Question: hmmpress error with a hmm database
gravatar for shyamgc01
6.4 years ago by
United States
shyamgc010 wrote:


I am trying to create a hmm database from individual hmm profiles downloaded from pfam db. I ran cat command on all the .hmm files and created a flat file of hmm database. when I ran hmmpress on this flat file i am getting the following error:

Error: bad file format in HMM file myhmm

Can anyone help me to solve this problem.


Thank you



hmmer hmm hmmpress • 5.9k views
ADD COMMENTlink modified 4.4 years ago by satanicodr150 • written 6.4 years ago by shyamgc010

Perhaps you have a mismatch between your versions of hmmpress and the models? I just ran through the same steps with a set of HMMs using hmmpress version 3.1b1 (the latest) and it worked just fine.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by SES8.4k
gravatar for satanicodr
4.4 years ago by
satanicodr150 wrote:

I found the answer elsewhere. To solve this issue you need to convert the different versions of the individual hmms to the most recent version using hmmconvert.

hmmconvert <old_hmm>  >  <new_hmm_name.hmm>

Then you can concatenate and press the database.

for i in `ls *hmm | sed 's/.hmm//g'`; do hmmconvert ${i}.hmm > ${i}_new.hmm;done
cat *_new.hmm >> database.hmm
hmmpress database.hmm
ADD COMMENTlink written 4.4 years ago by satanicodr150
gravatar for nkotowski
6.2 years ago by
nkotowski0 wrote:

Hi folks, I am facing the same issue here. I have double checked HMMER version, 3.1b1. I wonder if there are any limits related to the profile database size. I performed a cat on my HMMbuild profiles and ended up with a 14GB profile database. Is this a problem, I mean, is HMMPRESS able to process such a large profile database?

Help, please :)



ADD COMMENTlink written 6.2 years ago by nkotowski0
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