Issue with hmmcalibrate during tutorial.
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Entering edit mode
6 weeks ago
apcreyes29 • 0

Hi everyone. I'm trying to do the tutorial for hmmer but I seem to be having an issue for hmmcalibrate. I tried to use:

hmmcalibrate globin.hmm

But it says:

command 'hmm2calibrate' from deb hmmer2 (2.3.2+dfsg-6)

Try: sudo apt install <deb name>>

I already have hmmer 3.3.2 installed so I used hmm2calibrate instead and now this is what it says:

hmm2calibrate globin.hmm

FATAL: failed to open HMM file globin.hmm for reading.

Is there and issue with hmmcalibrate or with my file that I'm missing?

P.S. The globin.hmm file is a profile that I built using the globins4.sto file from the tutorial and hmmbuild.

hmmsearch hmmbuild hmmer hmmcalibrate • 406 views
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Entering edit mode
6 weeks ago
Mensur Dlakic ★ 23k

Pretty sure that hmmcalibrate does not exist in HMMer version 3+ as the models are internally calibrated. I think you are using a manual that is likely for HMMer 2. So you can either skip the calibration command and move on to the next, or install maybe HMMer 2.3.2 if you really want to follow the tutorial closely.

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Entering edit mode

If that's the case then I'll just proceed then. Thank you!