Class org.broadinstitute.hellbender.tools.IndexFeatureFileIntegrationTest
Tests
Test |
Duration |
Result |
testVCFIndexOnCloud |
2.033s |
passed |
Standard error
20:42:57.243 INFO IndexFeatureFile - ------------------------------------------------------------
20:42:57.243 INFO IndexFeatureFile - org.broadinstitute.hellbender.tools vUnavailable
20:42:57.243 INFO IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/
20:42:57.243 INFO IndexFeatureFile - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:42:57.243 INFO IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:42:57.243 INFO IndexFeatureFile - Start Date/Time: June 12, 2025 at 8:42:57 PM UTC
20:42:57.243 INFO IndexFeatureFile - ------------------------------------------------------------
20:42:57.243 INFO IndexFeatureFile - ------------------------------------------------------------
20:42:57.244 INFO IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:42:57.244 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:42:57.244 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:42:57.244 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:42:57.244 INFO IndexFeatureFile - Deflater: IntelDeflater
20:42:57.244 INFO IndexFeatureFile - Inflater: IntelInflater
20:42:57.244 INFO IndexFeatureFile - GCS max retries/reopens: 20
20:42:57.244 INFO IndexFeatureFile - Requester pays: disabled
20:42:57.244 INFO IndexFeatureFile - Initializing engine
20:42:57.244 INFO IndexFeatureFile - Done initializing engine
20:42:57.953 INFO FeatureManager - Using codec VCFCodec to read file gs://hellbender-test-logs/staging/testIndexOnCloud/f8c69df6-3175-4e4f-bc9a-bda452ab9f81.vcf
20:42:58.129 INFO ProgressMeter - Starting traversal
20:42:58.130 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:42:58.132 INFO ProgressMeter - unmapped 0.0 26 780000.0
20:42:58.132 INFO ProgressMeter - Traversal complete. Processed 26 total records in 0.0 minutes.
20:42:58.578 INFO IndexFeatureFile - Successfully wrote index to /staging/testIndexOnCloud/f8c69df6-3175-4e4f-bc9a-bda452ab9f81.vcf.idx
20:42:58.578 INFO IndexFeatureFile - Shutting down engine
[June 12, 2025 at 8:42:58 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2726297600