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GATK4.beta6 GenomicsDBimport error

I've been trying to run GenomicsDBimport on 2000+ samples. It worked on GATK4.beta3, but there was an error in the batch processing so I switched to beta6. In this version, I'm getting an error with the tiledb utilits.

My command was:

/gatk/gatk-launch GenomicsDBImport $input_samples --genomicsDBWorkspace tmp --intervals Chr01:1-100000 --batchSize 100

The resulting error was:

[January 1, 2018 4:04:59 AM UTC] Executing as [email protected] on Linux 3.10.0-693.5.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-0ubuntu1.16.04.2-b11; Version: 4.beta.6-SNAPSHOT
04:04:59.862 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 1
04:04:59.862 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
04:04:59.862 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
04:04:59.863 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
04:04:59.863 INFO  GenomicsDBImport - Deflater: IntelDeflater
04:04:59.863 INFO  GenomicsDBImport - Inflater: IntelInflater
04:04:59.863 INFO  GenomicsDBImport - GCS max retries/reopens: 20
04:04:59.863 INFO  GenomicsDBImport - Using google-cloud-java patch c035098b5e62cb4fe9155eff07ce88449a361f5d from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
04:04:59.863 INFO  GenomicsDBImport - Initializing engine
04:08:43.324 INFO  IntervalArgumentCollection - Processing 100000 bp from intervals
04:08:43.327 INFO  GenomicsDBImport - Done initializing engine
[TileDB::utils] Error: Cannot create directory '/root/.tiledb'; Permission denied.
[TileDB::StorageManager] Error: Cannot load metadata schema; Metadata '/root/.tiledb/master_catalog' does not exist.
Failed to create workspace /scratch/wild_gwas/genomicsdb/tmp
04:08:43.448 INFO  GenomicsDBImport - Shutting down engine
[January 1, 2018 4:08:43 AM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 3.73 minutes.

A USER ERROR has occurred: Error creating GenomicsDB workspace: tmp

I'm running it on a cluster where I do not have root access, so I'm not sure how to work around this.

Best Answer


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