Conflict between MAFFT and new PRANK installation

I had MAFFT running fine on my computer (MacOS 11.6), until I downloaded PRANK (a probabilistic multiple alignment program distributed by Wasabi) which also runs on its own MAFFT Unix executable file. The original MAFFT is located in the directory /usr/local/bin, and PRANK and its associated files live in another directory called /programs/prank/bin, both of which are in my $PATH variable, with the /usr/local/bin directory having priority. Now, not only is the MAFFT within PRANK giving the error below when I type the ‘prank’ command, but I also get this error when trying to use my original version of MAFFT by typing ‘mafft.’ Deleting my original MAFFT and only using the PRANK version does not fix things. If I fully delete PRANK and MAFFT and redownload MAFFT alone, I can get it to work again.

I’ve tried all the steps listed in the error output below. My $MAFFT_BINARIES file appears to be empty or nonexistent, and there is no MAFFT_BINARIES line in my .bash_profile or any of the other settings files listed.

Does anyone have any insight into what may be causing this or how I should go about fixing it? Has anyone experienced the same conflicts with PRANK? Please let me know if I can provide any additional information about my system or set-up that would be helpful. As you might be able to guess, I'm not particularly experienced in this level of digging around in the guts of my file directories, but I know just enough to get myself into trouble...

Error: Initial alignment with Mafft failed. The output generated was:

v7.490 != v7.450 (2019/Aug/23)

There is a problem in the configuration of your shell.
Check the MAFFT_BINARIES environmental variable by
$ echo $MAFFT_BINARIES

This variable must be *unset*, unless you have installed MAFFT
with a special configuration.  To unset this variable, type
$ unset MAFFT_BINARIES
or
% unsetenv MAFFT_BINARIES
Then retry
$ mafft input > output

To keep this change permanently, edit setting files
(.bash_profile, .profile, .cshrc, etc) in your home directory
to delete the MAFFT_BINARIES line.
On MacOSX, also edit or remove the .MacOSX/environment.plist file
and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7).

Please send a problem report to katoh@ifrec.osaka-u.ac.jp,
if this problem remains.

multiple-sequence-alignment bash prank mafft phylogenetics

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updated 2.9 years ago by Ram

• written 4.5 years ago by noramarie •

1 answer

There is no $MAFFT_BINARIES file, as this refers to an environmental variable. Whenever you see a $ sign followed by capital letters, that almost always is a system-defined environmental variable.

At the beginning of the error message it says v7.490 != v7.450 which I interpret to mean that PRANK "sees" an incorrect program version, most likely the one that you have globally installed in /usr/local/bin. I have never used PRANK, but an educated guess is that setting $MAFFT_BINARIES to /programs/prank/bin could potentially solve the problem.

If you use bash shell, that would mean entering the following in .bashrc:

export MAFFT_BINARIES="/programs/prank/bin/mafft"

Or for (t)csh shell, enter the following in .cshrc:

setenv MAFFT_BINARIES "/programs/prank/bin/mafft"

Note that both .bashrc and .cshrc have a dot in front, and they are located in your home directory. You may need to log out and back in for this to work. Also, some programs require directory location rather than file location, in which case you may need to delete /mafft in the lines above.

You should pat yourself on the back for laying out the problem so clearly. Most posters with your level of experience - and many with higher level - tend to write one or two sentences worth of description that require rounds of follow-up.

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written 4.5 years ago by Mensur Dlakic

Thank you, this helps a lot! I haven't tried setting the $MAFFT_BINARIES variable to a different path yet but it makes sense to me as a fix.

In case anyone comes across this with a similar problem, I also emailed the creator of MAFFT, who says that the prank-msa/mafft executable bundled in PRANK is actually a shell script that requires subprograms of MAFFT v7.450 in the location specified by the $MAFFT_BINARIES variable. The v7.450 MAFFT binaries are not bundled with PRANK, and the current version of MAFFT living in /usr/local/bin is v7.490. Dr. Katoh, the MAFFT creator was able to send me a PRANK package with the MAFFT binaries built in, where the "mafft" script automatically detects the location of itself and uses the bundled binaries in the "prank-msa" folder. Hopefully, this is how future PRANK downloads will be set up.

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written 4.5 years ago by noramarie •