Class org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testCoordinateSortedInRegion | 0.145s | passed |
| testFileToFileUsingReferenceBundle[0](print_reads.sam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[10](print_reads.sorted.sam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.104s | passed |
| testFileToFileUsingReferenceBundle[12](print_reads.sorted.bam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[13](print_reads.sorted.bam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.110s | passed |
| testFileToFileUsingReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.115s | passed |
| testFileToFileUsingReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.101s | passed |
| testFileToFileUsingReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.105s | passed |
| testFileToFileUsingReferenceBundle[18](print_reads.sorted.queryname.sam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[19](print_reads.sorted.queryname.sam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[1](print_reads.sam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.106s | passed |
| testFileToFileUsingReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.102s | passed |
| testFileToFileUsingReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.152s | passed |
| testFileToFileUsingReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.146s | passed |
| testFileToFileUsingReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.105s | passed |
| testFileToFileUsingReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.108s | passed |
| testFileToFileUsingReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.152s | passed |
| testFileToFileUsingReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta) | 0.104s | passed |
| testFileToFileUsingReferenceBundle[3](print_reads.bam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[4](print_reads.bam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta) | 0.106s | passed |
| testFileToFileUsingReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta) | 0.159s | passed |
| testFileToFileUsingReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta) | 0.150s | passed |
| testFileToFileUsingReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta) | 0.103s | passed |
| testFileToFileUsingReferenceBundle[9](print_reads.sorted.sam, .sam, null) | 0s | passed |
| testFileToFileWithMD5[0](print_reads.sam, .sam, null) | 0.147s | passed |
| testFileToFileWithMD5[10](print_reads.sorted.sam, .bam, null) | 0.092s | passed |
| testFileToFileWithMD5[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.100s | passed |
| testFileToFileWithMD5[12](print_reads.sorted.bam, .sam, null) | 0.146s | passed |
| testFileToFileWithMD5[13](print_reads.sorted.bam, .bam, null) | 0.095s | passed |
| testFileToFileWithMD5[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.101s | passed |
| testFileToFileWithMD5[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.154s | passed |
| testFileToFileWithMD5[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.102s | passed |
| testFileToFileWithMD5[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.103s | passed |
| testFileToFileWithMD5[18](print_reads.sorted.queryname.sam, .sam, null) | 0.148s | passed |
| testFileToFileWithMD5[19](print_reads.sorted.queryname.sam, .bam, null) | 0.143s | passed |
| testFileToFileWithMD5[1](print_reads.sam, .bam, null) | 0.148s | passed |
| testFileToFileWithMD5[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.098s | passed |
| testFileToFileWithMD5[21](print_reads.sorted.queryname.bam, .sam, null) | 0.146s | passed |
| testFileToFileWithMD5[22](print_reads.sorted.queryname.bam, .bam, null) | 0.143s | passed |
| testFileToFileWithMD5[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.107s | passed |
| testFileToFileWithMD5[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.150s | passed |
| testFileToFileWithMD5[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.146s | passed |
| testFileToFileWithMD5[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.100s | passed |
| testFileToFileWithMD5[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.102s | passed |
| testFileToFileWithMD5[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.152s | passed |
| testFileToFileWithMD5[2](print_reads.sam, .cram, print_reads.fasta) | 0.102s | passed |
| testFileToFileWithMD5[3](print_reads.bam, .sam, null) | 0.148s | passed |
| testFileToFileWithMD5[4](print_reads.bam, .bam, null) | 0.152s | passed |
| testFileToFileWithMD5[5](print_reads.bam, .cram, print_reads.fasta) | 0.100s | passed |
| testFileToFileWithMD5[6](print_reads.cram, .sam, print_reads.fasta) | 0.151s | passed |
| testFileToFileWithMD5[7](print_reads.cram, .bam, print_reads.fasta) | 0.151s | passed |
| testFileToFileWithMD5[8](print_reads.cram, .cram, print_reads.fasta) | 0.102s | passed |
| testFileToFileWithMD5[9](print_reads.sorted.sam, .sam, null) | 0.145s | passed |
| testFileToFileWithReferenceBundle[0](print_reads.sam, .sam, null) | 0.149s | passed |
| testFileToFileWithReferenceBundle[10](print_reads.sorted.sam, .bam, null) | 0.096s | passed |
| testFileToFileWithReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.108s | passed |
| testFileToFileWithReferenceBundle[12](print_reads.sorted.bam, .sam, null) | 0.145s | passed |
| testFileToFileWithReferenceBundle[13](print_reads.sorted.bam, .bam, null) | 0.098s | passed |
| testFileToFileWithReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.103s | passed |
| testFileToFileWithReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.151s | passed |
| testFileToFileWithReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.104s | passed |
| testFileToFileWithReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.110s | passed |
| testFileToFileWithReferenceBundle[18](print_reads.sorted.queryname.sam, .sam, null) | 0.145s | passed |
| testFileToFileWithReferenceBundle[19](print_reads.sorted.queryname.sam, .bam, null) | 0.144s | passed |
| testFileToFileWithReferenceBundle[1](print_reads.sam, .bam, null) | 0.148s | passed |
| testFileToFileWithReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.103s | passed |
| testFileToFileWithReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null) | 0.150s | passed |
| testFileToFileWithReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null) | 0.143s | passed |
| testFileToFileWithReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.101s | passed |
| testFileToFileWithReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.149s | passed |
| testFileToFileWithReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.149s | passed |
| testFileToFileWithReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.104s | passed |
| testFileToFileWithReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.104s | passed |
| testFileToFileWithReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.152s | passed |
| testFileToFileWithReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta) | 0.103s | passed |
| testFileToFileWithReferenceBundle[3](print_reads.bam, .sam, null) | 0.149s | passed |
| testFileToFileWithReferenceBundle[4](print_reads.bam, .bam, null) | 0.148s | passed |
| testFileToFileWithReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta) | 0.101s | passed |
| testFileToFileWithReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta) | 0.147s | passed |
| testFileToFileWithReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta) | 0.148s | passed |
| testFileToFileWithReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta) | 0.104s | passed |
| testFileToFileWithReferenceBundle[9](print_reads.sorted.sam, .sam, null) | 0.147s | passed |
| testFileToFile[0](print_reads.sam, .sam, null) | 0.154s | passed |
| testFileToFile[10](print_reads.sorted.sam, .bam, null) | 0.096s | passed |
| testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.116s | passed |
| testFileToFile[12](print_reads.sorted.bam, .sam, null) | 0.100s | passed |
| testFileToFile[13](print_reads.sorted.bam, .bam, null) | 0.104s | passed |
| testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.106s | passed |
| testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.157s | passed |
| testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.100s | passed |
| testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.105s | passed |
| testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null) | 0.151s | passed |
| testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null) | 0.150s | passed |
| testFileToFile[1](print_reads.sam, .bam, null) | 0.150s | passed |
| testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.106s | passed |
| testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null) | 0.145s | passed |
| testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null) | 0.148s | passed |
| testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.102s | passed |
| testFileToFile[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.156s | passed |
| testFileToFile[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.150s | passed |
| testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.106s | passed |
| testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.112s | passed |
| testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.103s | passed |
| testFileToFile[2](print_reads.sam, .cram, print_reads.fasta) | 0.123s | passed |
