I'm trying to validate PCR Primers. Jim Kent had suggested it would be possible to do stepSize 1, so I figured I would try it out.
I tried running it on 1/2 the genome (chr 1 - 8), but after 90 minutes it still hadn't finished tiling the genome (it only took 8 minutes to do it at step size 2), so I killed that process. Greg ----- Original Message ----- From: "Galt Barber" <[email protected]> To: "Gregory Dougherty" <[email protected]> Cc: "genome" <[email protected]> Sent: Wednesday, August 4, 2010 2:04:06 PM GMT -06:00 US/Canada Central Subject: Re: [Genome] Segmentation Fault running gfServer Even if it didn't segfault, you would not have enough memory to run stepSize 1, which is a very unusual option setting in any case. Typical users are setting stepSize to 11 (the default tileSize) or to 5 for a little extra sensitivity, at the cost of doubling the RAM required. What are you trying to align? If you need very small alignments then the many wonderful short-read-aligners like BWA do a good job. -Galt On 08/04/10 10:19, 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
