Hi, I'm trying to run FIMO on a single (pretty short) DNA motif. First I used the iupac2meme script to generate a MEME motif file for my sequence (WCCAAAYW). Then I took that output motif file and plugged it into FIMO without any additional modifications. This is what the input looks like:
MEME version 5.4.1 (Sat Aug 21 19:23:23 2021 -0700)
ALPHABET= ACGT
strands: + -
Background letter frequencies (from uniform background):
A 0.25000 C 0.25000 G 0.25000 T 0.25000
MOTIF WCCAAAYW WRTTTGGW
letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0
0.500000 0.000000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.500000 0.000000 0.500000
0.500000 0.000000 0.000000 0.500000
I keep running into this error, however:
Errors from MEME XML parser: Expected state IN_MEME not found! MEME XML parser returned error code 4. FATAL: An error occurred reading the motif file.
Has anyone else run into this? Why might it be happening? Thanks for your help.