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
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shyamgc01 •
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
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
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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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.