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Having trouble using the create-profmark tool in the HMMER suite

Hi all,

There is a tool in the HMMER suite that I'm particularly interested in using to divide a protein dataset, called create-profmark. This is the program that the developers used in designing pfam, and is deep in the code of HMMER (and not referenced in the HMMER manual). However, the program does have a readme on how to use it, which is attached below.

I have HMMER downloaded and have tried to follow the readme, by carrying out the command in the readme:

Usage: ./create-profmark <benchmark_prefix> <Stockholm MSA file> <FASTA sequence database>

When I do this, the command is not recognized. Should I be configuring HMMER differently? Or performing this function in a specific folder? Any advice would be highly appreciated.

Here is the readme and GitHub page for create-profmark, which is nested in the HMMER suite: https://github.com/EddyRivasLab/hmmer/blob/master/profmark/00README.md

Best,

Jacob

hmmer create-profmark
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written by Jacob • Jacob

1 answer

I have been using HMMer for >20 years and have never heard of this program. Apparently it does exist, but that doesn't mean that it is installed by default.

The way you are running the program is likely to be wrong:

./create-profmark <benchmark_prefix> <Stockholm MSA file> <FASTA sequence database>

This command, specifically the ./ at the beginning, means you are running this program from your current directory. That is unlikely to contain a copy of create-profmark even if it was installed. I suggest you try this:

which create-profmark

If that gives you in response something like /usr/bin/create-profmark, then you can run the program but without ./. If the response to the above command is create-profmark: Command not found., you either don't have create-profmark installed or it is in a directory that is not included in the $PATH variable. By googling Linux setting $PATH you should get enough information to explore the latter possibility.

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written by Mensur Dlakic Mensur Dlakic

Thank you so much for this information! It took me over the edge to get it up and running, I really appreciate it.

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written by Jacob • Jacob

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