Class picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest

107

tests

0

failures

0

ignored

1m50.87s

duration

100%

successful

Tests

Test Duration Result
pgRecordChainingTest[0](false, {1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2445ae0b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1eb499e5], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@dae62a4], 1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@68b350da, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@618f9e31, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5bce5854]}) 1.012s passed
pgRecordChainingTest[1](true, {1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6865af75], 1AAXX.3.1=[], 1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@775d4ca2, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6835376d]}) 1.045s passed
testBulkFragmentsNoDuplicates[0](.sam) 1.251s passed
testBulkFragmentsNoDuplicates[1](.bam) 1.339s passed
testBulkFragmentsNoDuplicates[2](.cram) 1.855s passed
testBulkFragmentsWithDuplicates[0](.sam) 1.457s passed
testBulkFragmentsWithDuplicates[1](.bam) 1.499s passed
testBulkFragmentsWithDuplicates[2](.cram) 2.445s passed
testBulkPairsNoDuplicates[0](.sam) 1.542s passed
testBulkPairsNoDuplicates[1](.bam) 1.484s passed
testBulkPairsNoDuplicates[2](.cram) 2.395s passed
testBulkPairsWithDuplicates[0](.sam) 1.073s passed
testBulkPairsWithDuplicates[1](.bam) 1.145s passed
testBulkPairsWithDuplicates[2](.cram) 1.496s passed
testDifferentChromosomesInOppositeOrder 0.883s passed
testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) 0.932s passed
testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) 0.937s passed
testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) 0.944s passed
testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) 0.945s passed
testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) 1.019s passed
testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) 0.913s passed
testMappedFragmentAndMappedPairFirstOfPairNonPrimary 0.955s passed
testMappedFragmentAndMatePairFirstUnmapped 1.027s passed
testMappedFragmentAndMatePairSecondUnmapped 0.955s passed
testMappedPairAndMappedFragmentAndMatePairFirstUnmapped 0.940s passed
testMappedPairAndMappedFragmentAndMatePairSecondUnmapped 0.925s passed
testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped 0.931s passed
testMappedPairAndMatePairFirstUnmapped 0.949s passed
testMappedPairAndMatePairSecondUnmapped 0.958s passed
testMappedPairWithFirstEndSamePositionAndOther 1.010s passed
testMappedPairWithSamePosition 0.873s passed
testMappedPairWithSamePositionSameCigar 0.957s passed
testMatePairFirstUnmapped 0.937s passed
testMatePairSecondUnmapped 0.986s passed
testOpticalDuplicateBehaviorNullRegex 0.952s passed
testOpticalDuplicateClusterOneEndSamePositionOneCluster 0.934s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance 0.903s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) 0.974s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) 0.954s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) 0.926s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) 0.941s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) 1.054s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) 0.972s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) 0.952s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) 0.972s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) 0.978s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) 0.965s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) 0.953s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) 1.012s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) 0.945s passed
testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) 0.980s passed
testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance 0.953s passed
testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate 0.943s passed
testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) 0.984s passed
testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) 1.013s passed
testOpticalDuplicateFinding 1.016s passed
testPathologicalOrderingAtTheSamePosition 0.981s passed
testSecondEndIsBeforeFirstInCoordinate 1.002s passed
testSingleMappedFragment 1.008s passed
testSingleMappedFragmentAndSingleMappedPair 0.907s passed
testSingleMappedFragmentAndTwoMappedPairs 0.937s passed
testSingleMappedPair 1.022s passed
testSingleUnmappedFragment 0.984s passed
testSingleUnmappedPair 1.007s passed
testStackOverFlowPairSetSwap 0.968s passed
testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs 0.949s passed
testThreeMappedPairs 0.945s passed
testThreeMappedPairsWithMatchingSecondMate 0.969s passed
testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs 0.975s passed
testTwoGroupsOnDifferentChromosomesOfTwoFragments 0.952s passed
testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs 0.970s passed
testTwoMappedFragments 0.952s passed
testTwoMappedPairWithSamePosition 0.964s passed
testTwoMappedPairWithSamePositionDifferentStrands 1.013s passed
testTwoMappedPairWithSamePositionDifferentStrands2 0.993s passed
testTwoMappedPairs 0.934s passed
testTwoMappedPairsAndMappedSecondaryFragment 0.996s passed
testTwoMappedPairsAndTerminalUnmappedFragment 0.983s passed
testTwoMappedPairsAndTerminalUnmappedPair 0.953s passed
testTwoMappedPairsMatesSoftClipped 0.960s passed
testTwoMappedPairsWithOppositeOrientations 1.023s passed
testTwoMappedPairsWithOppositeOrientationsNumberTwo 1.023s passed
testTwoMappedPairsWithSoftClipping 0.910s passed
testTwoMappedPairsWithSoftClippingBoth 0.958s passed
testTwoMappedPairsWithSoftClippingFirstOfPairOnly 0.899s passed
testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar 0.940s passed
testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) 1.021s passed
testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) 0.960s passed
testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) 0.937s passed
testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) 1.004s passed
testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) 0.922s passed
testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) 1.017s passed
testTwoMappedPairsWithSupplementaryReads[0](true, true, true) 0.937s passed
testTwoMappedPairsWithSupplementaryReads[1](true, false, true) 0.960s passed
testTwoMappedPairsWithSupplementaryReads[2](false, true, true) 1.056s passed
testTwoMappedPairsWithSupplementaryReads[3](true, true, false) 0.957s passed
testTwoMappedPairsWithSupplementaryReads[4](true, false, false) 1.047s passed
testTwoMappedPairsWithSupplementaryReads[5](false, true, false) 0.944s passed
testTwoUnmappedFragments 0.909s passed
testWithBarcodeComplex 0.974s passed
testWithBarcodeDuplicate 0.946s passed
testWithBarcodeFragmentDuplicate 0.958s passed
testWithIndividualReadBarcodes 1.039s passed
testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) 0.960s passed
testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) 0.971s passed
testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) 1.005s passed
testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) 0.975s passed

Standard error

[Thu Apr 24 13:04:15 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7897937372288214851/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7897937372288214851/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7897937372288214851/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:15	MarkDuplicates	Start of doWork freeMemory: 979690136; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:15	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:15	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:15	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:15	MarkDuplicates	Read 10000 records. 0 pairs never matched.
INFO	2025-04-24 13:04:16	MarkDuplicates	After buildSortedReadEndLists freeMemory: 916094000; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:16	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:16	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:16	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:16	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:16	MarkDuplicates	After generateDuplicateIndexes freeMemory: 979724048; totalMemory: 1612709888; maxMemory: 2147483648
INFO	2025-04-24 13:04:16	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:16	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:16	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:16	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:16	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:16	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:16	MarkDuplicates	Before output close freeMemory: 877820216; totalMemory: 1241513984; maxMemory: 2147483648
INFO	2025-04-24 13:04:16	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:16	MarkDuplicates	After output close freeMemory: 867334968; totalMemory: 1231028224; maxMemory: 2147483648
[Thu Apr 24 13:04:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1231028224
[Thu Apr 24 13:04:16 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2243669066579827599/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2243669066579827599/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2243669066579827599/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:17	MarkDuplicates	Start of doWork freeMemory: 979733464; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:17	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:17	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:17	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:17	MarkDuplicates	Read 10000 records. 0 pairs never matched.
INFO	2025-04-24 13:04:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 916087056; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:17	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:17	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:17	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:17	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:17	MarkDuplicates	After generateDuplicateIndexes freeMemory: 895835312; totalMemory: 1528823808; maxMemory: 2147483648
INFO	2025-04-24 13:04:17	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:17	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:17	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:17	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:17	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:17	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:17	MarkDuplicates	Before output close freeMemory: 873597400; totalMemory: 1237319680; maxMemory: 2147483648
INFO	2025-04-24 13:04:17	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:18	MarkDuplicates	After output close freeMemory: 870452152; totalMemory: 1234173952; maxMemory: 2147483648
[Thu Apr 24 13:04:18 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1234173952
[Thu Apr 24 13:04:18 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp112498351863795537/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp112498351863795537/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp112498351863795537/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester2903902155196002343/input.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:18	MarkDuplicates	Start of doWork freeMemory: 979504264; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:18	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:18	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:18	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:18	MarkDuplicates	Read 10000 records. 0 pairs never matched.
INFO	2025-04-24 13:04:19	MarkDuplicates	After buildSortedReadEndLists freeMemory: 915863392; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:19	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:19	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:19	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:19	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:19	MarkDuplicates	After generateDuplicateIndexes freeMemory: 979496224; totalMemory: 1612709888; maxMemory: 2147483648
INFO	2025-04-24 13:04:19	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:19	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:19	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:19	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:19	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:19	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:19	MarkDuplicates	Before output close freeMemory: 890658464; totalMemory: 1258291200; maxMemory: 2147483648
INFO	2025-04-24 13:04:19	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:19	MarkDuplicates	After output close freeMemory: 887510464; totalMemory: 1255145472; maxMemory: 2147483648
[Thu Apr 24 13:04:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1255145472
[Thu Apr 24 13:04:20 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15629499877382217818/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15629499877382217818/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15629499877382217818/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:20	MarkDuplicates	Start of doWork freeMemory: 971534704; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:20	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:20	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:20	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:20	MarkDuplicates	Read 21000 records. 0 pairs never matched.
INFO	2025-04-24 13:04:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 907097528; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:20	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:20	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:20	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:20	MarkDuplicates	After generateDuplicateIndexes freeMemory: 940069608; totalMemory: 1581252608; maxMemory: 2147483648
INFO	2025-04-24 13:04:20	MarkDuplicates	Marking 20000 records as duplicates.
INFO	2025-04-24 13:04:20	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:20	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:21	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:21	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:21	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:21	MarkDuplicates	Before output close freeMemory: 890591696; totalMemory: 1262485504; maxMemory: 2147483648
INFO	2025-04-24 13:04:21	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:21	MarkDuplicates	After output close freeMemory: 890595048; totalMemory: 1262485504; maxMemory: 2147483648
[Thu Apr 24 13:04:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1262485504
[Thu Apr 24 13:04:21 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17754840022769119520/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17754840022769119520/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17754840022769119520/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:21	MarkDuplicates	Start of doWork freeMemory: 971533864; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:21	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:21	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:21	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:21	MarkDuplicates	Read 21000 records. 0 pairs never matched.
