Class org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloaderIntegrationTest

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorDataSourceDownloaderIntegrationTest
tests
failures
ignored
0.424s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testDownloadDummySmallDataSources[0](true, true, false)	0.109s	passed
testDownloadDummySmallDataSources[1](true, false, false)	0.074s	passed
testDownloadDummySmallDataSources[2](true, true, true)	0.121s	passed
testDownloadDummySmallDataSources[3](true, false, true)	0.120s	passed
Standard error

20:45:07.488 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.492 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
20:45:07.492 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
20:45:07.492 INFO  FuncotatorDataSourceDownloader - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:45:07.492 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:45:07.492 INFO  FuncotatorDataSourceDownloader - Start Date/Time: June 12, 2025 at 8:45:07 PM UTC
20:45:07.492 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.492 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.493 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:45:07.493 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:45:07.493 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:45:07.493 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:45:07.493 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
20:45:07.493 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
20:45:07.493 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
20:45:07.493 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
20:45:07.493 INFO  FuncotatorDataSourceDownloader - Initializing engine
20:45:07.493 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
20:45:07.493 INFO  FuncotatorDataSourceDownloader - Done initializing engine
20:45:07.494 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
20:45:07.495 INFO  FuncotatorDataSourceDownloader - Collecting expected checksum...
20:45:07.495 INFO  FuncotatorDataSourceDownloader - Collection complete!
20:45:07.496 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources8342156406045545217/dummyDataSources.tar.gz
20:45:07.497 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
20:45:07.497 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
20:45:07.516 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.002 (@60235.29 kbps)
20:45:07.516 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@51612.60 kbps)
20:45:07.521 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
20:45:07.521 INFO  FuncotatorDataSourceDownloader - Integrity check on downloaded data sources succeeded.
20:45:07.522 INFO  FuncotatorDataSourceDownloader - IMPORTANT: You must unzip the downloaded data sources prior to using them with Funcotator.
20:45:07.522 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[June 12, 2025 at 8:45:07 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1071644672
20:45:07.592 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.592 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
20:45:07.592 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
20:45:07.592 INFO  FuncotatorDataSourceDownloader - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:45:07.592 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:45:07.592 INFO  FuncotatorDataSourceDownloader - Start Date/Time: June 12, 2025 at 8:45:07 PM UTC
20:45:07.592 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.593 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.593 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:45:07.593 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:45:07.593 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:45:07.593 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:45:07.593 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
20:45:07.593 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
20:45:07.593 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
20:45:07.593 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
20:45:07.593 INFO  FuncotatorDataSourceDownloader - Initializing engine
20:45:07.593 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
20:45:07.593 INFO  FuncotatorDataSourceDownloader - Done initializing engine
20:45:07.594 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
20:45:07.594 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources11364626262126990577/dummyDataSources.tar.gz
20:45:07.594 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
20:45:07.594 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
20:45:07.595 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@1024000.00 kbps)
20:45:07.596 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
20:45:07.596 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
20:45:07.596 INFO  FuncotatorDataSourceDownloader - IMPORTANT: You must unzip the downloaded data sources prior to using them with Funcotator.
20:45:07.596 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[June 12, 2025 at 8:45:07 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1071644672
20:45:07.665 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.666 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
20:45:07.666 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
20:45:07.666 INFO  FuncotatorDataSourceDownloader - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:45:07.666 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:45:07.666 INFO  FuncotatorDataSourceDownloader - Start Date/Time: June 12, 2025 at 8:45:07 PM UTC
20:45:07.666 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.666 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.666 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:45:07.666 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:45:07.666 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:45:07.667 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:45:07.667 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
20:45:07.667 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
20:45:07.667 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
20:45:07.667 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
20:45:07.667 INFO  FuncotatorDataSourceDownloader - Initializing engine
20:45:07.667 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
20:45:07.667 INFO  FuncotatorDataSourceDownloader - Done initializing engine
20:45:07.667 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
20:45:07.667 INFO  FuncotatorDataSourceDownloader - Collecting expected checksum...
