FIMO outputs only Chr1 hits

Question

[rbronste]

Ran the following fimo command with a meme PWM on a fasta file of about 10,000 sequences and for some reason it only output hits that map to the 1st chromosome in mm10? Any ideas? Thanks!

fimo /sonas-hs/hpc_norepl/home/MA0212.1.meme /sonas-hs/hpc_norepl/home/resOrderedFem.fa

[Satyajeet Khare]

I think FIMO is not able to go beyond Chr1 due to default parameters. Try playing with --max-stored-scores and --thresh parameters.