Hi, Shankar I tried to reproduce this error, but was unable to. I used a 34GB bedgraph file and had no trouble.
Since this problem may have been fixed somewhat recently, I suggest you try downloading a fresh version of bedGraphToBigWig and run it again. -Galt 3/14/2011 8:29 PM, Shankar Ajay Subramanian: > Hello, > > I'm trying to create a per-base coverage track from whole-genome sequencing > data and I opted to use the bigWig format to display this on the UCSC > browser. I downloaded the 64-bit linux 'bedGraphToBigWig' binary utility to > do so (Feb-18 version). > > The original read data are in BAM format (200GB), which I then converted to > bedGraph (49GB). When I tried to convert intermediate bedGraph file to > bigWig I end up getting the following error even though the process runs on > a machine with>100G RAM: > > needLargeMem: trying to allocate 34345569624 bytes (limit: 4294967296) > >> From talking to our sys admin it appears that the utility calls a library > where a hard-coded memory limit is specified for a 64-bit machine > (memalloc.c). Is there any way to get around this? I considered > down-sampling but didn't know if that would help since the bedGraph file is > likely to contain nearly as many data-points with Column4 values being > lower. > > Appreciate your help. > > Best, > Shankar > > Postdoctoral fellow > NIH/NHGRI _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
