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GATK v4.0.8.1 GenomicsDBImport Error (VariantStorageManagerException exception)

Hi, I am following the current best practice to prepare the consolidated GVCF from 5 samples of WGS for joint calling
with the following command and encounter an error
java -Djava.io.tmpdir=/work/TMP \ -Xmx40g -jar ~/bin/gatk-4.0.8.1/gatk-package-4.0.8.1-local.jar \ GenomicsDBImport \ -V /work/Analysis/III_3P_RG_DupMark.raw.snps.indels.g.vcf \ -V /work/Analysis/IV_11N_RG_DupMark.raw.snps.indels.g.vcf \ -V /work/Analysis/IV_8N_RG_DupMark.raw.snps.indels.g.vcf \ -V /work/Analysis/IV_10P_RG_DupMark.raw.snps.indels.g.vcf \ -V /work/Analysis/IV_20P_RG_DupMark.raw.snps.indels.g.vcf \ --genomicsdb-workspace-path /work/Analysis/wang_chr19_re \ --intervals chr19

Error Log

15:00:35.770 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/wang/bin/gatk-4.0.8.1/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
15:00:35.944 INFO GenomicsDBImport - ------------------------------------------------------------
15:00:35.944 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.8.1
15:00:35.945 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
15:00:35.945 INFO GenomicsDBImport - Executing as [email protected] on Linux v3.16.0-43-generic amd64
15:00:35.945 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-2~14.04-b11
15:00:35.945 INFO GenomicsDBImport - Start Date/Time: October 2, 2018 3:00:35 PM JST
15:00:35.945 INFO GenomicsDBImport - ------------------------------------------------------------
15:00:35.945 INFO GenomicsDBImport - ------------------------------------------------------------
15:00:35.946 INFO GenomicsDBImport - HTSJDK Version: 2.16.0
15:00:35.946 INFO GenomicsDBImport - Picard Version: 2.18.7
15:00:35.946 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:00:35.946 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:00:35.946 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:00:35.946 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:00:35.946 INFO GenomicsDBImport - Deflater: IntelDeflater
15:00:35.946 INFO GenomicsDBImport - Inflater: IntelInflater
15:00:35.946 INFO GenomicsDBImport - GCS max retries/reopens: 20
15:00:35.946 INFO GenomicsDBImport - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
15:00:35.946 INFO GenomicsDBImport - Initializing engine
15:00:38.360 INFO IntervalArgumentCollection - Processing 58617616 bp from intervals
15:00:38.366 INFO GenomicsDBImport - Done initializing engine
Created workspace /work/Analysis/wgs_chr19
15:00:38.849 INFO GenomicsDBImport - Vid Map JSON file will be written to /work/Analysis/wgs_chr19/vidmap.json
15:00:38.849 INFO GenomicsDBImport - Callset Map JSON file will be written to /work/Analysis/wgs_chr19/callset.json
15:00:38.849 INFO GenomicsDBImport - Complete VCF Header will be written to /work/Analysis/wgs_chr19/vcfheader.vcf
15:00:38.850 INFO GenomicsDBImport - Importing to array - /work/Analysis/wgs_chr19/genomicsdb_array
15:00:38.850 INFO ProgressMeter - Starting traversal
15:00:38.850 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute
15:00:39.771 INFO GenomicsDBImport - Importing batch 1 with 5 samples
Buffer resized from 28469bytes to 32688
Buffer resized from 28473bytes to 32630
Buffer resized from 28469bytes to 32745
Buffer resized from 28469bytes to 32717
Buffer resized from 28466bytes to 32648
Buffer resized from 32688bytes to 32758
Buffer resized from 32630bytes to 32726
Buffer resized from 32648bytes to 32703
Buffer resized from 32717bytes to 32751
Buffer resized from 32703bytes to 32765
Buffer resized from 32745bytes to 32768
Buffer resized from 32726bytes to 32763
Buffer resized from 32765bytes to 32767
Buffer resized from 32758bytes to 32765
Buffer resized from 32751bytes to 32762
Buffer resized from 32767bytes to 32769
Buffer resized from 32763bytes to 32768
Buffer resized from 32762bytes to 32768
Buffer resized from 32765bytes to 32767
Buffer resized from 32767bytes to 32769
Buffer resized from 32768bytes to 32769
Buffer resized from 32768bytes to 32769
Buffer resized from 32768bytes to 32769
terminate called after throwing an instance of 'VariantStorageManagerException'
what(): VariantStorageManagerException exception : Error while syncing array chr19$1$58617616 to disk
TileDB error message : [TileDB::utils] Error: Cannot sync file '/work/Analysis/wgs_chr19/chr19$1$58617616/.__a89fdd44-1241-43ba-9072-6fcf116fbc1d139627949156096_1538460040234'; File syncing error

things I have checked
I have confirmed there is enough disk space and the working directory is in a shared volume.
It would be appreciated if you can help me on the troubleshotting.

Thanks

Issue · Github
by bhanuGandham

Issue Number
5342
State
open
Last Updated
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Milestone
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