segment_juncs memory usage while running Tophat

[genec]

I'm looking for suggestions on decreasing memory usage by Tophat. I don't think I had this problem previously, but with my current data sets I'm seeing the segment_juncs process using close to 9 GB of RAM (and only 1.9% CPU). I had previously been able to run 4 tophat searches at a time, but I can barely run 2 now because they quickly use up all the available memory.

I'm running Tophat v1.0.13 and Bowtie version 0.12.2 on Mac OS X.

Thanks!

Gene

[biznatch]

I'm having the same problem, as I posted here.

I'm using Tophat to align ~33 million 100 bp paired end reads to the mouse genome using -p 8 and and when it gets about 1 hour into "Searching for junctions via segment mapping" memory usage jumps from a few GB to almost 20 GB which exceeds the 16GB on my computer and starts using the swap file. I'm also using the "butterfly-search" which the Tophat manual says will slow slow down the alignment but doesn't say it should use more memory. Is this amount of memory usage normal or did something go wrong?