INFO	2025-04-24 13:04:22	MarkDuplicates	After buildSortedReadEndLists freeMemory: 907096536; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:22	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:22	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 970477672; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:04:22	MarkDuplicates	Marking 20000 records as duplicates.
INFO	2025-04-24 13:04:22	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:22	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:22	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:22	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:22	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:22	MarkDuplicates	Before output close freeMemory: 896931280; totalMemory: 1268776960; maxMemory: 2147483648
INFO	2025-04-24 13:04:22	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:22	MarkDuplicates	After output close freeMemory: 890785408; totalMemory: 1262485504; maxMemory: 2147483648
[Thu Apr 24 13:04:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1262485504
[Thu Apr 24 13:04:23 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2545882483718425444/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2545882483718425444/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2545882483718425444/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester16567498800022500487/input.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:23	MarkDuplicates	Start of doWork freeMemory: 971180456; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:23	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:23	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:24	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:24	MarkDuplicates	Read 21000 records. 0 pairs never matched.
INFO	2025-04-24 13:04:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 906745704; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:24	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:24	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:24	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:24	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:24	MarkDuplicates	After generateDuplicateIndexes freeMemory: 612559856; totalMemory: 1254096896; maxMemory: 2147483648
INFO	2025-04-24 13:04:24	MarkDuplicates	Marking 20000 records as duplicates.
INFO	2025-04-24 13:04:24	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:24	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:25	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:25	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:25	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:25	MarkDuplicates	Before output close freeMemory: 881901152; totalMemory: 1254096896; maxMemory: 2147483648
INFO	2025-04-24 13:04:25	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:25	MarkDuplicates	After output close freeMemory: 882040824; totalMemory: 1254096896; maxMemory: 2147483648
[Thu Apr 24 13:04:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1254096896
[Thu Apr 24 13:04:25 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1196903007801833479/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1196903007801833479/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1196903007801833479/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:25	MarkDuplicates	Start of doWork freeMemory: 971012888; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:25	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:25	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:25	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:25	MarkDuplicates	Read 20200 records. 0 pairs never matched.
INFO	2025-04-24 13:04:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 905908464; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:26	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:26	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:26	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:26	MarkDuplicates	After generateDuplicateIndexes freeMemory: 967811968; totalMemory: 1609564160; maxMemory: 2147483648
INFO	2025-04-24 13:04:26	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:26	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:26	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:26	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:26	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:26	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:26	MarkDuplicates	Before output close freeMemory: 890072072; totalMemory: 1262485504; maxMemory: 2147483648
INFO	2025-04-24 13:04:26	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:26	MarkDuplicates	After output close freeMemory: 886020192; totalMemory: 1258291200; maxMemory: 2147483648
[Thu Apr 24 13:04:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1258291200
[Thu Apr 24 13:04:27 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5609673335269488945/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5609673335269488945/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5609673335269488945/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:27	MarkDuplicates	Start of doWork freeMemory: 971011968; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:27	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:27	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:27	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:27	MarkDuplicates	Read 20200 records. 0 pairs never matched.
INFO	2025-04-24 13:04:27	MarkDuplicates	After buildSortedReadEndLists freeMemory: 905907720; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:27	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:27	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:27	MarkDuplicates	After generateDuplicateIndexes freeMemory: 955230704; totalMemory: 1596981248; maxMemory: 2147483648
INFO	2025-04-24 13:04:27	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:27	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:27	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:28	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:28	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:28	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:28	MarkDuplicates	Before output close freeMemory: 893146824; totalMemory: 1265631232; maxMemory: 2147483648
INFO	2025-04-24 13:04:28	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:28	MarkDuplicates	After output close freeMemory: 890004448; totalMemory: 1262485504; maxMemory: 2147483648
[Thu Apr 24 13:04:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1262485504
[Thu Apr 24 13:04:29 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2243283229959559461/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2243283229959559461/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2243283229959559461/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester650686051114810634/input.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:29	MarkDuplicates	Start of doWork freeMemory: 970880496; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:29	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:29	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:29	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:29	MarkDuplicates	Read 20200 records. 0 pairs never matched.
INFO	2025-04-24 13:04:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 905773400; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:29	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:29	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:30	MarkDuplicates	After generateDuplicateIndexes freeMemory: 701385592; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:30	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:30	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:30	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:30	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:30	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:30	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:30	MarkDuplicates	Before output close freeMemory: 893135088; totalMemory: 1265631232; maxMemory: 2147483648
INFO	2025-04-24 13:04:30	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:30	MarkDuplicates	After output close freeMemory: 890131960; totalMemory: 1262485504; maxMemory: 2147483648
[Thu Apr 24 13:04:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1262485504
[Thu Apr 24 13:04:30 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13317055596671202718/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13317055596671202718/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13317055596671202718/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:31	MarkDuplicates	Start of doWork freeMemory: 981529488; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:31	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:31	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:31	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:31	MarkDuplicates	Read 6820 records. 0 pairs never matched.
INFO	2025-04-24 13:04:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 917870648; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:31	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:31	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:31	MarkDuplicates	After generateDuplicateIndexes freeMemory: 817946480; totalMemory: 1449132032; maxMemory: 2147483648
INFO	2025-04-24 13:04:31	MarkDuplicates	Marking 6200 records as duplicates.
INFO	2025-04-24 13:04:31	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:31	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:31	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:31	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:31	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:31	MarkDuplicates	Before output close freeMemory: 872326672; totalMemory: 1234173952; maxMemory: 2147483648
INFO	2025-04-24 13:04:31	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:31	MarkDuplicates	After output close freeMemory: 869323464; totalMemory: 1231028224; maxMemory: 2147483648
[Thu Apr 24 13:04:31 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1231028224
[Thu Apr 24 13:04:32 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16641064730227199867/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16641064730227199867/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16641064730227199867/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:32 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:32	MarkDuplicates	Start of doWork freeMemory: 981531040; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:32	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:32	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:32	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:32	MarkDuplicates	Read 6820 records. 0 pairs never matched.
INFO	2025-04-24 13:04:32	MarkDuplicates	After buildSortedReadEndLists freeMemory: 917869048; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:32	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:32	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1095817896; totalMemory: 1727004672; maxMemory: 2147483648
INFO	2025-04-24 13:04:32	MarkDuplicates	Marking 6200 records as duplicates.
INFO	2025-04-24 13:04:32	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:32	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:32	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:32	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:32	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:32	MarkDuplicates	Before output close freeMemory: 864987648; totalMemory: 1226833920; maxMemory: 2147483648
INFO	2025-04-24 13:04:32	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:33	MarkDuplicates	After output close freeMemory: 865127816; totalMemory: 1226833920; maxMemory: 2147483648
[Thu Apr 24 13:04:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1226833920
[Thu Apr 24 13:04:33 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9887636784151383858/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9887636784151383858/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9887636784151383858/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester12434642938989799117/input.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:33	MarkDuplicates	Start of doWork freeMemory: 981400432; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:33	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:33	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:04:33	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:33	MarkDuplicates	Read 6820 records. 0 pairs never matched.
INFO	2025-04-24 13:04:33	MarkDuplicates	After buildSortedReadEndLists freeMemory: 917741384; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:33	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:33	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:33	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 980346992; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:04:34	MarkDuplicates	Marking 6200 records as duplicates.
INFO	2025-04-24 13:04:34	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:34	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:34	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:34	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:34	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:34	MarkDuplicates	Before output close freeMemory: 879538232; totalMemory: 1241513984; maxMemory: 2147483648
INFO	2025-04-24 13:04:34	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:34	MarkDuplicates	After output close freeMemory: 872339912; totalMemory: 1234173952; maxMemory: 2147483648
[Thu Apr 24 13:04:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1234173952
[Thu Apr 24 13:04:34 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8532206634630329559/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8532206634630329559/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8532206634630329559/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:34	MarkDuplicates	Start of doWork freeMemory: 986647968; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:34	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:34	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:34	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932111240; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:34	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:35	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 630121888; totalMemory: 1256194048; maxMemory: 2147483648
INFO	2025-04-24 13:04:35	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:04:35	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:04:35	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:35	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:35	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:35	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:35	MarkDuplicates	Before output close freeMemory: 856421384; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:35	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:35	MarkDuplicates	After output close freeMemory: 856418312; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:35 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:35 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6046251151486385557/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6046251151486385557/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6046251151486385557/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:35	MarkDuplicates	Start of doWork freeMemory: 986636928; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:35	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:35	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:35	MarkDuplicates	Read 11 records. 0 pairs never matched.
INFO	2025-04-24 13:04:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932101912; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:35	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:35	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:36	MarkDuplicates	After generateDuplicateIndexes freeMemory: 768525128; totalMemory: 1394606080; maxMemory: 2147483648
INFO	2025-04-24 13:04:36	MarkDuplicates	Marking 8 records as duplicates.
INFO	2025-04-24 13:04:36	MarkDuplicates	Found 2 optical duplicate clusters.
INFO	2025-04-24 13:04:36	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:36	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:36	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:36	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:36	MarkDuplicates	Before output close freeMemory: 853267912; totalMemory: 1210056704; maxMemory: 2147483648
INFO	2025-04-24 13:04:36	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:36	MarkDuplicates	After output close freeMemory: 849070536; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:04:36 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:04:36 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3167532957326932460/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3167532957326932460/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3167532957326932460/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:36	MarkDuplicates	Start of doWork freeMemory: 986636176; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:36	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:36	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:36	MarkDuplicates	Read 11 records. 0 pairs never matched.
INFO	2025-04-24 13:04:36	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932101160; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:36	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:36	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:36	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:36	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:37	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717144152; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:37	MarkDuplicates	Marking 8 records as duplicates.
INFO	2025-04-24 13:04:37	MarkDuplicates	Found 2 optical duplicate clusters.
