"--text" option preventing outputs in FIMO command line version

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Ari Selzer

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Jul 25, 2013, 3:22:49 PM7/25/13
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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.

James Johnson

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Jul 25, 2013, 6:26:07 PM7/25/13
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FIMO has a default p-value threshold of 1e-4 but even with a perfect match your motif contains too little information to get a better p-value than 0.000864. If you set the "--thresh" option to 1e-3 then you will find your motif.

In text mode FIMO writes the output to standard output so you should use a redirect to store it in a file:

/apps1/meme/current/bin/fimo --thresh 1e-3 --text GGAGA_motif.txt chr1.fa > results.txt

You might want to look at Charles answer to another user with a similarly short motif:
FIMO returns no results when scanning large genomes
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