GDB feature request: silence buffer resize logging

[ldgauthier]

@nalinigans I have some very long-running jobs that I'm trying to track, but my stderr is choked with buffer resize outputs. Would it be possible to turn those off by default or add a flag to turn them off? It makes for huge log files and it's hard to track if the log is still being updated for jobs that run >24hrs.

[ldgauthier]

Looks like Nalini already took care of this a while ago.

[ldgauthier]

I just ran GATK 4.1.7.0 with GDB 1.2.1 and I'm seeing these logging messages again. Granted I've also built a few old jars lately, but after a clean build I'm still seeing it. @nalinigans can you run the latest and confirm or deny?

[droazen]

@ldgauthier Did you try GATK 4.1.8.0 or later as well? 4.1.8.0 introduced a major new release of GenomicsDB.

[droazen]

@ldgauthier Also, try running with the prebuilt jars (https://github.com/broadinstitute/gatk/releases/download/4.1.8.1/gatk-4.1.8.1.zip) and/or the latest docker image to eliminate your local build environment as a variable.

[nalinigans]

I just tried with gatk 4.1.7.0 and 4.1.8.0 released zips and cannot reproduce the issue. I can only see buffer resize logging messages when I use a debug version of libtiledbgenomicsdb.so in my private builds.

That said, gatk 4.1.7.0 picks up libtiledbgenomicsdb.so from the LD_LIBRARY_PATH, otherwise it extracts from the genomicsdb.jar. @ldgauthier, do you have an older version of the native libtiledbgenomicsdb.so in your LD_LIBRARY_PATH env? That could be one cause.

Otherwise, if you move to using gatk 4.1.8.1 as @droazen recommends, it will only pick up the native library packed with the genomicsdb 1.3.0 jar. To override the packed genomicsdb library, in versions 1.3.0+, one has to explicitly the path specify via java options -Dgenomicsdb.library.path=<path_to_libtiledbgenomicsdb.so>.