INFO	2025-04-24 13:04:37	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:37	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:37	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:37	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:37	MarkDuplicates	Before output close freeMemory: 863749640; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:04:37	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:37	MarkDuplicates	After output close freeMemory: 853267232; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:37 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14845855836644494541/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14845855836644494541/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14845855836644494541/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:37	MarkDuplicates	Start of doWork freeMemory: 986635464; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:37	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:37	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:37	MarkDuplicates	Read 11 records. 0 pairs never matched.
INFO	2025-04-24 13:04:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932100448; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:37	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:37	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:37	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 772717968; totalMemory: 1398800384; maxMemory: 2147483648
INFO	2025-04-24 13:04:38	MarkDuplicates	Marking 8 records as duplicates.
INFO	2025-04-24 13:04:38	MarkDuplicates	Found 2 optical duplicate clusters.
INFO	2025-04-24 13:04:38	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:38	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:38	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:38	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:38	MarkDuplicates	Before output close freeMemory: 863752208; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:04:38	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:38	MarkDuplicates	After output close freeMemory: 859554832; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:04:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:04:38 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7086493211468167601/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7086493211468167601/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7086493211468167601/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:38 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:38	MarkDuplicates	Start of doWork freeMemory: 986633608; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:38	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:38	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:38	MarkDuplicates	Read 11 records. 0 pairs never matched.
INFO	2025-04-24 13:04:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932098592; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:38	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:38	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:38	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:38	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717141584; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:38	MarkDuplicates	Marking 8 records as duplicates.
INFO	2025-04-24 13:04:38	MarkDuplicates	Found 2 optical duplicate clusters.
INFO	2025-04-24 13:04:38	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:38	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:38	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:38	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:39	MarkDuplicates	Before output close freeMemory: 859556048; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:04:39	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:39	MarkDuplicates	After output close freeMemory: 853261520; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:39 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16434486270906685917/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16434486270906685917/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16434486270906685917/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:39 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:39	MarkDuplicates	Start of doWork freeMemory: 986632904; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:39	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:39	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:39	MarkDuplicates	Read 11 records. 0 pairs never matched.
INFO	2025-04-24 13:04:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932097904; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:39	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:39	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1045345184; totalMemory: 1671430144; maxMemory: 2147483648
INFO	2025-04-24 13:04:39	MarkDuplicates	Marking 8 records as duplicates.
INFO	2025-04-24 13:04:39	MarkDuplicates	Found 2 optical duplicate clusters.
INFO	2025-04-24 13:04:39	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:39	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:39	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:39	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:40	MarkDuplicates	Before output close freeMemory: 863749656; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:04:40	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:40	MarkDuplicates	After output close freeMemory: 856406552; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:40 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3202788119641267709/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3202788119641267709/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3202788119641267709/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:40 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:40	MarkDuplicates	Start of doWork freeMemory: 986632200; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:40	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:40	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:40	MarkDuplicates	Read 11 records. 0 pairs never matched.
INFO	2025-04-24 13:04:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932097000; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:40	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:40	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:40	MarkDuplicates	After generateDuplicateIndexes freeMemory: 576630992; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:04:40	MarkDuplicates	Marking 8 records as duplicates.
INFO	2025-04-24 13:04:40	MarkDuplicates	Found 2 optical duplicate clusters.
INFO	2025-04-24 13:04:40	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:40	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:40	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:40	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:41	MarkDuplicates	Before output close freeMemory: 845923152; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:04:41	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:41	MarkDuplicates	After output close freeMemory: 845920080; totalMemory: 1202716672; maxMemory: 2147483648
[Thu Apr 24 13:04:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1202716672
[Thu Apr 24 13:04:41 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7948649373713093903/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7948649373713093903/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7948649373713093903/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:41 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:41	MarkDuplicates	Start of doWork freeMemory: 986637984; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:41	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:41	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:41	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:04:41	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932104288; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:41	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:41	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:41	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:41	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:41	MarkDuplicates	After generateDuplicateIndexes freeMemory: 772721016; totalMemory: 1398800384; maxMemory: 2147483648
INFO	2025-04-24 13:04:41	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:41	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:41	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:41	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:41	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:41	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:41	MarkDuplicates	Before output close freeMemory: 863755720; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:04:41	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:42	MarkDuplicates	After output close freeMemory: 856412616; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:42 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17501462573616826311/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17501462573616826311/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17501462573616826311/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:42 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:42	MarkDuplicates	Start of doWork freeMemory: 986636888; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:42	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:42	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:42	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:42	MarkDuplicates	Read 3 records. 0 pairs never matched.
INFO	2025-04-24 13:04:42	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932103112; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:42	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:42	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:42	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:42	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:42	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985580848; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:04:42	MarkDuplicates	Marking 1 records as duplicates.
INFO	2025-04-24 13:04:42	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:42	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:42	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:42	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:42	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:43	MarkDuplicates	Before output close freeMemory: 859560488; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:04:43	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:43	MarkDuplicates	After output close freeMemory: 856411712; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:43 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13218305081655760590/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13218305081655760590/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13218305081655760590/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:43	MarkDuplicates	Start of doWork freeMemory: 986636224; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:43	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:43	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:43	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:43	MarkDuplicates	Read 3 records. 0 pairs never matched.
INFO	2025-04-24 13:04:43	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932102432; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:43	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:43	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:43	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:43	MarkDuplicates	After generateDuplicateIndexes freeMemory: 877576840; totalMemory: 1503657984; maxMemory: 2147483648
INFO	2025-04-24 13:04:43	MarkDuplicates	Marking 1 records as duplicates.
INFO	2025-04-24 13:04:43	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:43	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:43	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:43	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:43	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:43	MarkDuplicates	Before output close freeMemory: 856414088; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:43	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:44	MarkDuplicates	After output close freeMemory: 856411040; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:44 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2126701740112919684/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2126701740112919684/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2126701740112919684/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:44 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:44	MarkDuplicates	Start of doWork freeMemory: 986633952; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:44	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:44	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:44	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:04:44	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932099800; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:44	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:44	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717142144; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:44	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:04:44	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:44	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:44	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:44	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:44	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:44	MarkDuplicates	Before output close freeMemory: 856411008; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:44	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:45	MarkDuplicates	After output close freeMemory: 853265352; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:45 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4796307963494374602/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4796307963494374602/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4796307963494374602/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:45 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:45	MarkDuplicates	Start of doWork freeMemory: 986632976; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:45	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:45	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:45	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:45	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:04:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932098840; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:45	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:45	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:45	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717138080; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:45	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:04:45	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:45	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:45	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:45	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:45	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:45	MarkDuplicates	Before output close freeMemory: 856410040; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:45	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:45	MarkDuplicates	After output close freeMemory: 853261240; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:45 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12394277088564068802/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12394277088564068802/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12394277088564068802/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:45 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:46	MarkDuplicates	Start of doWork freeMemory: 986632480; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:46	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:46	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:46	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:46	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932098408; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:46	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:46	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:46	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:46	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:46	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717140672; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:46	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:46	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:46	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:46	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:46	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:46	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:46	MarkDuplicates	Before output close freeMemory: 859551888; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:04:46	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:46	MarkDuplicates	After output close freeMemory: 853263784; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:46 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:46 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3817959123506445406/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3817959123506445406/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3817959123506445406/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:46 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:47	MarkDuplicates	Start of doWork freeMemory: 986631776; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:47	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:47	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:47	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:47	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:47	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932097704; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:47	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:47	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:47	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:47	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717136896; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:47	MarkDuplicates	Marking 1 records as duplicates.
INFO	2025-04-24 13:04:47	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:47	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:47	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:47	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:47	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:47	MarkDuplicates	Before output close freeMemory: 856408832; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:47	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:47	MarkDuplicates	After output close freeMemory: 853260032; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:47 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6556279545149033459/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6556279545149033459/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6556279545149033459/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:47 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:47	MarkDuplicates	Start of doWork freeMemory: 986630952; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:47	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:47	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:48	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:48	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932096880; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:48	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:48	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:48	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:48	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717136040; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:48	MarkDuplicates	Marking 1 records as duplicates.
INFO	2025-04-24 13:04:48	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:48	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:48	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:48	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:48	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:48	MarkDuplicates	Before output close freeMemory: 853262280; totalMemory: 1210056704; maxMemory: 2147483648
INFO	2025-04-24 13:04:48	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:48	MarkDuplicates	After output close freeMemory: 853259208; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:48 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12029643148482989649/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12029643148482989649/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12029643148482989649/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:48 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:48	MarkDuplicates	Start of doWork freeMemory: 986629680; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:48	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:48	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:48	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:48	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932095464; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:49	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:49	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:49	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:49	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:49	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985570272; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:04:49	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:49	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:49	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:49	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:49	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:49	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:49	MarkDuplicates	Before output close freeMemory: 866892552; totalMemory: 1223688192; maxMemory: 2147483648
INFO	2025-04-24 13:04:49	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:49	MarkDuplicates	After output close freeMemory: 856403720; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:49 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1197666574551634844/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1197666574551634844/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1197666574551634844/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:49 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:49	MarkDuplicates	Start of doWork freeMemory: 986630200; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:49	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:49	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:49	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:49	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:04:50	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932096224; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:50	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:50	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:50	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:50	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:50	MarkDuplicates	After generateDuplicateIndexes freeMemory: 576626120; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:04:50	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:50	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:50	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:50	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:50	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:50	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:50	MarkDuplicates	Before output close freeMemory: 845921560; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:04:50	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:50	MarkDuplicates	After output close freeMemory: 845918512; totalMemory: 1202716672; maxMemory: 2147483648
[Thu Apr 24 13:04:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1202716672
[Thu Apr 24 13:04:50 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4931822721477890543/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4931822721477890543/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4931822721477890543/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:50	MarkDuplicates	Start of doWork freeMemory: 986629344; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:50	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:50	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:50	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:50	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:04:51	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932095352; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:51	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:51	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:51	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:51	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:51	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717134432; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:51	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:51	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:51	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:51	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:51	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:51	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:51	MarkDuplicates	Before output close freeMemory: 856406456; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:51	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:51	MarkDuplicates	After output close freeMemory: 853257584; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:51 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12592448797705402632/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12592448797705402632/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12592448797705402632/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:51	MarkDuplicates	Start of doWork freeMemory: 986628616; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:51	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:51	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:51	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:51	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:04:51	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932094904; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:52	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:52	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:52	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:52	MarkDuplicates	After generateDuplicateIndexes freeMemory: 772711632; totalMemory: 1398800384; maxMemory: 2147483648
INFO	2025-04-24 13:04:52	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:52	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:52	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:52	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:52	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:52	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:52	MarkDuplicates	Before output close freeMemory: 856405576; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:52	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:52	MarkDuplicates	After output close freeMemory: 856406280; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:52 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15868819491037641465/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15868819491037641465/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15868819491037641465/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:52	MarkDuplicates	Start of doWork freeMemory: 986627864; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:52	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:52	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:04:52	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:04:52	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:04:52	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932094152; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:52	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:53	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:53	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:53	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:53	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717136352; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:53	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:04:53	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:53	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:53	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:53	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:53	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:53	MarkDuplicates	Before output close freeMemory: 856405504; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:53	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:53	MarkDuplicates	After output close freeMemory: 853256728; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:53 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4114463550182541513/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4114463550182541513/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4114463550182541513/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH  --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:53	MarkDuplicates	Start of doWork freeMemory: 986625376; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:53	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:53	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:53	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:53	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932091160; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:53	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:54	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:54	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:54	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:54	MarkDuplicates	After generateDuplicateIndexes freeMemory: 765368256; totalMemory: 1391460352; maxMemory: 2147483648
INFO	2025-04-24 13:04:54	MarkDuplicates	Marking 2 records as duplicates.
