FIMO (MEME Suite) Command Line Troubleshooting

Question

[na2]

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.

Answer 1

[Mensur Dlakic]

I think the problem is with this part:

Background letter frequencies (from uniform background): A 0.25000 C 0.25000 G 0.25000 T 0.25000

Don't know whether that is on a single line because you didn't format it properly, or it is actually a single line in your file. Either way, it should be:

Background letter frequencies
A 0.25000 C 0.25000 G 0.25000 T 0.25000

Here is the whole thing for the sake of completeness:

MEME version 5.4.1 (Sat Aug 21 19:23:23 2021 -0700)

ALPHABET= ACGT

strands: + -

Background letter frequencies
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

When I made that change, your motif worked fine:

Using motif +WCCAAAYW of width 8.
Using motif -WCCAAAYW of width 8.
Computing q-values.
  Estimating pi_0 from a uniformly sampled set of 10000 p-values.
  Estimating pi_0.
  Estimated pi_0=1