Class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark.pipelines > PrintReadsSparkIntegrationTest
65

tests
0

failures
1

ignored
20.020s

duration
100%

successful

Tests

Test Duration Result
testCoordinateSortedInRegion 2.413s passed
testFileToFile[0](print_reads.sam, .sam, null) 0.408s passed
testFileToFile[10](print_reads.sorted.sam, .bam, null) 0.237s passed
testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta) 0.244s passed
testFileToFile[12](print_reads.sorted.bam, .sam, null) 0.271s passed
testFileToFile[13](print_reads.sorted.bam, .bam, null) 0.338s passed
testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta) 0.287s passed
testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta) 0.237s passed
testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta) 0.268s passed
testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta) 0.253s passed
testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null) 0.194s passed
testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null) 0.216s passed
testFileToFile[1](print_reads.sam, .bam, null) 0.305s passed
testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) 0.213s passed
testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null) 0.375s passed
testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null) 0.413s passed
testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) 0.376s passed
testFileToFile[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) 0.329s passed
testFileToFile[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) 0.347s passed
testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) 0.301s passed
testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) 0.321s passed
testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) 0.310s passed
testFileToFile[2](print_reads.sam, .cram, print_reads.fasta) 0.371s passed
testFileToFile[3](print_reads.bam, .sam, null) 0.568s passed
testFileToFile[4](print_reads.bam, .bam, null) 0.445s passed
testFileToFile[5](print_reads.bam, .cram, print_reads.fasta) 0.436s passed
testFileToFile[6](print_reads.cram, .sam, print_reads.fasta) 0.382s passed
testFileToFile[7](print_reads.cram, .bam, print_reads.fasta) 0.367s passed
testFileToFile[8](print_reads.cram, .cram, print_reads.fasta) 0.391s passed
testFileToFile[9](print_reads.sorted.sam, .sam, null) 0.199s passed
testNonExistentReference 0.092s passed
testReadAndWriteCRAMAndReferenceOnHDFS - ignored
testReadFiltering 0.185s passed
testReadFiltering_asIntegrationTestSpec 0.194s passed
testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7) 0.175s passed
testReadFilters[10](print_reads.sorted.bam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 8) 0.253s passed
testReadFilters[11](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2) 0.267s passed
testReadFilters[12](print_reads.sorted.cram, print_reads.fasta, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2) 0.223s passed
testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8) 0.179s passed
testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8) 0.168s passed
testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8) 0.168s passed
testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) 0.165s passed
testReadFilters[5](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 200], 8) 0.178s passed
testReadFilters[6](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 1, --max-read-length, 10], 0) 0.172s passed
testReadFilters[7](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2) 0.171s passed
testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8) 0.262s passed
testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) 0.257s passed
testReadThatConsumesNoReferenceBases 0.258s passed
testSBIIndexGranularityArgument[0](1) 0.354s passed
testSBIIndexGranularityArgument[1](100) 0.339s passed
testSequenceDictionaryValidation 0.116s passed
testUnSorted 0.255s passed
testUnSortedRoundTrip 0.179s passed
testUnmappedReadInclusion[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [unmapped], [u1, u2, u3, u4, u5]) 0.264s passed
testUnmappedReadInclusion[10](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i]) 0.428s passed
testUnmappedReadInclusion[11](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000013, unmapped], [a, b, c, d, e, f, f, g, h, h, i, i]) 0.422s passed
testUnmappedReadInclusion[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped.intervals], [u1, u2, u3, u4, u5]) 0.265s passed
testUnmappedReadInclusion[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [1:200-300, unmapped], [a, b, c, u1, u2, u3, u4, u5]) 0.262s passed
testUnmappedReadInclusion[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [1:200-300, 4:700-701, unmapped], [a, b, c, k, u1, u2, u3, u4, u5]) 0.260s passed
testUnmappedReadInclusion[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped2.intervals], [a, b, c, k, u1, u2, u3, u4, u5]) 0.270s passed
testUnmappedReadInclusion[5](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [unmapped], [g, h, h, i, i]) 0.269s passed
testUnmappedReadInclusion[6](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000011], [a, b, c, d, e]) 0.268s passed
testUnmappedReadInclusion[7](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i]) 0.267s passed
testUnmappedReadInclusion[8](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000013, unmapped], [a, b, c, d, e, f, f, g, h, h, i, i]) 0.257s passed
testUnmappedReadInclusion[9](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [unmapped], [g, h, h, i, i]) 0.362s passed

Standard output

--------------------------------------------------------------------------------
[19:12:50] Executing test PrintReadsSparkIntegrationTest:testReadFiltering_asIntegrationTestSpec

Standard error

[May 19, 2025 at 7:12:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 7:12:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 7:12:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 7:12:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 7:12:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:46 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:46 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:46 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:49 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:49 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:49 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:57 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 7:12:57 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=933232640
[May 19, 2025 at 7:12:58 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=933232640
[May 19, 2025 at 7:12:58 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=933232640
[May 19, 2025 at 7:12:58 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=933232640