WARNING	2025-04-24 13:04:54	MarkDuplicates	Skipped optical duplicate cluster discovery; library size estimation may be inaccurate!
INFO	2025-04-24 13:04:54	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:54	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:54	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:54	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:54	MarkDuplicates	Before output close freeMemory: 859548424; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:04:54	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:54	MarkDuplicates	After output close freeMemory: 856399648; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:54 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5182519452012571341/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5182519452012571341/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5182519452012571341/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:54	MarkDuplicates	Start of doWork freeMemory: 986624152; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:54	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:54	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:54	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:54	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932089856; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:54	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:55	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:55	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:55	MarkDuplicates	After generateDuplicateIndexes freeMemory: 716083552; totalMemory: 1342177280; maxMemory: 2147483648
INFO	2025-04-24 13:04:55	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:04:55	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:04:55	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:55	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:55	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:55	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:55	MarkDuplicates	Before output close freeMemory: 859546568; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:04:55	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:55	MarkDuplicates	After output close freeMemory: 853252040; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:55 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14830341533991190494/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14830341533991190494/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14830341533991190494/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:55	MarkDuplicates	Start of doWork freeMemory: 986621040; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:55	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:55	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:55	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:55	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932086760; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:55	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:56	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 768509408; totalMemory: 1394606080; maxMemory: 2147483648
INFO	2025-04-24 13:04:56	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:04:56	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:56	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:56	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:56	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:56	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:56	MarkDuplicates	Before output close freeMemory: 859543640; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:04:56	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:56	MarkDuplicates	After output close freeMemory: 853251760; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:56 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:56 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14342329724830382557/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14342329724830382557/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14342329724830382557/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:56	MarkDuplicates	Start of doWork freeMemory: 986620304; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:56	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:56	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:56	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932086024; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:56	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:56	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:57	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717128448; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:57	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:04:57	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:57	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:57	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:57	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:57	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:57	MarkDuplicates	Before output close freeMemory: 856397176; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:04:57	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:57	MarkDuplicates	After output close freeMemory: 853248376; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:57 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17214842730936175271/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17214842730936175271/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17214842730936175271/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:57	MarkDuplicates	Start of doWork freeMemory: 986619640; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:57	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:57	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:57	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:57	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932082472; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:57	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:57	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:57	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:57	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:58	MarkDuplicates	After generateDuplicateIndexes freeMemory: 768507992; totalMemory: 1394606080; maxMemory: 2147483648
INFO	2025-04-24 13:04:58	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:04:58	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:58	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:58	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:58	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:58	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:58	MarkDuplicates	Before output close freeMemory: 859542232; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:04:58	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:58	MarkDuplicates	After output close freeMemory: 853247704; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:04:58 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:04:58 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16089089746252566791/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16089089746252566791/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16089089746252566791/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:58	MarkDuplicates	Start of doWork freeMemory: 986618944; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:58	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:58	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:58	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:58	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932084664; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:58	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:58	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:58	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:58	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:04:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717123976; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:04:59	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:04:59	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:04:59	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:04:59	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:04:59	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:04:59	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:04:59	MarkDuplicates	Before output close freeMemory: 863735848; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:04:59	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:04:59	MarkDuplicates	After output close freeMemory: 856392744; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:04:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:04:59 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11229284706840374060/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11229284706840374060/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11229284706840374060/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:04:59	MarkDuplicates	Start of doWork freeMemory: 986618256; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:59	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:04:59	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:04:59	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:04:59	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932083960; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:04:59	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:04:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:04:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:04:59	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 768506608; totalMemory: 1394606080; maxMemory: 2147483648
INFO	2025-04-24 13:05:00	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:00	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:00	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:00	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:00	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:00	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:00	MarkDuplicates	Before output close freeMemory: 856391840; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:00	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:00	MarkDuplicates	After output close freeMemory: 856395192; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:00 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4140496770213923191/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4140496770213923191/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4140496770213923191/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:00	MarkDuplicates	Start of doWork freeMemory: 986617560; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:00	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:00	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:00	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:00	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932083264; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:00	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:00	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:00	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:00	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717125688; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:00	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:00	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:00	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:00	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:00	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:00	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:01	MarkDuplicates	Before output close freeMemory: 859540152; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:01	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:01	MarkDuplicates	After output close freeMemory: 859539728; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:01 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3521456391645883774/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3521456391645883774/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3521456391645883774/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:01	MarkDuplicates	Start of doWork freeMemory: 986616864; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:01	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:01	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:01	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:01	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932082568; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:01	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:01	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:01	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:01	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:01	MarkDuplicates	After generateDuplicateIndexes freeMemory: 775845248; totalMemory: 1401946112; maxMemory: 2147483648
INFO	2025-04-24 13:05:01	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:01	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:01	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:01	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:01	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:01	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:02	MarkDuplicates	Before output close freeMemory: 856393728; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:02	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:02	MarkDuplicates	After output close freeMemory: 856390656; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:02 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:02 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6296674495157710904/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6296674495157710904/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6296674495157710904/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:02	MarkDuplicates	Start of doWork freeMemory: 986616168; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:02	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:02	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:02	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:02	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932081888; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:02	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:02	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:02	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:02	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:02	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985556664; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:02	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:02	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:02	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:02	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:02	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:02	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:03	MarkDuplicates	Before output close freeMemory: 863733072; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:05:03	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:03	MarkDuplicates	After output close freeMemory: 856389992; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:03 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:03 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17787386566944200741/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17787386566944200741/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17787386566944200741/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:03	MarkDuplicates	Start of doWork freeMemory: 986615384; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:03	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:03	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:03	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:03	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932080920; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:03	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:03	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:03	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:03	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:03	MarkDuplicates	After generateDuplicateIndexes freeMemory: 772698056; totalMemory: 1398800384; maxMemory: 2147483648
INFO	2025-04-24 13:05:03	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:03	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:03	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:03	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:03	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:03	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:04	MarkDuplicates	Before output close freeMemory: 866878016; totalMemory: 1223688192; maxMemory: 2147483648
INFO	2025-04-24 13:05:04	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:04	MarkDuplicates	After output close freeMemory: 856389184; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:04 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:04 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11982589475168964913/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11982589475168964913/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11982589475168964913/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:04	MarkDuplicates	Start of doWork freeMemory: 986614696; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:04	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:04	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:04	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:04	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932080400; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:04	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:04	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:04	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:04	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717122824; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:04	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:04	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:04	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:04	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:04	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:04	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:05	MarkDuplicates	Before output close freeMemory: 859537288; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:05	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:05	MarkDuplicates	After output close freeMemory: 856388512; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:05 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:05 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16202525773709730336/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16202525773709730336/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16202525773709730336/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:05	MarkDuplicates	Start of doWork freeMemory: 986614000; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:05	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:05	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:05	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:05	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932079720; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:05	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:05	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:05	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:05	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:05	MarkDuplicates	After generateDuplicateIndexes freeMemory: 775842400; totalMemory: 1401946112; maxMemory: 2147483648
INFO	2025-04-24 13:05:05	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:05	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:05	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:05	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:05	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:05	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:05	MarkDuplicates	Before output close freeMemory: 859536600; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:05	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:06	MarkDuplicates	After output close freeMemory: 859536176; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:06 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2986999893165726351/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2986999893165726351/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2986999893165726351/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:06 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:06	MarkDuplicates	Start of doWork freeMemory: 986613288; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:06	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:06	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:06	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:06	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932078992; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:06	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:06	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:06	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:06	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:06	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717118312; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:06	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:06	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:06	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:06	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:06	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:06	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:06	MarkDuplicates	Before output close freeMemory: 859535880; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:06	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:07	MarkDuplicates	After output close freeMemory: 849049696; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:05:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:05:07 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14167968500862624569/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14167968500862624569/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14167968500862624569/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:07	MarkDuplicates	Start of doWork freeMemory: 986612592; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:07	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:07	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:07	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:07	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932078232; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:07	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:07	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:07	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:07	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:07	MarkDuplicates	After generateDuplicateIndexes freeMemory: 765355152; totalMemory: 1391460352; maxMemory: 2147483648
INFO	2025-04-24 13:05:07	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:07	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:07	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:07	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:07	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:07	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:07	MarkDuplicates	Before output close freeMemory: 859535120; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:07	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:07	MarkDuplicates	After output close freeMemory: 859532072; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:07 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16816213374739349838/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16816213374739349838/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16816213374739349838/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:08	MarkDuplicates	Start of doWork freeMemory: 986611832; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:08	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:08	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:08	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:08	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932077536; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:08	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:08	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:08	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:08	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:08	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985555416; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:08	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:08	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:08	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:08	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:08	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:08	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:08	MarkDuplicates	Before output close freeMemory: 856388696; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:08	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:09	MarkDuplicates	After output close freeMemory: 856385624; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:09 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8825991288685076440/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8825991288685076440/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8825991288685076440/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:09 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:09	MarkDuplicates	Start of doWork freeMemory: 986611080; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:09	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:09	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:09	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:09	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932076616; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:09	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:09	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:09	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:09	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:09	MarkDuplicates	After generateDuplicateIndexes freeMemory: 877551352; totalMemory: 1503657984; maxMemory: 2147483648
INFO	2025-04-24 13:05:09	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:09	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:09	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:09	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:09	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:09	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:09	MarkDuplicates	Before output close freeMemory: 856387952; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:09	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:09	MarkDuplicates	After output close freeMemory: 856387528; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:09 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5760826449260131263/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5760826449260131263/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5760826449260131263/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:09 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:10	MarkDuplicates	Start of doWork freeMemory: 986610712; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:10	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:10	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:10	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:10	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932073584; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:10	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:10	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:10	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:10	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:10	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717118688; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:10	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:10	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:10	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:10	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:10	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:10	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:10	MarkDuplicates	Before output close freeMemory: 863727800; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:05:10	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:10	MarkDuplicates	After output close freeMemory: 859530448; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:10 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:10 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12241536796148232198/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12241536796148232198/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12241536796148232198/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:10 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:11	MarkDuplicates	Start of doWork freeMemory: 986609664; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:11	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:11	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:11	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:11	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932075384; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:11	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:11	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:11	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:11	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717117200; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:11	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:11	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:11	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:11	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:11	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:11	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:11	MarkDuplicates	Before output close freeMemory: 856386552; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:11	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:11	MarkDuplicates	After output close freeMemory: 849043448; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:05:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:05:11 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4193561616124287306/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4193561616124287306/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4193561616124287306/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:11 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:11	MarkDuplicates	Start of doWork freeMemory: 986607648; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:11	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:11	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:11	MarkDuplicates	Read 6 records. 0 pairs never matched.
