Hello, It seems like you are using your own mirror and trying to upload there as a native track? From a first look, you are out of disc space.
Double check that you have space, then perhaps try an alternate format designed for large datasets, such as bigBed or bigWig. And finally, breaking the data up per-chromosome is always an option. We do this for many tracks internally. Hiram may have more to add later on, Thanks, Jennifer ps. Just to double check, your mySQL version is still 4, but we are on 5. Be certain that you are using a consistent source code tree for all (data and software). Some changes were made to several utilities when the switch to v5 was made. See the genome-mirror mailing list archives for exact changes. http://genome.ucsc.edu/contacts.html#mirror ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "WANG Wuqi" <[email protected]> wrote: > From: "WANG Wuqi" <[email protected]> > To: "[email protected]" <[email protected]> > Cc: "Jennifer Jackson" <[email protected]>, [email protected], "WANG Wuqi" > <[email protected]> > Sent: Tuesday, November 10, 2009 7:39:38 PM GMT -08:00 US/Canada Pacific > Subject: UCSC data loading error - needMem: Out of memory > > Hi Hiram, > > When we upload BED data format with 12 columns to encounter below > error: > ................ > $ hgLoadBed hg18 RHM005_final_gff_noFILT RHM005_final_gff_noFILT.bed > Reading RHM005_final_gff_noFILT.bed > needMem: Out of memory - request size 89 bytes, errno: 12 > ................ > > The size of this data file is about 3GB. When we take part of data, > for example, 1000 rows > to do custom track or load, both are ok. > > Our server: > Linux ucsc.fugu-sg.org 2.6.9-67.0.22.ELsmp #1 SMP Wed Jul 23 17:30:51 > EDT 2008 i686 i686 i386 GNU/Linux > > MySQL: Ver 14.7 Distrib 4.1.22, for pc-linux-gnu (i686) using readline > 4.3 > > > Thanks & regards > > Wuqi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
