hmmpress error with a hmm database

Question

[shyamgc01]

Hi:

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

GSC

[SES]

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.

Answer 1

[satanicodr]

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

[cmclark8]

for i in ls *hmm | sed 's/.hmm//g'; do hmmconvert ${i}.hmm > ${i}_new.hmm;done

Should be

for i in ls *hmm | sed 's/\.hmm//g'; do hmmconvert ${i}.hmm > ${i}_new.hmm;done

Otherwise any directory or filename with hmm will be removed

Answer 2

[nkotowski]

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 :)

Regards,

Nelson.