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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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usage of HMMer format profiles #69

Open margoschuller opened 6 years ago

margoschuller commented 6 years ago

hh-suite v2.0.16 from the Linux tar release

I would like to use the hh-suite similarity searches using HMMer format files. hh-suites documentation states that it is able to handle HMMer format files, but I have not been able to make it to work.

What I tried is running hhsearch using HMMer format files like described in the documentation, though it gave me an ERROR and no output. This command line does work for the hh-suite profiles.

command used: multithread.pl '*.hmm' 'hhsearch -i $file -d hmm_db' -cpu 15

ERROR code: Use of HMMER format as input will result in severe loss of sensitivity!

So my questions are: Can I use hh-suite with HMMer profiles? And how should I do this? Do you have extra information or feedback about the reduced performance of hh-suite when using HMMer format profiles apart?

With kind regards,

Margo Schuller

milot-mirdita commented 6 years ago

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

margoschuller commented 6 years ago

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

milot-mirdita commented 6 years ago

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

margoschuller commented 6 years ago

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)

Done

VOG0001.hhm.txt VOG0001.hmm.txt

TaehyungKwon commented 3 years ago

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

milot-mirdita commented 3 years ago

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

TaehyungKwon commented 3 years ago

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

LicoriceLin commented 4 months ago

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? image

LicoriceLin commented 4 months ago

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? image

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