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

all > org.broadinstitute.hellbender.tools.funcotator > FuncotatorDataSourceDownloaderIntegrationTest
tests
failures
ignored
0.408s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testDownloadDummySmallDataSources[0](true, true, false)	0.096s	passed
testDownloadDummySmallDataSources[1](true, false, false)	0.077s	passed
testDownloadDummySmallDataSources[2](true, true, true)	0.128s	passed
testDownloadDummySmallDataSources[3](true, false, true)	0.107s	passed
Standard error

22:38:02.304 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.308 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
22:38:02.308 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
22:38:02.308 INFO  FuncotatorDataSourceDownloader - Executing as runner@fv-az2219-44 on Linux v6.8.0-1021-azure amd64
22:38:02.308 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:38:02.308 INFO  FuncotatorDataSourceDownloader - Start Date/Time: March 28, 2025 at 10:38:02 PM UTC
22:38:02.308 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.308 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.309 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:38:02.309 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:38:02.309 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:38:02.309 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:38:02.309 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
22:38:02.309 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
22:38:02.309 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
22:38:02.309 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
22:38:02.309 INFO  FuncotatorDataSourceDownloader - Initializing engine
22:38:02.309 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
22:38:02.310 INFO  FuncotatorDataSourceDownloader - Done initializing engine
22:38:02.310 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
22:38:02.311 INFO  FuncotatorDataSourceDownloader - Collecting expected checksum...
22:38:02.311 INFO  FuncotatorDataSourceDownloader - Collection complete!
22:38:02.312 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources13603528813821645221/dummyDataSources.tar.gz
22:38:02.313 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
22:38:02.313 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
22:38:02.319 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@256000.00 kbps)
22:38:02.320 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@149494.95 kbps)
22:38:02.325 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
22:38:02.325 INFO  FuncotatorDataSourceDownloader - Integrity check on downloaded data sources succeeded.
22:38:02.325 INFO  FuncotatorDataSourceDownloader - IMPORTANT: You must unzip the downloaded data sources prior to using them with Funcotator.
22:38:02.325 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[March 28, 2025 at 10:38:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
22:38:02.398 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.398 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
22:38:02.398 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
22:38:02.398 INFO  FuncotatorDataSourceDownloader - Executing as runner@fv-az2219-44 on Linux v6.8.0-1021-azure amd64
22:38:02.398 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:38:02.398 INFO  FuncotatorDataSourceDownloader - Start Date/Time: March 28, 2025 at 10:38:02 PM UTC
22:38:02.398 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.399 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.399 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:38:02.399 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:38:02.399 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:38:02.399 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:38:02.399 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
22:38:02.399 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
22:38:02.399 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
22:38:02.399 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
22:38:02.399 INFO  FuncotatorDataSourceDownloader - Initializing engine
22:38:02.399 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
22:38:02.399 INFO  FuncotatorDataSourceDownloader - Done initializing engine
22:38:02.399 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
22:38:02.400 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources7935660069022020522/dummyDataSources.tar.gz
22:38:02.400 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
22:38:02.400 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
22:38:02.401 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@1024000.00 kbps)
22:38:02.402 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
22:38:02.402 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
22:38:02.402 INFO  FuncotatorDataSourceDownloader - IMPORTANT: You must unzip the downloaded data sources prior to using them with Funcotator.
22:38:02.402 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[March 28, 2025 at 10:38:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
22:38:02.476 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.476 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
22:38:02.476 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
22:38:02.477 INFO  FuncotatorDataSourceDownloader - Executing as runner@fv-az2219-44 on Linux v6.8.0-1021-azure amd64
22:38:02.477 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:38:02.477 INFO  FuncotatorDataSourceDownloader - Start Date/Time: March 28, 2025 at 10:38:02 PM UTC
22:38:02.477 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.477 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.477 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:38:02.477 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:38:02.477 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:38:02.477 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:38:02.477 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
22:38:02.478 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
22:38:02.478 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
22:38:02.478 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
22:38:02.478 INFO  FuncotatorDataSourceDownloader - Initializing engine
22:38:02.478 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
22:38:02.478 INFO  FuncotatorDataSourceDownloader - Done initializing engine
22:38:02.478 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
22:38:02.478 INFO  FuncotatorDataSourceDownloader - Collecting expected checksum...
22:38:02.478 INFO  FuncotatorDataSourceDownloader - Collection complete!
22:38:02.479 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources10432301022658151042/dummyDataSources.tar.gz
22:38:02.479 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
22:38:02.479 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
22:38:02.481 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@512000.00 kbps)
22:38:02.481 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
22:38:02.482 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
22:38:02.482 INFO  FuncotatorDataSourceDownloader - Integrity check on downloaded data sources succeeded.
