Hello, SVGenotyperWalker is crashing with the error. Please see attached files for the output and error logs.
A java crash like this is often some system-dependent issue (because we aren't executing any native code).
My first thought would be to check to make sure LSF or SGE (if you are using something like this) didn't terminate the process. I note that the process had run for almost exactly 3 days when it died.
I'm also surprised it ran for so long, since it looks like you are running 1000 sites per process. I would suggest looking at the log to figure out the last site that was genotyped successfully and then try to run just the next site alone to see if the problem is reproducible. I would also suggest looking at the log messages to see if there is a pattern for whether some sites are taking a long time to genotype. It looks like you are using just 20 samples, so this performance seems quite slow unless these are very large sites. It looks like in the beginning of the run, you are taking just a few seconds per site, which is more like what I would expect. The time per site to genotype will grow linearly with site length (megabase sites might take a few minutes).
Thanks. Yes, it was LSF hitting the time limit (3 days). Not sure why it is so slow though. I'll try to look for a pattern as you suggest.