hmmpress error with a hmm database
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7.6 years ago
shyamgc01 • 0

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

hmm hmmer hmmpress • 7.5k views
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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.

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5.6 years ago
satanicodr ▴ 160

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
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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

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7.4 years ago
nkotowski • 0

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.

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