I'm using the FIMO analysis tool to look for the small motif "GGAGA" (
motif link saved and used as a .txt file) in the first chromosome split up into 5kb long sequences (
fasta input sequence). I only want the plain text output file so I'd like to use the "--text" option given. However, whenever I do so the program runs, but no directory or output file is created. I have tried manually assigning a directory (-o and -oc options). I have also tried only using a very limited part of the first chromosome (all the way down to only using only one 5kb long sequence) to see if there would be any difference, with no avail.
here is my command line input:
/apps1/meme/current/bin/fimo --text GGAGA_motif.txt chr1.fa
and the information given while the program runs:
Warning: text mode turns off computation of q-values
Reading txt file vmajor: 4, vminor: 9, vbug: 0
Using nucleotide alphabet (ACGTRYKMSWBDHVN).
Using background frequencies from NR sequence database.
Reading motif 1.
Reverse complementing: +1 -1
Motif Seq Start Stop Log-odds p-value Site
Using motif +1 of width 5.
Using motif -1 of width 5.
when the changes listed above were administered there was still no output.