Error in creating bowtie index

[sbaheti]

Hi
I am trying to run methylcode and while running it creates the bowtie index for *.fr.c2t.fa(human) that time it fails to create the index file required.

i get this error message
Error: Reference sequence has more than 2^32-1 characters! Please divide the
reference into batches or chunks of about 3.6 billion characters or less each
and index each independently.

I tried using 64 bit version of bowtie but it didn't help, do you know what i doing incorrectly or how should i solve this

du -hs *.fr.c2t.fa
6.5G which is double the size of human reference genome hg19.

Thanks

Saurabh