A frg library was created from NCBI traces using the method described here:
for wgs built from trunk on 2014_07_03. When run like this it segfaults in one of the "2" files. Change the order around and it goes more or less entries, but always segfaults.
/home/mathog/wgs_project/wgs_trunk_2014_07_03/Linux-amd64/bin/gatekeeper \ -o /home/mathog/wgs_project/corrected_Spur_PACBIO/temppacbio_corrected/asm.gkpStore.BUILDING \ -F \ /home/mathog/wgs_project/NCBI_traces/strongylocentrotus_purpuratus.1.lib.frg \ /home/mathog/wgs_project/NCBI_traces/strongylocentrotus_purpuratus.2.001.frg \ /home/mathog/wgs_project/NCBI_traces/strongylocentrotus_purpuratus.2.002.frg
Using gdb I traced this down to what appears to be a basic memory allocation error in AS_GKP_checkFrag.C. The attached patch resolved that error and let the program run longer. It is currently grinding through the 26 "2" frg files, and I expect it will finish.
Perhaps there was a change recently in that file? It is hard to see how this bug could have been around for long.
I do not know yet if this patch results in correctly constructed output, just that it keeps gatekeeper from crashing on this input.
Log in to post a comment.