AndyMenzies

@cjfields I think I was trying to parse Uberon at the time, its quite large and I don't have a concise file that triggers the problem. http://purl.obolibrary.org/obo/uberon/ext.obo

Take a look at the pull request I just added [#21](https://github.com/data61/gossamer/pull/21). It doesn't attempt to change the threading, but it does mitigate the hanging problem by having multiple exit points...

GATK BaseRecalibration is almost certainly the issue. Most of our tools are written to use Illumina standard quality scores, BaseRecalibration will push the quality scores well outside the expected ranges....