mosaik jump database

[amcrisan]

Hello,

I am uncertain as how to make use of the mosaik jump database. I built my reference sequence as per the documentation, and when running the alignment I give it the following command:

./MosaikAligner -in /DIRECTORY/LANE_moasik_exports.dat -out LANE_aligned.dat -ia DIRECTORY/human_all_mosaik.dat -hs 15 -mm 6 -act 25 -p 8 -mhp 100 -j h.sapiens_15

and I get the error: ERROR: Could not open h.sapiens_15_keys.jmp for reading.

I am uncertain what pre-step I need to do to make this work. If I run it without the -j option, the alignment will exectue, although is does eat up the promised 57 gigs of RAM.

Ideally I'd like to get it down to 19 gigs, and if anyone knows any optimization tricks to get it even lower, that would best.

[sdriscoll]

run the following to make your jump database

MosaikJump -ia <yourpath>/human_all_mosaik.dat -out <yourpath>/human_all_mosaik_15 -hs 15

replace <yourpath> with the path to where your reference dat files are so that the files produced by this command are in the same place. when you run MosaikAligner make sure in include that path after the -j option. your command will then look like this:

./MosaikAligner -in DIRECTORY/LANE_moasik_exports.dat -out LANE_aligned.dat -ia DIRECTORY/human_all_mosaik.dat -hs 15 -mm 6 -act 25 -p 8 -mhp 100 -j DIRECTORY/human_all_mosaik_15