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
