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GenomicsDBImport error: File2TileDBBinaryException
Hello, I've been trying to get the HaplotypeCaller-in-gVCF-mode to work for a combination of exome samples, some of which are diploid individuals, and others of which are bulks with ploidies ~20. For about 20% of my chromosomes, The GenomicsDBImport step fails, with the following error message:
09:58:45.656 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 09:58:46.530 INFO GenomicsDBImport - Importing batch 1 with 6 samples terminate called after throwing an instance of 'File2TileDBBinaryException' what(): File2TileDBBinaryException : read_one_line_fully && "Buffer did not have space to hold a line fully - increase buffer size"
I'm not sure what this means, and a google search brings up next to nothing.
I am working with mosquito exome data, 150bp PE illumina reads, GATK 18.104.22.168, java 1.8.0_181. I've been following the Broad best practices pretty closely, although I haven't managed to figure out how to bootstrap base recalibration yet.
Example GenomicsDBImport command:
gatk --java-options '-Xmx5G' GenomicsDBImport \ --genomicsdb-workspace-path ../vcfs/combined_gvcfs/NW_021837046.1 \ --intervals NW_021837046.1 \ -V ../vcfs/gvcfs/BH2.gvcf \ -V ../vcfs/gvcfs/BH3.gvcf \ -V ../vcfs/gvcfs/K01.gvcf \ -V ../vcfs/gvcfs/K02.gvcf \ -V ../vcfs/gvcfs/M01.gvcf \ -V ../vcfs/gvcfs/M02.gvcf