSAs. Using hmmer profiles isn't supported anymore.

These hmm relevant operations are still in HH-suite's documentation. How about remove them to avoid future complain?

As I executed this command, it reported error directly and generated a null .hhm file

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