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GenomicsDBImport problem with versions 0.9.0 and 0.9.2

Hi,

I don't know if it's a bug, but whenever I try to do a GenomicsDBImport I get an error, no matter which file I use. The command I run is (using GATK 4.0):

gatk GenomicsDBImport -V AD0616.10.g.vcf.gz --genomicsdb-workspace-path gdbworkspace-gatk -L 10

And the error I get is:

Using GATK jar /apps/GATK/4.0/gatk-package-4.0.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /apps/GATK/4.0/gatk-package-4.0.0.0-local.jar GenomicsDBImport -V /scratch/production/cluengo/genomicsdb/AD0616.10.g.vcf.gz --genomicsdb-workspace-path gdbworkspace-gatk -L 10
17:00:53.658 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/apps/GATK/4.0/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
17:00:53.770 INFO GenomicsDBImport - ------------------------------------------------------------
17:00:53.771 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.0.0
17:00:53.771 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
17:00:53.771 INFO GenomicsDBImport - Executing as [email protected] on Linux v2.6.32-696.13.2.el6.Bull.128.x86_64 amd64
17:00:53.771 INFO GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_102-b14
17:00:53.771 INFO GenomicsDBImport - Start Date/Time: March 8, 2018 5:00:53 PM CET
17:00:53.771 INFO GenomicsDBImport - ------------------------------------------------------------
17:00:53.771 INFO GenomicsDBImport - ------------------------------------------------------------
17:00:53.772 INFO GenomicsDBImport - HTSJDK Version: 2.13.2
17:00:53.772 INFO GenomicsDBImport - Picard Version: 2.17.2
17:00:53.772 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 1
17:00:53.772 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:00:53.772 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:00:53.772 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:00:53.772 INFO GenomicsDBImport - Deflater: IntelDeflater
17:00:53.772 INFO GenomicsDBImport - Inflater: IntelInflater
17:00:53.772 INFO GenomicsDBImport - GCS max retries/reopens: 20
17:00:53.772 INFO GenomicsDBImport - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
17:00:53.772 INFO GenomicsDBImport - Initializing engine
17:00:54.197 INFO IntervalArgumentCollection - Processing 135534747 bp from intervals
17:00:54.200 INFO GenomicsDBImport - Done initializing engine
Created workspace /scratch/production/cluengo/genomicsdb/gdbworkspace-gatk
17:00:54.418 INFO GenomicsDBImport - Vid Map JSON file will be written to gdbworkspace-gatk/vidmap.json
17:00:54.418 INFO GenomicsDBImport - Callset Map JSON file will be written to gdbworkspace-gatk/callset.json
17:00:54.418 INFO GenomicsDBImport - Complete VCF Header will be written to gdbworkspace-gatk/vcfheader.vcf
17:00:54.418 INFO GenomicsDBImport - Importing to array - gdbworkspace-gatk/genomicsdb_array
17:00:54.470 INFO ProgressMeter - Starting traversal
17:00:54.470 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute
17:00:54.488 INFO GenomicsDBImport - Importing batch 1 with 1 samples
terminate called after throwing an instance of 'FileBasedVidMapperException'
what(): FileBasedVidMapperException : type_index_iter != VidMapper::m_typename_string_to_type_index.end() && "Unhandled field type"
[login1:01909] *** Process received signal ***
[login1:01909] Signal: Aborted (6)
[login1:01909] Signal code: (-6)
[login1:01909] [ 0] /lib64/libpthread.so.0[0x30bfa0f7e0]
[login1:01909] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x30bf6325e5]
[login1:01909] [ 2] /lib64/libc.so.6(abort+0x175)[0x30bf633dc5]
[login1:01909] [ 3] /apps/GCC/6.3.0/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x15d)[0x7f507f7018ed]
[login1:01909] [ 4] /apps/GCC/6.3.0/lib64/libstdc++.so.6(+0x8e8a6)[0x7f507f6ff8a6]
[login1:01909] [ 5] /apps/GCC/6.3.0/lib64/libstdc++.so.6(+0x8e8f1)[0x7f507f6ff8f1]
[login1:01909] [ 6] /apps/GCC/6.3.0/lib64/libstdc++.so.6(+0x8eb08)[0x7f507f6ffb08]
[login1:01909] [ 7] /apps/GENOMICSDB/0.9.2/lib/libtiledbgenomicsdb.so(+0x151df1)[0x7f507fb56df1]
[login1:01909] [ 8] /apps/GENOMICSDB/0.9.2/lib/libtiledbgenomicsdb.so(+0x1434d9)[0x7f507fb484d9]
[login1:01909] [ 9] /apps/GENOMICSDB/0.9.2/lib/libtiledbgenomicsdb.so(+0x1489f9)[0x7f507fb4d9f9]
[login1:01909] [10] /apps/GENOMICSDB/0.9.2/lib/libtiledbgenomicsdb.so(+0x12c78e)[0x7f507fb3178e]
[login1:01909] [11] /apps/GENOMICSDB/0.9.2/lib/libtiledbgenomicsdb.so(+0x12d7b4)[0x7f507fb327b4]
[login1:01909] [12] /apps/GENOMICSDB/0.9.2/lib/libtiledbgenomicsdb.so(+0x11f80d)[0x7f507fb2480d]
[login1:01909] [13] /apps/GENOMICSDB/0.9.2/lib/libtiledbgenomicsdb.so(Java_com_intel_genomicsdb_GenomicsDBImporter_jniSetupGenomicsDBLoader+0x98)[0x7f507fb99c78]
[login1:01909] [14] [0x7f50f1015814]
[login1:01909] *** End of error message ***

Thanks in advance!

Cristina.

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