| testFileToFile[3](print_reads.bam, .sam, null) | 0.153s | passed |
| testFileToFile[4](print_reads.bam, .bam, null) | 0.166s | passed |
| testFileToFile[5](print_reads.bam, .cram, print_reads.fasta) | 0.111s | passed |
| testFileToFile[6](print_reads.cram, .sam, print_reads.fasta) | 0.158s | passed |
| testFileToFile[7](print_reads.cram, .bam, print_reads.fasta) | 0.154s | passed |
| testFileToFile[8](print_reads.cram, .cram, print_reads.fasta) | 0.111s | passed |
| testFileToFile[9](print_reads.sorted.sam, .sam, null) | 0.101s | passed |
| testNoConflictPG | 0.146s | passed |
| testNonExistentReference | 0.094s | passed |
| testReadFiltering | 0.096s | passed |
| testReadFiltering_asIntegrationTestSpec | 0.096s | passed |
| testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7) | 0.145s | passed |
| testReadFilters[10](print_reads.sorted.bam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 8) | 0.143s | 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) | 0.146s | 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) | 0.143s | passed |
| testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.144s | passed |
| testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8) | 0.141s | passed |
| testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.144s | passed |
| testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.143s | passed |
| testReadFilters[5](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 200], 8) | 0.141s | passed |
| testReadFilters[6](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 1, --max-read-length, 10], 0) | 0.143s | 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) | 0.150s | passed |
| testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.147s | passed |
| testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.142s | passed |
| testReadThatConsumesNoReferenceBases | 0.147s | passed |
| testSequenceDictionaryValidation | 0.097s | passed |
| testUnSorted | 0.145s | 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]) | 0.143s | 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]) | 0.209s | 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]) | 0.210s | 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]) | 0.146s | 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]) | 0.146s | 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]) | 0.092s | 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]) | 0.094s | 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]) | 0.142s | 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]) | 0.154s | 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]) | 0.146s | 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]) | 0.144s | 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]) | 0.207s | passed |
Standard output
-------------------------------------------------------------------------------- [13:51:31] Executing test PrintReadsIntegrationTest:testReadFiltering_asIntegrationTestSpec
Standard error
[May 27, 2025 at 1:51:22 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:22 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:22 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:22 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:22 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:23 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:23 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:23 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:23 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:23 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:23 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:23 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:23 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:24 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:24 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:24 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:24 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:24 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:24 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:24 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:24 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:25 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:25 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:25 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:25 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:25 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:25 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:25 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:25 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:26 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:26 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:26 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:26 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:26 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:26 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:26 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:26 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:27 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:28 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:28 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:28 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:28 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:28 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:28 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:28 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:29 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:30 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:30 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:30 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:30 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:30 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:30 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:30 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:32 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:32 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:32 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:32 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:32 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:32 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:32 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:33 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:33 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:33 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:33 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:33 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:33 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:33 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:34 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:34 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:34 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:34 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:34 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:34 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:34 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:34 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:35 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:35 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:35 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:35 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:35 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:35 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:36 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:36 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:36 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:36 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:36 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:36 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:36 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:37 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:37 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:37 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:37 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:37 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:37 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:37 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:37 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:38 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:38 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:38 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:38 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:38 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:38 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:38 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:38 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:39 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:39 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:39 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:39 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:39 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:39 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:39 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:51:40 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000