[Genome] BLAT against mm9.2bit

[Hiram Clawson]

Good Afternoon Sukhinder:

A blat against the entire genome requires on the order of 3 to 8 Gb of memory
in the machine.

As a work around, run the blat individually on each chromosome, then combine
all the results.

--Hiram

Sukhinder Sandhu wrote:
> Hi
> 
> I can do small BLAts but when I try to BLAT the same file against the whole
> genome build, I get the following error:
> 
> [CANCER-W8706199WOH:~/Desktop/usr/blatSuite] sand60% ./blat /Volumes/MAC\
> USERS\$/sand60/mm9.2bit
> /Users/sand60/Desktop/FRA_LOH_DEl/humanMirs_known.fasta ./aug31_try1.psl
> Loaded 2725765481 letters in 35 sequences
> blat(627) malloc: *** vm_allocate(size=879542272) failed (error code=3)
> blat(627) malloc: *** error: can't allocate region
> blat(627) malloc: *** set a breakpoint in szone_error to debug
> needHugeMen: Out of huge memory - request size 879541876 bytes
> 
> What would be the best way around this? Any suggestions are greatly
> appreciated. Thanks a lot.
> 
> sukhinder