Jim has said in another email that he will not make a blat version that uses 64-bit pointers until most machines ship with >16GB ram.
-Galt On Tue, Jul 17, 2012 at 2:19 PM, Hiram Clawson <[email protected]> wrote: > Good Afternoon Tony: > > We know why blat will crash on this sequence: > Homo_sapiens.GRCh37.67.dna.toplevel.fa.gz > > The internals of the program has 32-bit integers that can > not count past 4 GiB. This fasta file has 20 GiB of sequence. > It will not function as a single .2bit file. I'm not sure > you would want it to either. Each of the haplotypes in this > file reproduce the entire chromosome that the haplotype is contained > within. There are eight complete copies of chr1, five complete > copies of chr2, etc. It has two different copies of chrY, one > completely empty of sequence. > > --Hiram > > Tony Travis wrote: > > If I've got time, I'll do some more debugging - It might be a memory > > leak that only shows up when indexing >4GiB DB files. As I said here, > > the same query files run fine against the hg19.2bit DB I downloaded. > > However, using this DB "blat" only uses about 3.9GiB RAM. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
