Class org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest

all > org.broadinstitute.hellbender.tools > PrintReadsIntegrationTest
91

tests
0

failures
0

ignored
11.856s

duration
100%

successful

Tests

Test Duration Result
testCoordinateSortedInRegion 0.098s passed
testFileToFileWithMD5[0](print_reads.sam, .sam, null) 0.140s passed
testFileToFileWithMD5[10](print_reads.sorted.sam, .bam, null) 0.099s passed
testFileToFileWithMD5[11](print_reads.sorted.sam, .cram, print_reads.fasta) 0.103s passed
testFileToFileWithMD5[12](print_reads.sorted.bam, .sam, null) 0.146s passed
testFileToFileWithMD5[13](print_reads.sorted.bam, .bam, null) 0.100s passed
testFileToFileWithMD5[14](print_reads.sorted.bam, .cram, print_reads.fasta) 0.100s passed
testFileToFileWithMD5[15](print_reads.sorted.cram, .sam, print_reads.fasta) 0.147s passed
testFileToFileWithMD5[16](print_reads.sorted.cram, .bam, print_reads.fasta) 0.101s passed
testFileToFileWithMD5[17](print_reads.sorted.cram, .cram, print_reads.fasta) 0.104s passed
testFileToFileWithMD5[18](print_reads.sorted.queryname.sam, .sam, null) 0.151s passed
testFileToFileWithMD5[19](print_reads.sorted.queryname.sam, .bam, null) 0.151s passed
testFileToFileWithMD5[1](print_reads.sam, .bam, null) 0.142s passed
testFileToFileWithMD5[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) 0.095s passed
testFileToFileWithMD5[21](print_reads.sorted.queryname.bam, .sam, null) 0.154s passed
testFileToFileWithMD5[22](print_reads.sorted.queryname.bam, .bam, null) 0.141s passed
testFileToFileWithMD5[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) 0.099s passed
testFileToFileWithMD5[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) 0.147s passed
testFileToFileWithMD5[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) 0.142s passed
testFileToFileWithMD5[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) 0.105s passed
testFileToFileWithMD5[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) 0.113s passed
testFileToFileWithMD5[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) 0.146s passed
testFileToFileWithMD5[2](print_reads.sam, .cram, print_reads.fasta) 0.098s passed
testFileToFileWithMD5[3](print_reads.bam, .sam, null) 0.147s passed
testFileToFileWithMD5[4](print_reads.bam, .bam, null) 0.141s passed
testFileToFileWithMD5[5](print_reads.bam, .cram, print_reads.fasta) 0.103s passed
testFileToFileWithMD5[6](print_reads.cram, .sam, print_reads.fasta) 0.145s passed
testFileToFileWithMD5[7](print_reads.cram, .bam, print_reads.fasta) 0.144s passed
testFileToFileWithMD5[8](print_reads.cram, .cram, print_reads.fasta) 0.102s passed
testFileToFileWithMD5[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) 0.102s passed
testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta) 0.104s passed
testFileToFile[12](print_reads.sorted.bam, .sam, null) 0.159s passed
testFileToFile[13](print_reads.sorted.bam, .bam, null) 0.098s passed
testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta) 0.104s passed
testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta) 0.149s passed
testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta) 0.094s passed
testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta) 0.105s passed
testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null) 0.150s passed
testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null) 0.095s passed
testFileToFile[1](print_reads.sam, .bam, null) 0.153s passed
testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) 0.104s passed
testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null) 0.147s passed
testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null) 0.146s passed
testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) 0.101s passed
testFileToFile[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) 0.145s passed
testFileToFile[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) 0.146s passed
testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) 0.100s passed
testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) 0.106s passed
testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) 0.156s passed
testFileToFile[2](print_reads.sam, .cram, print_reads.fasta) 0.115s passed
testFileToFile[3](print_reads.bam, .sam, null) 0.172s passed
testFileToFile[4](print_reads.bam, .bam, null) 0.145s passed
testFileToFile[5](print_reads.bam, .cram, print_reads.fasta) 0.103s passed
testFileToFile[6](print_reads.cram, .sam, print_reads.fasta) 0.150s passed
testFileToFile[7](print_reads.cram, .bam, print_reads.fasta) 0.154s passed
testFileToFile[8](print_reads.cram, .cram, print_reads.fasta) 0.109s passed
testFileToFile[9](print_reads.sorted.sam, .sam, null) 0.156s passed
testNoConflictPG 0.145s passed
testNonExistentReference 0.091s passed
testReadFiltering 0.104s passed
testReadFiltering_asIntegrationTestSpec 0.091s passed
testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7) 0.146s passed
testReadFilters[10](print_reads.sorted.bam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 8) 0.142s 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) 0.144s 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) 0.150s passed
testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8) 0.140s passed
testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8) 0.139s passed
testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8) 0.145s passed
testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) 0.142s 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) 0.139s 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) 0.139s passed
testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8) 0.141s passed
testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) 0.139s passed
testReadThatConsumesNoReferenceBases 0.092s passed
testSequenceDictionaryValidation 0.091s 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]) 0.140s 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]) 0.184s 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]) 0.197s 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]) 0.143s 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]) 0.140s 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]) 0.102s 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]) 0.093s 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]) 0.143s 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]) 0.141s 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]) 0.141s 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]) 0.143s 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]) 0.210s passed

Standard output

--------------------------------------------------------------------------------
[20:48:11] Executing test PrintReadsIntegrationTest:testReadFiltering_asIntegrationTestSpec

Standard error

[June 12, 2025 at 8:48:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:12 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:12 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:12 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:12 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:12 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:12 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:12 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:12 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:13 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:13 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:13 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:13 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:13 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:13 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:13 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:14 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:14 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:14 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:14 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:14 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:14 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:14 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:15 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:15 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:15 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:15 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:15 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:15 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:15 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:16 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:16 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:16 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:16 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:16 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:16 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:16 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:16 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:17 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:17 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:17 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:17 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:17 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:17 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:17 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:17 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:18 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:18 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:18 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:18 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:18 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:18 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:18 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:18 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:19 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:19 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000