I'm validating already created primers. One of the things I'm doing is telling the users if their primers will target anything else in the genome. Since a 20 base primer with, oh, an A to T mismatch at position 10 is still going to bind quite adequately, I need to be able to find those situations before they bite my users. (IOW, one of the main purposes of the program I'm working on is to warn the users when their primer pair is also going to bind and amplify someplace else. For that I need to find less than perfect matches.)
Other than setting MACHTYPE to x86_64, is there anything I need to do to make sure it all compiles 64 bit? Thanks, Greg ----- Original Message ----- From: "Jim Kent" <[email protected]> To: "Gregory Dougherty" <[email protected]> Cc: "genome" <[email protected]> Sent: Wednesday, August 4, 2010 2:57:33 PM GMT -06:00 US/Canada Central Subject: Re: [Genome] Segmentation Fault running gfServer Try it on a larger machine, and make sure you're runing a version compiled with 64 bit. You are pushing the envelope here Greg. _Why_ do you need to have less of the 3' end match perfectly? Are you amplifying non-human DNA with human primers? On Aug 4, 2010, at 10:19 AM, Gregory Dougherty wrote: > On a server w/ 8 GB of RAM I tried running gfServer with a stepSize of 1, > tileSize of 11, on hg18. I got a Segmentation Fault. Running it with > stepSize of 2 works, and on a 4GB machine the stepSize of 2 generates a "not > enough memory" error rather than a segfault. > > Is this a known problem? The machine is x86_64, running Linux. > > TIA, > > Greg > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
