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

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

tests
0

failures
1

ignored
20.514s

duration
100%

successful

Tests

Test Duration Result
testCoordinateSortedInRegion 2.424s passed
testFileToFile[0](print_reads.sam, .sam, null) 0.405s passed
testFileToFile[10](print_reads.sorted.sam, .bam, null) 0.246s passed
testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta) 0.250s passed
testFileToFile[12](print_reads.sorted.bam, .sam, null) 0.291s passed
testFileToFile[13](print_reads.sorted.bam, .bam, null) 0.318s passed
testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta) 0.299s passed
testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta) 0.256s passed
testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta) 0.276s passed
testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta) 0.260s passed
testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null) 0.203s passed
testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null) 0.204s passed
testFileToFile[1](print_reads.sam, .bam, null) 0.340s passed
testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) 0.213s passed
testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null) 0.372s passed
testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null) 0.371s passed
testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) 0.378s passed
testFileToFile[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) 0.342s passed
testFileToFile[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) 0.318s passed
testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) 0.323s passed
testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) 0.320s passed
testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) 0.312s passed
testFileToFile[2](print_reads.sam, .cram, print_reads.fasta) 0.357s passed
testFileToFile[3](print_reads.bam, .sam, null) 0.563s passed
testFileToFile[4](print_reads.bam, .bam, null) 0.455s passed
testFileToFile[5](print_reads.bam, .cram, print_reads.fasta) 0.497s passed
testFileToFile[6](print_reads.cram, .sam, print_reads.fasta) 0.453s passed
testFileToFile[7](print_reads.cram, .bam, print_reads.fasta) 0.397s passed
testFileToFile[8](print_reads.cram, .cram, print_reads.fasta) 0.385s passed
testFileToFile[9](print_reads.sorted.sam, .sam, null) 0.210s passed
testNonExistentReference 0.092s passed
testReadAndWriteCRAMAndReferenceOnHDFS - ignored
testReadFiltering 0.193s passed
testReadFiltering_asIntegrationTestSpec 0.204s passed
testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7) 0.173s passed
testReadFilters[10](print_reads.sorted.bam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 8) 0.266s 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) 0.228s passed
testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8) 0.177s passed
testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8) 0.190s passed
testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8) 0.170s passed
testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) 0.173s passed
testReadFilters[5](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 200], 8) 0.185s passed
testReadFilters[6](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 1, --max-read-length, 10], 0) 0.177s 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) 0.191s passed
testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8) 0.257s passed
testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) 0.257s passed
testReadThatConsumesNoReferenceBases 0.268s passed
testSBIIndexGranularityArgument[0](1) 0.375s passed
testSBIIndexGranularityArgument[1](100) 0.355s passed
testSequenceDictionaryValidation 0.127s passed
testUnSorted 0.259s passed
testUnSortedRoundTrip 0.194s 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]) 0.270s 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]) 0.452s 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]) 0.440s 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]) 0.269s 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]) 0.275s 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]) 0.268s 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]) 0.271s 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]) 0.278s 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]) 0.269s 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]) 0.271s 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]) 0.266s 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]) 0.369s passed

Standard output

--------------------------------------------------------------------------------
[20:58:54] Executing test PrintReadsSparkIntegrationTest:testReadFiltering_asIntegrationTestSpec

Standard error

[June 12, 2025 at 8:58:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:46 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:46 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:49 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:49 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:49 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:50 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:55 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:56 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:57 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:57 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:57 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:58 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:58 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:58 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:58 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:58 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:59 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:59 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:58:59 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:59:00 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:59:00 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:59:00 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:59:00 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:59:01 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:59:01 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=750780416
[June 12, 2025 at 8:59:02 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=750780416
[June 12, 2025 at 8:59:02 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
[June 12, 2025 at 8:59:02 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
[June 12, 2025 at 8:59:03 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416