New digenome User - Basic Questions

[bredler]

I am a novice when it comes to analyzing NGS data. I have done some local protein blast in the past, but that is as close as I get. Here's the gist of what I'm doing:

1. I have Illumina sequencing reads from an experiment I just ran.
2. The file I would like to analyze is a .fastq file that contains all of the Read 2 sequence information for one index/sample.
3. The sample is an in vitro digested genome that I want to use to find target and off target hits of Cas9
4. I used bwa index to generate a bam and bai file of my data aligned to Drosophila melanogaster dm6 genome
5. I then used digenome-toolkit to analyze the aligned Read 2 bam file
6. digenome 'found' 1800+ chromosomes and produced ~6k files as output. When I try to view my data in IGV, it recognizes that I have...1800+ chromosomes which isn't very useful.

Is there something obvious that I'm missing?