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

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorDataSourceDownloaderIntegrationTest
tests
failures
ignored
0.508s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testDownloadDummySmallDataSources[0](true, true, false)	0.111s	passed
testDownloadDummySmallDataSources[1](true, false, false)	0.087s	passed
testDownloadDummySmallDataSources[2](true, true, true)	0.198s	passed
testDownloadDummySmallDataSources[3](true, false, true)	0.112s	passed
Standard error

15:36:42.337 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.341 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:36:42.341 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
15:36:42.341 INFO  FuncotatorDataSourceDownloader - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:36:42.342 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:36:42.342 INFO  FuncotatorDataSourceDownloader - Start Date/Time: May 19, 2025 at 3:36:42 PM UTC
15:36:42.342 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.342 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.342 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:36:42.342 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:36:42.342 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:36:42.342 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:36:42.342 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
15:36:42.343 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
15:36:42.343 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
15:36:42.343 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
15:36:42.343 INFO  FuncotatorDataSourceDownloader - Initializing engine
15:36:42.343 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
15:36:42.343 INFO  FuncotatorDataSourceDownloader - Done initializing engine
15:36:42.343 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
15:36:42.345 INFO  FuncotatorDataSourceDownloader - Collecting expected checksum...
15:36:42.345 INFO  FuncotatorDataSourceDownloader - Collection complete!
15:36:42.346 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources13221880595658568146/dummyDataSources.tar.gz
15:36:42.347 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
15:36:42.347 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
15:36:42.353 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@256000.00 kbps)
15:36:42.354 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@149494.95 kbps)
15:36:42.366 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
15:36:42.367 INFO  FuncotatorDataSourceDownloader - Integrity check on downloaded data sources succeeded.
15:36:42.367 INFO  FuncotatorDataSourceDownloader - IMPORTANT: You must unzip the downloaded data sources prior to using them with Funcotator.
15:36:42.367 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[May 19, 2025 at 3:36:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=996147200
15:36:42.388 INFO  BlockManagerInfo - Removed broadcast_11_piece0 on localhost:37979 in memory (size: 2.4 KiB, free: 1920.0 MiB)
15:36:42.391 INFO  BlockManagerInfo - Removed broadcast_12_piece0 on localhost:37979 in memory (size: 2.4 KiB, free: 1920.0 MiB)
15:36:42.446 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.447 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:36:42.447 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
15:36:42.447 INFO  FuncotatorDataSourceDownloader - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:36:42.447 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:36:42.447 INFO  FuncotatorDataSourceDownloader - Start Date/Time: May 19, 2025 at 3:36:42 PM UTC
15:36:42.447 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.447 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.447 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:36:42.447 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:36:42.447 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:36:42.447 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:36:42.447 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
15:36:42.448 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
15:36:42.448 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
15:36:42.448 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
15:36:42.448 INFO  FuncotatorDataSourceDownloader - Initializing engine
15:36:42.448 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
15:36:42.448 INFO  FuncotatorDataSourceDownloader - Done initializing engine
15:36:42.448 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
15:36:42.452 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources7609829137938531385/dummyDataSources.tar.gz
15:36:42.452 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
15:36:42.452 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
15:36:42.454 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@1024000.00 kbps)
15:36:42.454 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
15:36:42.454 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
15:36:42.454 INFO  FuncotatorDataSourceDownloader - IMPORTANT: You must unzip the downloaded data sources prior to using them with Funcotator.
15:36:42.454 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[May 19, 2025 at 3:36:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=996147200
15:36:42.530 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.530 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:36:42.530 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
15:36:42.530 INFO  FuncotatorDataSourceDownloader - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:36:42.530 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:36:42.530 INFO  FuncotatorDataSourceDownloader - Start Date/Time: May 19, 2025 at 3:36:42 PM UTC
15:36:42.531 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.531 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.531 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:36:42.531 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:36:42.531 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:36:42.531 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:36:42.531 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
15:36:42.531 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
15:36:42.532 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
15:36:42.532 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
15:36:42.532 INFO  FuncotatorDataSourceDownloader - Initializing engine
15:36:42.532 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
15:36:42.532 INFO  FuncotatorDataSourceDownloader - Done initializing engine
15:36:42.532 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
15:36:42.532 INFO  FuncotatorDataSourceDownloader - Collecting expected checksum...
15:36:42.532 INFO  FuncotatorDataSourceDownloader - Collection complete!
15:36:42.533 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources2977041776866910940/dummyDataSources.tar.gz
15:36:42.533 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
15:36:42.533 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
15:36:42.535 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@512000.00 kbps)
15:36:42.535 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
15:36:42.535 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
15:36:42.535 INFO  FuncotatorDataSourceDownloader - Integrity check on downloaded data sources succeeded.
15:36:42.536 INFO  IOUtils - Extracting data from archive: file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources2977041776866910940/dummyDataSources.tar.gz
15:36:42.536 INFO  IOUtils - Extracting file: dummyDataSources/
15:36:42.537 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/
15:36:42.537 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/
15:36:42.538 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/
15:36:42.538 INFO  IOUtils - Extracting file: dummyDataSources/MANIFEST.txt
15:36:42.539 INFO  IOUtils - Extracting file: dummyDataSources/README.txt
15:36:42.540 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/
15:36:42.540 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg38
15:36:42.541 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/familial.config
15:36:42.541 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:36:42.542 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/
15:36:42.542 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/
15:36:42.543 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
15:36:42.543 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
15:36:42.560 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
15:36:42.561 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
15:36:42.572 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/
15:36:42.572 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/
15:36:42.573 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
15:36:42.573 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:36:42.574 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
15:36:42.575 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config
15:36:42.575 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[May 19, 2025 at 3:36:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=996147200
15:36:42.726 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.726 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
15:36:42.726 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
15:36:42.727 INFO  FuncotatorDataSourceDownloader - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:36:42.727 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:36:42.727 INFO  FuncotatorDataSourceDownloader - Start Date/Time: May 19, 2025 at 3:36:42 PM UTC
15:36:42.727 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.727 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
15:36:42.728 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:36:42.728 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:36:42.728 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:36:42.728 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:36:42.728 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
15:36:42.728 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
15:36:42.728 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
15:36:42.728 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
15:36:42.728 INFO  FuncotatorDataSourceDownloader - Initializing engine
15:36:42.728 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
15:36:42.728 INFO  FuncotatorDataSourceDownloader - Done initializing engine
15:36:42.729 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
15:36:42.729 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources10672993965795105339/dummyDataSources.tar.gz
15:36:42.729 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
15:36:42.729 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
15:36:42.730 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@1024000.00 kbps)
15:36:42.730 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
15:36:42.730 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
15:36:42.730 INFO  IOUtils - Extracting data from archive: file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources10672993965795105339/dummyDataSources.tar.gz
15:36:42.731 INFO  IOUtils - Extracting file: dummyDataSources/
15:36:42.731 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/
15:36:42.732 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/
15:36:42.732 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/
15:36:42.733 INFO  IOUtils - Extracting file: dummyDataSources/MANIFEST.txt
15:36:42.733 INFO  IOUtils - Extracting file: dummyDataSources/README.txt
15:36:42.734 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/
15:36:42.734 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg38
15:36:42.735 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/familial.config
15:36:42.735 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:36:42.736 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/
15:36:42.736 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/
15:36:42.737 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
15:36:42.737 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
15:36:42.750 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
15:36:42.751 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
15:36:42.760 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/
15:36:42.760 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/
15:36:42.760 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
15:36:42.761 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:36:42.761 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
15:36:42.762 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config
15:36:42.762 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[May 19, 2025 at 3:36:42 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=880803840