GSNAP genome directory problems

[KJam]

Hi All,

I was wondering if anyone could help me running GSNAP, I assume I've got a fairly simple problem.
I first used gmap_build to build a reference
gmap_build -d /Users/kjames/Documents/Chapter5NGS/ROD/GMAP/ RODRef.fasta

And then when I try to run GSNAP it has problems finding -d
gsnap -d /Users/kjames/Documents/Chapter5NGS/ROD/GMAP/ -m 5 -A sam RODc_1.fastq RODc_2.fastq

And it gives the error:

Unable to find genome directory /usr/local/share//Users/kjames/Documents/Chapter5NGS/ROD/GMAP. Either recompile the GMAP package
to have the correct default directory (seen by doing gmap --version),
or use the -D flag to gmap to specify the correct genome directory.

I'm wondering if it's hidden the reference elsewhere but I can't see an obvious location.

Any help would be great appreciated,

Kat

[GenoMax]

Since you did not create your genome indexes in the "genome" directory you may have to specify (NOTE: Capital D) "-D /Users/kjames/Documents/Chapter5NGS/ROD/GMAP/".

See quote from GMAP help below:

we assume that you have installed a
genome database called <genome> in your GMAPDB directory. (If your
database is located elsewhere, you can specify the -D flag to gmap or
set the environment variable GMAPDB to point to that directory.)

[KJam]

Thanks so much GenoMax! I had my directories and databases muddled up, all working brilliantly now.

Kat