INFO	2025-04-24 13:05:12	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932073120; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:12	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:12	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:12	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:12	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:12	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985551088; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:12	MarkDuplicates	Marking 4 records as duplicates.
INFO	2025-04-24 13:05:12	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:12	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:12	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:12	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:12	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:12	MarkDuplicates	Before output close freeMemory: 856384696; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:12	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:12	MarkDuplicates	After output close freeMemory: 856381624; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:12 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4291705184714309033/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4291705184714309033/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4291705184714309033/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:13	MarkDuplicates	Start of doWork freeMemory: 986607592; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:13	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:13	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:13	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:13	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932073112; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:13	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:13	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:13	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:13	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:13	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717115568; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:13	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:13	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:13	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:13	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:13	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:13	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:13	MarkDuplicates	Before output close freeMemory: 859530216; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:13	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:13	MarkDuplicates	After output close freeMemory: 853235688; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:13 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2184791307909559173/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2184791307909559173/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2184791307909559173/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:13	MarkDuplicates	Start of doWork freeMemory: 986607952; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:13	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:13	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:14	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:14	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:05:14	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932073976; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:14	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:14	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:14	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:14	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:14	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985551616; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:14	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:14	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:14	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:14	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:14	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:14	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:14	MarkDuplicates	Before output close freeMemory: 859530824; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:14	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:14	MarkDuplicates	After output close freeMemory: 859527752; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:14 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:14 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9171803729411274064/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9171803729411274064/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9171803729411274064/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:14	MarkDuplicates	Start of doWork freeMemory: 986607856; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:14	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:14	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:15	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:15	MarkDuplicates	Read 1 records. 0 pairs never matched.
INFO	2025-04-24 13:05:15	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932074144; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:15	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:15	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:15	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:15	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:15	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985551800; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:15	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:15	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:15	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:15	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:15	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:15	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:15	MarkDuplicates	Before output close freeMemory: 856385728; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:15	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:15	MarkDuplicates	After output close freeMemory: 856382656; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:15 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:15 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17100417945165030879/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17100417945165030879/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17100417945165030879/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:15	MarkDuplicates	Start of doWork freeMemory: 986605840; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:15	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:15	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:16	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:16	MarkDuplicates	Read 3 records. 0 pairs never matched.
INFO	2025-04-24 13:05:16	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932071768; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:16	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:16	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:16	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:16	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:16	MarkDuplicates	After generateDuplicateIndexes freeMemory: 576604848; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:05:16	MarkDuplicates	Marking 1 records as duplicates.
INFO	2025-04-24 13:05:16	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:16	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:16	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:16	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:16	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:16	MarkDuplicates	Before output close freeMemory: 845897328; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:05:16	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:16	MarkDuplicates	After output close freeMemory: 845894256; totalMemory: 1202716672; maxMemory: 2147483648
[Thu Apr 24 13:05:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1202716672
[Thu Apr 24 13:05:16 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12327402503372000117/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12327402503372000117/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12327402503372000117/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:16	MarkDuplicates	Start of doWork freeMemory: 986603600; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:16	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:16	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:16	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:16	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932069288; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:17	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:17	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:17	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:17	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:17	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717111792; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:17	MarkDuplicates	Marking 3 records as duplicates.
INFO	2025-04-24 13:05:17	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:17	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:17	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:17	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:17	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:17	MarkDuplicates	Before output close freeMemory: 859526624; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:17	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:17	MarkDuplicates	After output close freeMemory: 853232048; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:17 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:17 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7423156055018174737/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7423156055018174737/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7423156055018174737/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:17	MarkDuplicates	Start of doWork freeMemory: 986604704; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:17	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:17	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:17	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:17	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:05:18	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932070712; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:18	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:18	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:18	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:18	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985545008; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:18	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:18	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:18	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:18	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:18	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:18	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:18	MarkDuplicates	Before output close freeMemory: 856382000; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:18	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:18	MarkDuplicates	After output close freeMemory: 853233200; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:18 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:18 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp649924277660184224/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp649924277660184224/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp649924277660184224/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:18	MarkDuplicates	Start of doWork freeMemory: 986604672; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:18	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:18	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:18	MarkDuplicates	Read 0 records. 0 pairs never matched.
INFO	2025-04-24 13:05:19	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932070968; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:19	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:19	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:19	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:19	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:19	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717113272; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:19	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:19	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:19	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:19	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:19	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:19	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:19	MarkDuplicates	Before output close freeMemory: 859528600; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:19	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:19	MarkDuplicates	After output close freeMemory: 859525528; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:19 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15961181722955916677/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15961181722955916677/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15961181722955916677/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:19	MarkDuplicates	Start of doWork freeMemory: 986603496; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:19	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:19	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:19	MarkDuplicates	Read 0 records. 0 pairs never matched.
INFO	2025-04-24 13:05:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932069992; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:20	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:20	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:20	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:20	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985547568; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:20	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:20	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:20	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:20	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:20	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:20	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:20	MarkDuplicates	Before output close freeMemory: 863721736; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:05:20	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:20	MarkDuplicates	After output close freeMemory: 863721312; totalMemory: 1220542464; maxMemory: 2147483648
[Thu Apr 24 13:05:20 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1220542464
[Thu Apr 24 13:05:20 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4449820951935425591/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4449820951935425591/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4449820951935425591/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:20	MarkDuplicates	Start of doWork freeMemory: 986490456; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:20	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:20	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:20	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 931926968; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:21	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:21	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:21	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:21	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:21	MarkDuplicates	After generateDuplicateIndexes freeMemory: 716969424; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:21	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:21	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:21	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:21	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:21	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:21	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:21	MarkDuplicates	Before output close freeMemory: 859325424; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:21	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:21	MarkDuplicates	After output close freeMemory: 859325000; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:21 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3971029272313180136/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3971029272313180136/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3971029272313180136/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:21	MarkDuplicates	Start of doWork freeMemory: 986590368; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:21	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:21	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:21	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:21	MarkDuplicates	Read 18 records. 0 pairs never matched.
INFO	2025-04-24 13:05:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932054232; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:22	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:22	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 778964320; totalMemory: 1405091840; maxMemory: 2147483648
INFO	2025-04-24 13:05:22	MarkDuplicates	Marking 12 records as duplicates.
INFO	2025-04-24 13:05:22	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:22	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:22	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:22	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:22	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:22	MarkDuplicates	Before output close freeMemory: 859513160; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:22	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:22	MarkDuplicates	After output close freeMemory: 853221280; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:22 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5170026202520022496/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5170026202520022496/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5170026202520022496/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:22	MarkDuplicates	Start of doWork freeMemory: 986597504; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:22	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:22	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:22	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:22	MarkDuplicates	Read 6 records. 0 pairs never matched.
INFO	2025-04-24 13:05:22	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932063032; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:23	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:23	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:23	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:23	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:23	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717105696; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:23	MarkDuplicates	Marking 4 records as duplicates.
INFO	2025-04-24 13:05:23	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:23	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:23	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:23	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:23	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:23	MarkDuplicates	Before output close freeMemory: 859520528; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:23	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:23	MarkDuplicates	After output close freeMemory: 856371728; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:23 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:23 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11971410120849350283/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11971410120849350283/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11971410120849350283/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:23	MarkDuplicates	Start of doWork freeMemory: 986596248; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:23	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:23	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:23	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:23	MarkDuplicates	Read 6 records. 0 pairs never matched.
INFO	2025-04-24 13:05:23	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932061792; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:23	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:24	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:24	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:24	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:24	MarkDuplicates	After generateDuplicateIndexes freeMemory: 772678672; totalMemory: 1398800384; maxMemory: 2147483648
INFO	2025-04-24 13:05:24	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:24	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:24	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:24	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:24	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:24	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:24	MarkDuplicates	Before output close freeMemory: 859518776; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:24	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:24	MarkDuplicates	After output close freeMemory: 853224248; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:24 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1023846307908418651/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1023846307908418651/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1023846307908418651/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:24	MarkDuplicates	Start of doWork freeMemory: 986591296; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:24	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:24	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:24	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:24	MarkDuplicates	Read 12 records. 0 pairs never matched.
