Dear Mailing list, Please can someone help me fix a problem using a local version of BLAT? I want to align nucleotides to the human genome.
I have this version: blat - Standalone BLAT v. 34 fast sequence search command line tool My workstation has a Core i 7 processor and 12Gb of ram. I indexed the genome doing: faToTwoBit hg18.fa hg18.2bit However, if I take a single sequence and align it with blat, this happens: j...@john-desktop:~/data/genome$ blat -out=blast9 hg18.2bit test test_seq_blas9.out Loaded 3107677273 letters in 49 sequences needHugeMen: Out of huge memory - request size 957189248 bytes If I am looking right, this amounts to 1Gb of memory but the machine has 12Gb. Is there a line of code in the source I can modify to get around this problem or am I missing something? Thanks for any advice. ps. I saw other similar posts but they have work arounds and as I have a lot of data to analyse, it would be great to sort it out so it works. John. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
