Hello Tim,
This is an elusive, rare bug that has come up just a few times in the past. We will work with you about this on the bug report thread submitted about the same issue on the private galaxy-bugs mailing list (dated 3/2).
We do appreciate your sending in the example. It is difficult to reproduce and the new example is very helpful. We have had one other example (so far) from another user recently and will be getting back to you both as soon as possible.
Thanks!
Jen Galaxy team
On 3/1/12 2:19 PM, Tim Reddy wrote:
Hello,
I'm getting this problem a lot when I'm trying to intersect data sets. There errors are similar to:
Skipped 4 invalid lines of 1st dataset, 1st line #19614: "chr10 135498863 135499333 chr10.6783 1000 + 0.4037 15.3 -1 236 ", problem: 536870912 is larger than the size of this BitSet (536870912).
This is on the main public server with the hg19 genome while running "overlapping pieces of intervals" on pairs of datasets in the attached history. I've tried different format types, changing the strand, confirming that the provided files to not extend past end of chromosomes, to no avail.
Public history: http://main.g2.bx.psu.edu/u/timreddy/h/unnamed-history
Seems there was an error to this extent in the archives from 2009, but no response.
Tx, Tim