22:38:02.482 INFO  IOUtils - Extracting data from archive: file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources10432301022658151042/dummyDataSources.tar.gz
22:38:02.483 INFO  IOUtils - Extracting file: dummyDataSources/
22:38:02.483 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/
22:38:02.484 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/
22:38:02.485 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/
22:38:02.485 INFO  IOUtils - Extracting file: dummyDataSources/MANIFEST.txt
22:38:02.486 INFO  IOUtils - Extracting file: dummyDataSources/README.txt
22:38:02.487 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/
22:38:02.487 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg38
22:38:02.488 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/familial.config
22:38:02.488 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
22:38:02.489 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/
22:38:02.490 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/
22:38:02.490 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
22:38:02.491 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
22:38:02.506 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
22:38:02.506 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
22:38:02.515 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/
22:38:02.516 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/
22:38:02.516 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
22:38:02.517 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
22:38:02.518 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
22:38:02.518 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config
22:38:02.519 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[March 28, 2025 at 10:38:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
22:38:02.599 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.599 INFO  FuncotatorDataSourceDownloader - org.broadinstitute.hellbender.tools.funcotator vUnavailable
22:38:02.599 INFO  FuncotatorDataSourceDownloader - For support and documentation go to https://software.broadinstitute.org/gatk/
22:38:02.599 INFO  FuncotatorDataSourceDownloader - Executing as runner@fv-az2219-44 on Linux v6.8.0-1021-azure amd64
22:38:02.599 INFO  FuncotatorDataSourceDownloader - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:38:02.599 INFO  FuncotatorDataSourceDownloader - Start Date/Time: March 28, 2025 at 10:38:02 PM UTC
22:38:02.599 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.599 INFO  FuncotatorDataSourceDownloader - ------------------------------------------------------------
22:38:02.599 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:38:02.599 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:38:02.600 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:38:02.600 INFO  FuncotatorDataSourceDownloader - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:38:02.600 INFO  FuncotatorDataSourceDownloader - Deflater: IntelDeflater
22:38:02.600 INFO  FuncotatorDataSourceDownloader - Inflater: IntelInflater
22:38:02.600 INFO  FuncotatorDataSourceDownloader - GCS max retries/reopens: 20
22:38:02.600 INFO  FuncotatorDataSourceDownloader - Requester pays: disabled
22:38:02.600 INFO  FuncotatorDataSourceDownloader - Initializing engine
22:38:02.600 INFO  FuncotatorDataSourceDownloader - Overwrite ENABLED.  Will overwrite existing data sources download.
22:38:02.600 INFO  FuncotatorDataSourceDownloader - Done initializing engine
22:38:02.600 INFO  FuncotatorDataSourceDownloader - TESTING data sources selected.
22:38:02.601 INFO  NioFileCopierWithProgressMeter - Initiating copy from file:///home/runner/work/gatk/gatk/src/test/resources/large/funcotator/dummyDataSources.tar.gz to file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources1697165743279551318/dummyDataSources.tar.gz
22:38:02.601 INFO  NioFileCopierWithProgressMeter - File size: 1180641 bytes (1 MB).
22:38:02.601 INFO  NioFileCopierWithProgressMeter - Please wait.  This could take a while...
22:38:02.602 INFO  NioFileCopierWithProgressMeter -     Transfer:  80.00% complete.  Est. time remaining: 00.000 (@1024000.00 kbps)
22:38:02.602 INFO  NioFileCopierWithProgressMeter -     Transfer:  100.00% complete.  Est. time remaining: 00.000 (@Infinity kbps)
22:38:02.602 INFO  NioFileCopierWithProgressMeter - Download Complete! - Total elapsed time: 0s
22:38:02.603 INFO  IOUtils - Extracting data from archive: file:///tmp/FuncotatorDataSourceDownloaderIntegrationTest_testDownloadDummySmallDataSources1697165743279551318/dummyDataSources.tar.gz
22:38:02.603 INFO  IOUtils - Extracting file: dummyDataSources/
22:38:02.604 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/
22:38:02.604 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/
22:38:02.604 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/
22:38:02.605 INFO  IOUtils - Extracting file: dummyDataSources/MANIFEST.txt
22:38:02.605 INFO  IOUtils - Extracting file: dummyDataSources/README.txt
22:38:02.606 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/
22:38:02.606 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg38
22:38:02.607 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/familial.config
22:38:02.607 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
22:38:02.608 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/
22:38:02.608 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/
22:38:02.609 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
22:38:02.609 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
22:38:02.622 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
22:38:02.622 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
22:38:02.631 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/
22:38:02.631 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/
22:38:02.632 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
22:38:02.632 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
22:38:02.633 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
22:38:02.633 INFO  IOUtils - Extracting file: dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config
22:38:02.634 INFO  FuncotatorDataSourceDownloader - Shutting down engine
[March 28, 2025 at 10:38:02 PM UTC] org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560