I can't tell why you have a problem with memory. When I run your test here I can see the blat process reach a maximum size of just under 4 Gb as it operates. Can you indicate what source version you have or where you picked it up from ?
The procedure you indicate where you operate one chromosome at a time is actually a more efficient procedure of running through a number of query sequences. You can also make it operate much faster with a pre-computed ooc file. Use the command: blat hg19.2bit /dev/null /dev/null -tileSize=11 -makeOoc=hg19.11.ooc -repMatch=1024 Then, in each of your per-chromosome mapping operations, use the -ooc flag: blat hg19.2bit:chr12 -ooc=hg19.11.ooc test.fa test.psl --Hiram ----- Original Message ----- From: "Jinyan Huang" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Monday, June 13, 2011 9:35:50 AM Subject: Re: [Genome] Blat problem If I do like this: blat ~/bin/blat/hg19.2bit:chr12 test.fa test.psl it works. But I really do not like it. I have lots of query. blat ~/bin/blat/hg19.2bit:chr12 test.fa test.psl Loaded 133851895 letters in 1 sequences Searched 243 bases in 1 sequences Thanks. On Mon, Jun 13, 2011 at 6:33 PM, Jinyan Huang <[email protected]> wrote: > Here is my test.fa > >>probe_set:HuEx-1_0-st-v2:2315101; Assembly=build-34/hg16; Seqname=chr1; >>Start=1788; Stop=2030; Strand=+; > TGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTC > TTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAG > GGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGG > ATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAG > GCA > > On Mon, Jun 13, 2011 at 6:29 PM, Hiram Clawson <[email protected]> wrote: >> Can you say anything about your query sequence in test.fa ? >> >> ----- Original Message ----- >> From: "Jinyan Huang" <[email protected]> >> To: [email protected] >> Sent: Monday, June 13, 2011 6:17:18 AM >> Subject: [Genome] Blat problem >> >> Dear list, >> >> When I run blat local. I always get this error. >> >>>blat ~/bin/blat/hg19.2bit test.fa test.psl >> >> Loaded 3137161264 letters in 93 sequences >> needHugeMen: Out of huge memory - request size 962165992 bytes >> >> In fact, my machine have 48G memory. I have set: >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