INFO	2025-04-24 13:05:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932056000; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:24	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:25	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:25	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:25	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:25	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717099384; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:25	MarkDuplicates	Marking 8 records as duplicates.
INFO	2025-04-24 13:05:25	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:25	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:25	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:25	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:25	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:25	MarkDuplicates	Before output close freeMemory: 853222752; totalMemory: 1210056704; maxMemory: 2147483648
INFO	2025-04-24 13:05:25	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:25	MarkDuplicates	After output close freeMemory: 849025376; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:05:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:05:25 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2049527185883681267/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2049527185883681267/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2049527185883681267/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:25	MarkDuplicates	Start of doWork freeMemory: 986595912; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:25	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:25	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:25	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:25	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:25	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932061976; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:25	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:26	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:26	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:26	MarkDuplicates	After generateDuplicateIndexes freeMemory: 768484640; totalMemory: 1394606080; maxMemory: 2147483648
INFO	2025-04-24 13:05:26	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:26	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:26	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:26	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:26	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:26	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:26	MarkDuplicates	Before output close freeMemory: 856373792; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:26	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:26	MarkDuplicates	After output close freeMemory: 856370720; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:26 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1466717139282279202/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1466717139282279202/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1466717139282279202/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:26	MarkDuplicates	Start of doWork freeMemory: 986592336; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:26	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:26	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:26	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:26	MarkDuplicates	Read 8 records. 0 pairs never matched.
INFO	2025-04-24 13:05:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932057520; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:26	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:27	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:27	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717100424; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:27	MarkDuplicates	Marking 4 records as duplicates.
INFO	2025-04-24 13:05:27	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:27	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:27	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:27	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:27	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:27	MarkDuplicates	Before output close freeMemory: 863709552; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:05:27	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:27	MarkDuplicates	After output close freeMemory: 859512176; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:27 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:27 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9072007399716826323/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9072007399716826323/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9072007399716826323/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:27	MarkDuplicates	Start of doWork freeMemory: 986595448; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:27	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:27	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:27	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:27	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:05:27	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932061656; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:27	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:27	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 768484160; totalMemory: 1394606080; maxMemory: 2147483648
INFO	2025-04-24 13:05:28	MarkDuplicates	Marking 1 records as duplicates.
INFO	2025-04-24 13:05:28	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:28	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:28	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:28	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:28	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:28	MarkDuplicates	Before output close freeMemory: 853227592; totalMemory: 1210056704; maxMemory: 2147483648
INFO	2025-04-24 13:05:28	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:28	MarkDuplicates	After output close freeMemory: 853224520; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:28 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11660845974124501691/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11660845974124501691/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11660845974124501691/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:28	MarkDuplicates	Start of doWork freeMemory: 986593192; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:28	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:28	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:28	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:28	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932058960; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:28	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:28	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:28	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:28	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717100928; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:29	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:29	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:29	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:29	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:29	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:29	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:29	MarkDuplicates	Before output close freeMemory: 859516024; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:29	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:29	MarkDuplicates	After output close freeMemory: 853224144; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:29 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:29 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4629385109064828444/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4629385109064828444/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4629385109064828444/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:29	MarkDuplicates	Start of doWork freeMemory: 986592520; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:29	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:29	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:29	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:29	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932058304; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:29	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:29	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:30	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1145968312; totalMemory: 1772093440; maxMemory: 2147483648
INFO	2025-04-24 13:05:30	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:30	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:30	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:30	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:30	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:30	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:30	MarkDuplicates	Before output close freeMemory: 866855576; totalMemory: 1223688192; maxMemory: 2147483648
INFO	2025-04-24 13:05:30	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:30	MarkDuplicates	After output close freeMemory: 866855152; totalMemory: 1223688192; maxMemory: 2147483648
[Thu Apr 24 13:05:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1223688192
[Thu Apr 24 13:05:30 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5716946053216611991/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5716946053216611991/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5716946053216611991/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:30	MarkDuplicates	Start of doWork freeMemory: 986591712; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:30	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:30	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:30	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:30	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:30	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932057480; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:30	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:30	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:30	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:30	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:31	MarkDuplicates	After generateDuplicateIndexes freeMemory: 716051328; totalMemory: 1342177280; maxMemory: 2147483648
INFO	2025-04-24 13:05:31	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:31	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:31	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:31	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:31	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:31	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:31	MarkDuplicates	Before output close freeMemory: 853223272; totalMemory: 1210056704; maxMemory: 2147483648
INFO	2025-04-24 13:05:31	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:31	MarkDuplicates	After output close freeMemory: 849028544; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:05:31 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:05:31 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11744150073132467729/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11744150073132467729/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11744150073132467729/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:31 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:31	MarkDuplicates	Start of doWork freeMemory: 986590656; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:31	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:31	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:31	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:31	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932056424; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:31	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:31	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717098392; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:32	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:32	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:32	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:32	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:32	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:32	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:32	MarkDuplicates	Before output close freeMemory: 859513680; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:32	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:32	MarkDuplicates	After output close freeMemory: 856364880; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:32 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14164665599239800669/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14164665599239800669/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14164665599239800669/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:32 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:32	MarkDuplicates	Start of doWork freeMemory: 986589112; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:32	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:32	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:32	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:32	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:32	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932054896; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:32	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:32	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:33	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985532776; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:33	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:33	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:33	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:33	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:33	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:33	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:33	MarkDuplicates	Before output close freeMemory: 863706584; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:05:33	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:33	MarkDuplicates	After output close freeMemory: 849026096; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:05:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:05:33 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4693753651605165378/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4693753651605165378/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4693753651605165378/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:33	MarkDuplicates	Start of doWork freeMemory: 986588392; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:33	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:33	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:33	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:33	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:33	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932054176; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:33	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:33	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:33	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:33	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717096600; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:33	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:33	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:33	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:33	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:33	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:33	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:34	MarkDuplicates	Before output close freeMemory: 856366048; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:34	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:34	MarkDuplicates	After output close freeMemory: 856362976; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:34 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8504268676789538620/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8504268676789538620/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8504268676789538620/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:34	MarkDuplicates	Start of doWork freeMemory: 986587088; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:34	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:34	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:34	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:34	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932052872; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:34	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:34	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:34	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:34	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717095296; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:34	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:34	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:34	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:34	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:34	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:34	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:35	MarkDuplicates	Before output close freeMemory: 859510472; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:35	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:35	MarkDuplicates	After output close freeMemory: 853218520; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:35 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:35 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15315529855215739859/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15315529855215739859/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15315529855215739859/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:35	MarkDuplicates	Start of doWork freeMemory: 986587032; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:35	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:35	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:35	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:35	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932052816; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:35	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:35	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717094784; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:35	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:35	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:35	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:35	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:35	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:35	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:36	MarkDuplicates	Before output close freeMemory: 859509888; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:36	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:36	MarkDuplicates	After output close freeMemory: 856361016; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:36 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:36 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13231557751424580982/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13231557751424580982/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13231557751424580982/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:36	MarkDuplicates	Start of doWork freeMemory: 986585888; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:36	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:36	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:36	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:36	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:36	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932051656; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:36	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:36	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:36	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:36	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:36	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985526464; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:36	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:36	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:36	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:36	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:36	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:36	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:37	MarkDuplicates	Before output close freeMemory: 856362944; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:37	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:37	MarkDuplicates	After output close freeMemory: 856359872; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:37 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2875113876763416684/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2875113876763416684/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2875113876763416684/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:37	MarkDuplicates	Start of doWork freeMemory: 986585016; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:37	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:37	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:37	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:37	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932050784; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:37	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:37	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:37	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:37	MarkDuplicates	After generateDuplicateIndexes freeMemory: 986577240; totalMemory: 1612709888; maxMemory: 2147483648
INFO	2025-04-24 13:05:37	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:37	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:37	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:37	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:37	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:37	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:38	MarkDuplicates	Before output close freeMemory: 859507848; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:38	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:38	MarkDuplicates	After output close freeMemory: 856359048; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:38 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12455113249775410931/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12455113249775410931/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12455113249775410931/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:38 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:38	MarkDuplicates	Start of doWork freeMemory: 986584048; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:38	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:38	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:38	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:38	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932049816; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:38	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:38	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:38	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:38	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 577628528; totalMemory: 1203765248; maxMemory: 2147483648
INFO	2025-04-24 13:05:38	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:38	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:38	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:38	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:38	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:38	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:38	MarkDuplicates	Before output close freeMemory: 846923976; totalMemory: 1203765248; maxMemory: 2147483648
INFO	2025-04-24 13:05:38	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:39	MarkDuplicates	After output close freeMemory: 846920904; totalMemory: 1203765248; maxMemory: 2147483648
[Thu Apr 24 13:05:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1203765248
[Thu Apr 24 13:05:39 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1467084527998625752/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1467084527998625752/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1467084527998625752/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:39 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:39	MarkDuplicates	Start of doWork freeMemory: 986583128; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:39	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:39	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:39	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:39	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932048912; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:39	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:39	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717088224; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:39	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:39	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:39	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:39	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:39	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:39	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:39	MarkDuplicates	Before output close freeMemory: 859505920; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:39	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:40	MarkDuplicates	After output close freeMemory: 853211392; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:40 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16893283105583430554/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16893283105583430554/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16893283105583430554/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:40 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:40	MarkDuplicates	Start of doWork freeMemory: 986583432; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:40	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:40	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:40	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:40	MarkDuplicates	Read 2 records. 2 pairs never matched.
