command line Meme-chip fail to write seqs-centered

[c.w....@gmail.com]

I'm trying to run meme with the following command:

meme-chip -db etc/motif_databases/JASPAR_CORE_2009_vertebrates.meme etc/motif_databases/uniprobe_mouse.meme file.fa

My file is full of entries as below (though for the occasional entry there is no accompanying DNA sequence, only a blank line before the next entry):

>chr_cStart:cEnd

atgcDNAsequence

However, I get the following error:

WARNING: skipped shuffle_seqs due to missing requirement center_seqs.

meme memechip_out/seqs-centered -oc memechip_out/meme_out -dna -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile memechip_out/background -revcomp -nostatus

HOME/.cshrc

No sequences found in file `memechip_out/seqs-centered'.  Check file format.

WARNING: skipped dreme due to missing requirement center_seqs.

centrimo -noflip -seqlen 0 -verbosity 1 -oc memechip_out/centrimo_out -bgfile memechip_out/background memechip_out/uniprobe_mouse.meme meme_4.9.0/etc/motif_databases/JASPAR_CORE_2009_vertebrates.meme

FATAL: Failed to read a single sequence from the given FASTA file.

Would someone please help me?

Thanks,

C

[CharlesEGrant]

Hi C,

Some of the scripts used in MEME-ChIP (fasta-center for example) won't run if the input sequence file contains empty sequences. Before you can run MEME-ChIP on your data you'll need to filter out those sequences that have a header line '>chr_cStart:cEnd', but don't contain any sequence data.

There is also a problem with your command line:

meme-chip -db etc/motif_databases/JASPAR_CORE_2009_vertebrates.meme etc/motif_databases/uniprobe_mouse.meme file.fa

When specifying two motif databases you need to repeat the '-db' flag, so your command line should be

meme-chip -db etc/motif_databases/JASPAR_CORE_2009_vertebrates.meme -db etc/motif_databases/uniprobe_mouse.meme file.fa