Class picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest
|
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