INFO	2025-04-24 13:05:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932049520; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:40	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:40	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:40	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717091344; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:40	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:40	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:40	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:40	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:40	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:40	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:40	MarkDuplicates	Before output close freeMemory: 853215112; totalMemory: 1210056704; maxMemory: 2147483648
INFO	2025-04-24 13:05:40	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:41	MarkDuplicates	After output close freeMemory: 849020384; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:05:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:05:41 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17102341359307635698/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17102341359307635698/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17102341359307635698/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:41 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:41	MarkDuplicates	Start of doWork freeMemory: 986579872; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:41	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:41	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:41	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:41	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932045592; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:41	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:41	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:41	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:41	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:41	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717087864; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:41	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:41	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:41	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:41	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:41	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:41	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:41	MarkDuplicates	Before output close freeMemory: 856356760; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:41	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:41	MarkDuplicates	After output close freeMemory: 853207960; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:05:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:05:41 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4721920575636366950/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4721920575636366950/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4721920575636366950/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:41 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:42	MarkDuplicates	Start of doWork freeMemory: 986579088; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:42	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:42	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:42	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:42	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932044792; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:42	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:42	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:42	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:42	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:42	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717087064; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:42	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:42	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:42	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:42	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:42	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:42	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:42	MarkDuplicates	Before output close freeMemory: 859501696; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:42	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:42	MarkDuplicates	After output close freeMemory: 856352824; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:42 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2129363431034420923/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2129363431034420923/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2129363431034420923/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:42 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:43	MarkDuplicates	Start of doWork freeMemory: 986578384; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:43	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:43	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:43	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:43	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932041256; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:43	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:43	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:43	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:43	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985518704; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:43	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:43	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:43	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:43	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:43	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:43	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:43	MarkDuplicates	Before output close freeMemory: 859500992; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:05:43	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:43	MarkDuplicates	After output close freeMemory: 859497920; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:44 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12766434977266958908/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12766434977266958908/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12766434977266958908/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:44 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:44	MarkDuplicates	Start of doWork freeMemory: 986577680; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:44	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:44	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:44	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:44	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932043216; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:44	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:44	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 768465896; totalMemory: 1394606080; maxMemory: 2147483648
INFO	2025-04-24 13:05:44	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:44	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:44	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:44	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:44	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:44	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:44	MarkDuplicates	Before output close freeMemory: 856354568; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:44	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:44	MarkDuplicates	After output close freeMemory: 856354416; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:44 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16628270717090668305/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16628270717090668305/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16628270717090668305/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:44 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:45	MarkDuplicates	Start of doWork freeMemory: 986576984; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:45	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:45	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:45	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932042520; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:45	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:45	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:45	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985520432; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:05:45	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:45	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:45	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:45	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:45	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:45	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:45	MarkDuplicates	Before output close freeMemory: 856353872; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:45	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:45	MarkDuplicates	After output close freeMemory: 856353448; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:46 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12597134417524408920/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12597134417524408920/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12597134417524408920/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:46 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:46	MarkDuplicates	Start of doWork freeMemory: 986576288; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:46	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:46	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:46	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932041824; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:46	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:46	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:46	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:46	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:46	MarkDuplicates	After generateDuplicateIndexes freeMemory: 775804536; totalMemory: 1401946112; maxMemory: 2147483648
INFO	2025-04-24 13:05:46	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:46	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:46	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:46	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:46	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:46	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:46	MarkDuplicates	Before output close freeMemory: 856353176; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:46	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:46	MarkDuplicates	After output close freeMemory: 856350104; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:46 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:46 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13295102763324621362/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13295102763324621362/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13295102763324621362/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:46 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:47	MarkDuplicates	Start of doWork freeMemory: 986574592; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:47	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:47	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:47	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:47	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932040296; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:47	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:47	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:47	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:47	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717079464; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:47	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:47	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:47	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:47	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:47	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:47	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:47	MarkDuplicates	Before output close freeMemory: 863691688; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:05:47	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:47	MarkDuplicates	After output close freeMemory: 859496960; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:47 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9304835939880778976/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9304835939880778976/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9304835939880778976/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:47 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:48	MarkDuplicates	Start of doWork freeMemory: 986573880; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:48	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:48	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:48	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932039600; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:48	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:48	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:48	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:48	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 772656400; totalMemory: 1398800384; maxMemory: 2147483648
INFO	2025-04-24 13:05:48	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:48	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:48	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:48	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:48	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:48	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:48	MarkDuplicates	Before output close freeMemory: 856350952; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:48	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:48	MarkDuplicates	After output close freeMemory: 856350488; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:48 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1968364125799835225/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1968364125799835225/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1968364125799835225/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:48 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:49	MarkDuplicates	Start of doWork freeMemory: 986573184; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:49	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:49	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:49	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932036016; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:49	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:49	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:49	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:49	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:49	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717080736; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:05:49	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:49	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:49	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:49	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:49	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:49	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:49	MarkDuplicates	Before output close freeMemory: 866836008; totalMemory: 1223688192; maxMemory: 2147483648
INFO	2025-04-24 13:05:49	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:49	MarkDuplicates	After output close freeMemory: 859492904; totalMemory: 1216348160; maxMemory: 2147483648
[Thu Apr 24 13:05:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:05:49 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17907731748672626539/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17907731748672626539/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17907731748672626539/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:49 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:50	MarkDuplicates	Start of doWork freeMemory: 986572480; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:50	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:50	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:50	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:50	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932035576; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:50	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:50	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:50	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:50	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:50	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1042139032; totalMemory: 1668284416; maxMemory: 2147483648
INFO	2025-04-24 13:05:50	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:50	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:50	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:50	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:50	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:50	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:50	MarkDuplicates	Before output close freeMemory: 856349552; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:50	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:50	MarkDuplicates	After output close freeMemory: 856349128; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:50 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17087263844350060088/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17087263844350060088/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17087263844350060088/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:51	MarkDuplicates	Start of doWork freeMemory: 986571784; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:51	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:51	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:51	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:51	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932037304; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:51	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:51	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:51	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:51	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:51	MarkDuplicates	After generateDuplicateIndexes freeMemory: 576570120; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:05:51	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:51	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:51	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:51	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:51	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:51	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:51	MarkDuplicates	Before output close freeMemory: 845863088; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:05:51	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:51	MarkDuplicates	After output close freeMemory: 845860016; totalMemory: 1202716672; maxMemory: 2147483648
[Thu Apr 24 13:05:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1202716672
[Thu Apr 24 13:05:51 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16641347816766720452/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16641347816766720452/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16641347816766720452/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:51	MarkDuplicates	Start of doWork freeMemory: 986571080; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:51	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:51	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:51	MarkDuplicates	Read 5 records. 0 pairs never matched.
INFO	2025-04-24 13:05:52	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932036800; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:52	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:52	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:52	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:52	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1052623392; totalMemory: 1678770176; maxMemory: 2147483648
INFO	2025-04-24 13:05:52	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:52	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:52	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:52	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:52	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:52	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:52	MarkDuplicates	Before output close freeMemory: 863688184; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:05:52	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:52	MarkDuplicates	After output close freeMemory: 856347728; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:52 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6294233343607922451/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6294233343607922451/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6294233343607922451/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:52	MarkDuplicates	Start of doWork freeMemory: 986572568; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:52	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:52	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:52	MarkDuplicates	Read 0 records. 0 pairs never matched.
INFO	2025-04-24 13:05:53	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932038880; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:53	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:53	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:53	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:53	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:53	MarkDuplicates	After generateDuplicateIndexes freeMemory: 576568896; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:05:53	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:53	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:53	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:53	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:53	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:53	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:53	MarkDuplicates	Before output close freeMemory: 845865016; totalMemory: 1202716672; maxMemory: 2147483648
INFO	2025-04-24 13:05:53	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:53	MarkDuplicates	After output close freeMemory: 845864520; totalMemory: 1202716672; maxMemory: 2147483648
[Thu Apr 24 13:05:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1202716672
[Thu Apr 24 13:05:53 EDT 2025] MarkDuplicates --ADD_PG_TAG_TO_READS true --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MarkDuplicates/merge1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MarkDuplicates/merge2.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MarkDuplicates/merge3.sam --OUTPUT /tmp/MarkDuplicates.tmp14598916492476715494/MarkDuplicates.sam --METRICS_FILE /tmp/MarkDuplicates.tmp14598916492476715494/MarkDuplicates.duplicate_metrics --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:53	MarkDuplicates	Start of doWork freeMemory: 986577008; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:53	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:53	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:05:53	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2025-04-24 13:05:53	MarkDuplicates	Read 6 records. 0 pairs never matched.
INFO	2025-04-24 13:05:54	MarkDuplicates	After buildSortedReadEndLists freeMemory: 923653024; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:54	MarkDuplicates	Will retain up to 67108864 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:54	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:54	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:54	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:54	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985516656; totalMemory: 1610612736; maxMemory: 2147483648
INFO	2025-04-24 13:05:54	MarkDuplicates	Marking 4 records as duplicates.
INFO	2025-04-24 13:05:54	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:54	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:54	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:54	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:54	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:54	MarkDuplicates	Before output close freeMemory: 986280080; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:54	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:54	MarkDuplicates	After output close freeMemory: 986277152; totalMemory: 1073741824; maxMemory: 2147483648
[Thu Apr 24 13:05:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:05:54 EDT 2025] MarkDuplicates --ADD_PG_TAG_TO_READS true --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MarkDuplicates/merge1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MarkDuplicates/merge2.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MarkDuplicates/merge3.sam --OUTPUT /tmp/MarkDuplicates.tmp15066552959357322905/MarkDuplicates.sam --METRICS_FILE /tmp/MarkDuplicates.tmp15066552959357322905/MarkDuplicates.duplicate_metrics  --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:54	MarkDuplicates	Start of doWork freeMemory: 986576096; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:54	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:54	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
WARNING	2025-04-24 13:05:54	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2025-04-24 13:05:54	MarkDuplicates	Read 6 records. 0 pairs never matched.
INFO	2025-04-24 13:05:55	MarkDuplicates	After buildSortedReadEndLists freeMemory: 923652288; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:55	MarkDuplicates	Will retain up to 67108864 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:55	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:55	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:55	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985519184; totalMemory: 1610612736; maxMemory: 2147483648
INFO	2025-04-24 13:05:55	MarkDuplicates	Marking 4 records as duplicates.
