Andrew Bromage

_(32bit linked)_ Assuming that this means what I think this means, that's your problem right there. Compiling Xenome as a 32-bit program is unsupported. I'm a bit surprised that it...

Thank you! That helps a lot. I've been looking for an incompatibility, but it sounds like it's actually a longstanding bug. Everyone has probably worked out by now that you...

The problem is a concurrency issue. And it's a nasty one. This is why it works on short reference genomes: there isn't enough work for multithreading to be an issue.

"I've now tried running xenome index with -T 1 and -T 8, could it potentially work with other values of -T?" If the bug is what we think it is,...