GenomicsDBImport GATK v4.0.9.0 BookKeeping error

Hi,

I'm trying to use the latest version of GATK and on the GenomicsDBImport step I can't import any gvcf on my machine.

I keep getting the following error with any input options:

12:27:39.237 INFO  GenomicsDBImport - ------------------------------------------------------------
12:27:39.238 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.9.0
12:27:39.238 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
12:27:39.239 INFO  GenomicsDBImport - Executing as **** on Linux v2.6.32-696.16.1.el6.x86_64 amd64
12:27:39.239 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_151-b12
12:27:39.240 INFO  GenomicsDBImport - Start Date/Time: September 27, 2018 12:27:37 PM EDT
12:27:39.240 INFO  GenomicsDBImport - ------------------------------------------------------------
12:27:39.240 INFO  GenomicsDBImport - ------------------------------------------------------------
12:27:39.240 INFO  GenomicsDBImport - HTSJDK Version: 2.16.1
12:27:39.240 INFO  GenomicsDBImport - Picard Version: 2.18.13
12:27:39.240 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:27:39.240 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:27:39.241 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:27:39.241 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:27:39.241 INFO  GenomicsDBImport - Deflater: IntelDeflater
12:27:39.241 INFO  GenomicsDBImport - Inflater: IntelInflater
12:27:39.241 INFO  GenomicsDBImport - GCS max retries/reopens: 20
12:27:39.241 INFO  GenomicsDBImport - Requester pays: disabled
12:27:39.241 INFO  GenomicsDBImport - Initializing engine
12:27:39.701 INFO  IntervalArgumentCollection - Processing 103110 bp from intervals
12:27:39.704 INFO  GenomicsDBImport - Done initializing engine
Created workspace /path/to/workspace
12:27:40.053 INFO  GenomicsDBImport - Vid Map JSON file will be written to /path/to/workspace/vidmap.json
12:27:40.053 INFO  GenomicsDBImport - Callset Map JSON file will be written to /path/to/workspace/callset.json
12:27:40.053 INFO  GenomicsDBImport - Complete VCF Header will be written to /path/to/workspace/vcfheader.vcf
12:27:40.054 INFO  GenomicsDBImport - Importing to array - /path/to/workspace/genomicsdb_array
12:27:40.054 INFO  ProgressMeter - Starting traversal
12:27:40.054 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute
12:27:40.225 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
terminate called after throwing an instance of 'VariantStorageManagerException'
  what():  VariantStorageManagerException exception : Error while finalizing TileDB array chr22$4514591$4617700
TileDB error message : [TileDB::BookKeeping] Error: Cannot finalize book-keeping; Writing domain size failed

An example command:

gatk-4.0.9.0/gatk --java-options "-Xms4g -XX:ParallelGCThreads=4" GenomicsDBImport \
-ip 250 \
--overwrite-existing-genomicsdb-workspace true \
-L chr22:4514841-4617450 \
--genomicsdb-workspace-path /path/to/workspace/ \
--tmp-dir /path/to/large/tmp/dir \
-V v1.chr22.g.vcf.gz

The error message isn't informative and so far I wasn't able to track down the origin of this problem. The only thing that I'm certain about is that importing work relatively stable for me on version 4.0.5.1 and doesn't work on any newer versions - I get the very same error. Do you have any solutions to this problem?

Thank you,
Timur

Answers

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