20:45:07.667 INFO  FuncotatorDataSourceDownloader - Collection complete!
20:45:07.668 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources10280077119666206720/dummyDataSources.tar.gz
20:45:07.668 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
20:45:07.668 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
20:45:07.670 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@512000.00 kbps)
20:45:07.670 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
20:45:07.671 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
20:45:07.671 INFO  FuncotatorDataSourceDownloader - Integrity check on downloaded data sources succeeded.
20:45:07.671 INFO  IOUtils - Extracting data from archive: file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources10280077119666206720/dummyDataSources.tar.gz
20:45:07.672 INFO  IOUtils - Extracting file: dummyDataSources/
20:45:07.672 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/
20:45:07.673 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/
20:45:07.673 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/
20:45:07.674 INFO  IOUtils - Extracting file: dummyDataSources/MANIFEST.txt
20:45:07.675 INFO  IOUtils - Extracting file: dummyDataSources/README.txt
20:45:07.675 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/
20:45:07.676 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg38
20:45:07.677 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/familial.config
20:45:07.677 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
20:45:07.678 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/
20:45:07.678 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/
20:45:07.679 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
20:45:07.679 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
20:45:07.692 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
20:45:07.693 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
20:45:07.701 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/
20:45:07.702 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/
20:45:07.703 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
20:45:07.703 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
20:45:07.704 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
20:45:07.705 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config
20:45:07.705 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[June 12, 2025 at 8:45:07 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1071644672
20:45:07.777 INFO  BlockManagerInfo - Removed broadcast_12_piece0 on localhost:44963 in memory (size: 2.4 KiB, free: 1920.0 MiB)
20:45:07.780 INFO  BlockManagerInfo - Removed broadcast_11_piece0 on localhost:44963 in memory (size: 2.4 KiB, free: 1920.0 MiB)
20:45:07.794 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.794 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
20:45:07.794 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
20:45:07.795 INFO  FuncotatorDataSourceDownloader - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:45:07.795 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:45:07.795 INFO  FuncotatorDataSourceDownloader - Start Date/Time: June 12, 2025 at 8:45:07 PM UTC
20:45:07.795 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.795 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
20:45:07.795 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:45:07.795 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:45:07.795 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:45:07.796 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:45:07.796 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
20:45:07.796 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
20:45:07.796 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
20:45:07.796 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
20:45:07.796 INFO  FuncotatorDataSourceDownloader - Initializing engine
20:45:07.796 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
20:45:07.796 INFO  FuncotatorDataSourceDownloader - Done initializing engine
20:45:07.796 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
20:45:07.799 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources6956742716084449625/dummyDataSources.tar.gz
20:45:07.799 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
20:45:07.800 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
20:45:07.801 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@1024000.00 kbps)
20:45:07.801 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
20:45:07.801 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
20:45:07.801 INFO  IOUtils - Extracting data from archive: file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources6956742716084449625/dummyDataSources.tar.gz
20:45:07.802 INFO  IOUtils - Extracting file: dummyDataSources/
20:45:07.802 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/
20:45:07.803 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/
20:45:07.803 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/
20:45:07.803 INFO  IOUtils - Extracting file: dummyDataSources/MANIFEST.txt
20:45:07.804 INFO  IOUtils - Extracting file: dummyDataSources/README.txt
20:45:07.804 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/
20:45:07.805 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg38
20:45:07.805 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/familial.config
20:45:07.806 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
20:45:07.806 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/
20:45:07.807 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/
20:45:07.807 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
20:45:07.808 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
20:45:07.821 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
20:45:07.822 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
20:45:07.831 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/
20:45:07.831 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/
20:45:07.831 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
20:45:07.832 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
20:45:07.833 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
20:45:07.833 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config
20:45:07.834 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[June 12, 2025 at 8:45:07 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1071644672