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MARVEL all_vogs_hmm_profiles issue

I'm trying to run MARVEL on mac. I've followed installations steps, installed dependencies, but I keep running into a recurring problem. MARVEL unpacks a tar.gz file called "AllvogHMMprofiles.tar.gz" and searches for all_vogs_hmm_profiles_feb2018.hmm but cannot find it. I've manually searched through the tar file and cannot find all_vogs_hmm_profiles_feb2018.hmm. Any ideas?

marvel prophage phage genomics
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updated by Mensur Dlakic Mensur Dlakic • written by ams686 • ams686

1 answer

A similar question was already answered here.

Briefly, the archive contains individual HMM files, but you still need to concatenate them to make a final HMM.

tar -zxvf AllvogHMMprofiles.tar.gz
cat AllvogHMMprofiles/* > all_vogs_hmm_profiles_feb2018.hmm
hmmpress all_vogs_hmm_profiles_feb2018.hmm
rm -rf AllvogHMMprofiles
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written by Mensur Dlakic Mensur Dlakic

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