Off topic:Indexing Genome Commands in Linux (hummingbird-ucsc)

Question

[Scott McKay]

Hey all,

I am having trouble indexing my reference genome (mm10) with bowtie 2. It keeps stalling / lagging after it starts indexing. As in it begins, but then gets stuck in a loop soon after and cannot finish. Anyone else run into this problem? Or know another way to go through indexing a genome for Chip-Seq?