FATAL: glam2: error reading alphabet file: found T twice

[Michiel Karrenbelt]

during make test this occurs:

FAIL: glam2_1 (differences in glam2.txt)

and when trying to run glam2 I get: 

FATAL: glam2: error reading alphabet file: found T twice

Can someone help me out here? 

[James Johnson]

In reply to your first question - Are you using MEME 4.10.1 patch 2? There was an issue with the previous versions where Mac OS was getting different results due to differences in random number generation. We switched to using a bundled random number generator to fix the issue (or so we hoped).

So if you're using a version prior to MEME 4.10.1 patch 2 I recommend updating. If you are already using patch 2 then please send us the file "MEME_DIR/tests/results/glam2_1/glam2.txt" so we can try to figure out where the problem is.


In reply to your second question - I strongly suspect you have not listed the alphabet in the command and it is trying to read your sequence file as it it is an alphabet file.

For DNA you must specify 'n':

glam2 n my_seqs.fna

And for Protein you must specify 'p':

glam2 p my_seqs.faa

If you try to specify anything else it will attempt to read it as a GLAM2 alphabet file:
http://meme-suite.org/doc/glam2_alphabet.html