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GenomicsDB
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BookKeeping error while using GATK4 GenomicsDBImport #222

Open TimurIs opened 6 years ago

TimurIs commented 6 years ago

Hello,

While using the GATK4 GenomicsDBImport (version >= 4.0.6.0) I'm keep getting the following error:

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

This error happens on any type input.

I suspect that the dollar sign in the name of the directories can cause this on my system (although, I'm not 100% sure). I've posted similar question on the GATK forum and got a suggestion to try to communicate with the DB developers.

I'm ready to provide more information if necessary,

Thank you, Timur

nalinigans commented 6 years ago

Was it working on versions below 4.0.6.0?

TimurIs commented 6 years ago

Was it working on versions below 4.0.6.0?

Yes, it works fine with 4.0.3.0 With 4.0.5.1 some imports look like "empty", but it still works. It stopped working with introduction of multiple intervals as input

nalinigans commented 6 years ago

Are you using docker? On what platform(s)? What would be the best way to reproduce this issue?

nalinigans commented 6 years ago

Hello @TimurIs. Are you still seeing the issue?