Good Afternoon John: Your login shell may have default memory limits for processes to avoid run-away procedures from hogging all your memory.
If you are in bash, you can raise your shell limits with the commands: ulimit -d 10240000 ulimit -v 10240000 To set 10 Gb memory limits. If you are working in the C-shell (csh/tcsh) use the limit command: limit datasize 10240m limit vmemorysize 10240m The usual method to avoid this problem is to break up your alignment problem into smaller parts. For example, align each of your query sequences to a single chromosome in the target genome. You can specify a single chromosome target sequence, for example: hg19.2bit:chr1 to blat just to chr1 in hg19. --Hiram John Herbert wrote: > 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
