Dear Dr. Galt. I am grateful to you for your help. Bellow, I will list the required informations that you solicited in last e-mail: - PC: 64 bits architecture, AMD Atlon X2 dual core proc, 8 GB-RAM, Linux Fedora 9 64 bits; - UCSC Blat: http://genome-test.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip - Genome database: ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/ -only reference sequence genome, build 36.3; -I downloaded fasta files of 1-22, X and Y chromossomos, and agrupated each one in a single file (fasta format): approximatedely 3GB. -UCSC Blat command line user: #./blat hs_ref_chr_all.fas query.fas output.out -t=dna -q=dna -stepSize=5 -minScore=0 -minIdentity=0 -minMatch=25 I got an error message related to: not enough system memory. However, I certified that my system has 8GBRAM, and the graphical interface was not loaded. Thanks!! Herai.
> > By the way, normally questions should be addressed to > [email protected] > > Thanks for the specific info about your machine. > > Can you also show me example commandlines that > you are using to run BLAT? > > Also, where did you get blat, > and where did you get the human chromosome data? > > BLAT on DNA with -stepSize=5 for extra sensitivity > takes about 6GB of RAM for the entire human genome. > > But a 32-bit compiled blat won't be able to use more > than 4GB address space. > > Thanks! > > -Galt > > > On Thu, 19 Mar 2009, [email protected] wrote: > >> >> >> Dear Dr. Galt. >> I'me using USCS Blat standalone version >> and wants to load and use the interely human genome in my experiments. >> At >> the moment, I doing the experiments with isolated human chromosomes, >> because my computer can't load all the chromosomes in memory. Probably, >> I >> done some mistakes in the Blat configuration, because my computer is >> good. It is a 64 bits architecture, AMD Atlon X2 dual core processor, >> with >> 8 GB-RAM, Linux Fedora 64 bits. Like the input data to Blat program, I >> using the human genome, in fasta format, that has approximatedely 3GB. >> How >> can I try to run, perfectly, the Blat? >> Thank you >> very much. >> Regards, >> >> Herai. >> _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