INFO	2025-04-24 13:05:55	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:55	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:55	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:55	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:55	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:55	MarkDuplicates	Before output close freeMemory: 986280824; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:55	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:55	MarkDuplicates	After output close freeMemory: 986280328; totalMemory: 1073741824; maxMemory: 2147483648
[Thu Apr 24 13:05:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 13:05:55	MarkDuplicates	Start of doWork freeMemory: 986595152; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:55	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:55	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
INFO	2025-04-24 13:05:55	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 923671472; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:56	MarkDuplicates	Will retain up to 67108864 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:56	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985537584; totalMemory: 1610612736; maxMemory: 2147483648
INFO	2025-04-24 13:05:56	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:56	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:56	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:56	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:56	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:56	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:56	MarkDuplicates	Before output close freeMemory: 986402304; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:56	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:56	MarkDuplicates	After output close freeMemory: 986399232; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:56	MarkDuplicates	Start of doWork freeMemory: 986594432; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:56	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:56	MarkDuplicates	Will retain up to 7780737 data points before spilling to disk.
INFO	2025-04-24 13:05:56	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:57	MarkDuplicates	After buildSortedReadEndLists freeMemory: 923673072; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:57	MarkDuplicates	Will retain up to 67108864 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:57	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:57	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:57	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:57	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985539640; totalMemory: 1610612736; maxMemory: 2147483648
INFO	2025-04-24 13:05:57	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:57	MarkDuplicates	Found 1 optical duplicate clusters.
INFO	2025-04-24 13:05:57	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:57	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:57	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:57	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:57	MarkDuplicates	Before output close freeMemory: 986401232; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:57	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:57	MarkDuplicates	After output close freeMemory: 986398160; totalMemory: 1073741824; maxMemory: 2147483648
[Thu Apr 24 13:05:57 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4911208455857522232/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4911208455857522232/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4911208455857522232/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:57	MarkDuplicates	Start of doWork freeMemory: 986563192; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:57	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:57	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:05:57	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:05:57	MarkDuplicates	Read 2 records. 2 pairs never matched.
INFO	2025-04-24 13:05:58	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932029224; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:58	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:58	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:58	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:58	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:58	MarkDuplicates	After generateDuplicateIndexes freeMemory: 877503632; totalMemory: 1503657984; maxMemory: 2147483648
INFO	2025-04-24 13:05:58	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:05:58	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:58	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:58	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:58	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:58	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:58	MarkDuplicates	Before output close freeMemory: 856340392; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:05:58	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:58	MarkDuplicates	After output close freeMemory: 856339968; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:05:58 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:05:58 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11505960217194865580/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11505960217194865580/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11505960217194865580/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:58	MarkDuplicates	Start of doWork freeMemory: 986559408; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:58	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:58	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:58	MarkDuplicates	Read 6 records. 0 pairs never matched.
INFO	2025-04-24 13:05:58	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932024704; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:59	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:05:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:05:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:05:59	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:05:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 716018800; totalMemory: 1342177280; maxMemory: 2147483648
INFO	2025-04-24 13:05:59	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:05:59	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:05:59	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:05:59	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:05:59	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:05:59	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:05:59	MarkDuplicates	Before output close freeMemory: 863676128; totalMemory: 1220542464; maxMemory: 2147483648
INFO	2025-04-24 13:05:59	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:05:59	MarkDuplicates	After output close freeMemory: 848992992; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:05:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:05:59 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2790923537669763745/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2790923537669763745/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2790923537669763745/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:05:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:05:59	MarkDuplicates	Start of doWork freeMemory: 986559928; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:05:59	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:05:59	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:05:59	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:05:59	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932025632; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:00	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:06:00	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:06:00	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:06:00	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:06:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717067360; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:06:00	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:06:00	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:06:00	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:06:00	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:06:00	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:06:00	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:06:00	MarkDuplicates	Before output close freeMemory: 856336848; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:06:00	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:06:00	MarkDuplicates	After output close freeMemory: 856336352; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:06:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:06:00 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12773831259504016866/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12773831259504016866/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12773831259504016866/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:06:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:06:00	MarkDuplicates	Start of doWork freeMemory: 986560592; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:00	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:06:00	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:06:00	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
INFO	2025-04-24 13:06:00	MarkDuplicates	Read 2 records. 0 pairs never matched.
INFO	2025-04-24 13:06:00	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932026816; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:00	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:06:01	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:06:01	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:06:01	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:06:01	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717065752; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:06:01	MarkDuplicates	Marking 1 records as duplicates.
INFO	2025-04-24 13:06:01	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:06:01	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:06:01	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:06:01	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:06:01	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:06:01	MarkDuplicates	Before output close freeMemory: 859484056; totalMemory: 1216348160; maxMemory: 2147483648
INFO	2025-04-24 13:06:01	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:06:01	MarkDuplicates	After output close freeMemory: 856337904; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:06:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:06:01 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_ONE_BARCODE_TAG BX --READ_TWO_BARCODE_TAG BX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11619908446091283358/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11619908446091283358/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11619908446091283358/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:06:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:06:01	MarkDuplicates	Start of doWork freeMemory: 986556504; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:01	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:06:01	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
INFO	2025-04-24 13:06:01	MarkDuplicates	Read 6 records. 0 pairs never matched.
INFO	2025-04-24 13:06:01	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932021968; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:02	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:06:02	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:06:02	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:06:02	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:06:02	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985499216; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:06:02	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:06:02	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:06:02	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:06:02	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:06:02	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:06:02	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:06:02	MarkDuplicates	Before output close freeMemory: 856333112; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:06:02	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:06:02	MarkDuplicates	After output close freeMemory: 856330040; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:06:02 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432
[Thu Apr 24 13:06:02 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI false --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1447630769038144938/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1447630769038144938/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1447630769038144938/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:06:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:06:02	MarkDuplicates	Start of doWork freeMemory: 986554216; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:02	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:06:02	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:06:02	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number.
INFO	2025-04-24 13:06:02	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:06:02	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932020160; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:02	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:06:03	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:06:03	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:06:03	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:06:03	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717061888; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:06:03	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:06:03	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:06:03	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:06:03	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:06:03	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:06:03	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:06:03	MarkDuplicates	Before output close freeMemory: 856331840; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:06:03	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:06:03	MarkDuplicates	After output close freeMemory: 853183040; totalMemory: 1210056704; maxMemory: 2147483648
[Thu Apr 24 13:06:03 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1210056704
[Thu Apr 24 13:06:03 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI false --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7120701200248249214/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7120701200248249214/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7120701200248249214/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:06:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:06:03	MarkDuplicates	Start of doWork freeMemory: 986553768; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:03	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:06:03	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:06:03	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number.
INFO	2025-04-24 13:06:03	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:06:03	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932019536; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:03	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:06:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:06:04	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:06:04	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:06:04	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717061264; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:06:04	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:06:04	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:06:04	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:06:04	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:06:04	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:06:04	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:06:04	MarkDuplicates	Before output close freeMemory: 848991192; totalMemory: 1205862400; maxMemory: 2147483648
INFO	2025-04-24 13:06:04	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:06:04	MarkDuplicates	After output close freeMemory: 848988120; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:06:04 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:06:04 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI true --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3467955636481138456/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3467955636481138456/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3467955636481138456/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:06:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:06:04	MarkDuplicates	Start of doWork freeMemory: 986553048; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:04	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:06:04	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:06:04	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number.
INFO	2025-04-24 13:06:04	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:06:04	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932017624; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:04	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:06:05	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:06:05	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:06:05	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:06:05	MarkDuplicates	After generateDuplicateIndexes freeMemory: 985494888; totalMemory: 1611661312; maxMemory: 2147483648
INFO	2025-04-24 13:06:05	MarkDuplicates	Marking 2 records as duplicates.
INFO	2025-04-24 13:06:05	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:06:05	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:06:05	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:06:05	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:06:05	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:06:05	MarkDuplicates	Before output close freeMemory: 848989344; totalMemory: 1205862400; maxMemory: 2147483648
INFO	2025-04-24 13:06:05	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:06:05	MarkDuplicates	After output close freeMemory: 848986272; totalMemory: 1205862400; maxMemory: 2147483648
[Thu Apr 24 13:06:05 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1205862400
[Thu Apr 24 13:06:05 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI true --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11353630259124807190/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11353630259124807190/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11353630259124807190/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:06:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:06:05	MarkDuplicates	Start of doWork freeMemory: 986551200; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:05	MarkDuplicates	Reading input file and constructing read end information.
INFO	2025-04-24 13:06:05	MarkDuplicates	Will retain up to 6628035 data points before spilling to disk.
WARNING	2025-04-24 13:06:05	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number.
INFO	2025-04-24 13:06:05	MarkDuplicates	Read 4 records. 0 pairs never matched.
INFO	2025-04-24 13:06:05	MarkDuplicates	After buildSortedReadEndLists freeMemory: 932016968; totalMemory: 1073741824; maxMemory: 2147483648
INFO	2025-04-24 13:06:05	MarkDuplicates	Will retain up to 33554432 duplicate indices before spilling to disk.
INFO	2025-04-24 13:06:06	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2025-04-24 13:06:06	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2025-04-24 13:06:06	MarkDuplicates	Sorting list of duplicate records.
INFO	2025-04-24 13:06:06	MarkDuplicates	After generateDuplicateIndexes freeMemory: 717059392; totalMemory: 1343225856; maxMemory: 2147483648
INFO	2025-04-24 13:06:06	MarkDuplicates	Marking 0 records as duplicates.
INFO	2025-04-24 13:06:06	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2025-04-24 13:06:06	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2025-04-24 13:06:06	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2025-04-24 13:06:06	MarkDuplicates	Duplicate Index cleanup.
INFO	2025-04-24 13:06:06	MarkDuplicates	Getting Memory Stats.
INFO	2025-04-24 13:06:06	MarkDuplicates	Before output close freeMemory: 856328648; totalMemory: 1213202432; maxMemory: 2147483648
INFO	2025-04-24 13:06:06	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2025-04-24 13:06:06	MarkDuplicates	After output close freeMemory: 856325576; totalMemory: 1213202432; maxMemory: 2147483648
[Thu Apr 24 13:06:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1213202432