Nalini Ganapati

> As you can see we ran java with relatively low RAM, but left ~150G for the C++ layer. I'm surprised this isnt good enough. Joint genotyping runs on jvm...

@bbimber, not sure what is happening here - the total of the GenomicsDB timers is `0.113811361+0.8294423339999996+0.018747005+0.04312843799999999+0.029110260000000002+0.007382536+0.029079955999999997+0.006077208000000001+0.30639567500000026+0.016806184 seconds` which is minuscule compared to the 25 minutes. Any chance of running this...

@droazen, @lbergelson, any pointers for remote java profiling for @bbimber?

Would it still be possible to try the profiler with this workspace for some insight?

> If you have a multi-NT variant that starts within 1050-1150, but extends outside (i.e. deletion or insertion starting at 1148), this could be a problem. The GenomicsDB workspace created...

@bbimber, did you use `GenomicsDBImport` from v4.2.5.0 as well? How large is your /home/exacloud/gscratch/prime-seq/cachedData/16b9ede7-6db8-103a-9262-f8f3fc86a851/WGS_Feb22_1852.gdb/1$1$223616942/__9b9a9e96-139c-4105-81ec-ab1455d1f01d140490873108224_1597099702436/__book_keeping.tdb.gz file? Anyway, you can share it with us?

There was an issue with the compressed write of book-keeping files. The import would seem to have succeeded, but the issue would show up during queries sometimes. This was fixed...

Another question, did `GenotypesGVCFs` succeed before with the same workspace?

Thanks @bbimber. Just tested with the files you shared and the book keeping file uncompresses and loads fine. So, no problem on that count. As you have noticed, consolidation is...

Yes, 60G should be sufficient. I will run a native consolidation with some data we have for profiling and see what I come with. Also, what OS and version are...