Class picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| pgRecordChainingTest[0](false, {1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7d87aa0c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7df41283], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1e29ac18], 1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@53903a78, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@13873dcc, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4e3a5535]}) | 1.015s | passed |
| pgRecordChainingTest[1](true, {1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@79fdee34], 1AAXX.3.1=[], 1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@360a57d2, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@68c67ccc]}) | 0.907s | passed |
| testBulkFragmentsNoDuplicates[0](.sam) | 1.481s | passed |
| testBulkFragmentsNoDuplicates[1](.bam) | 1.397s | passed |
| testBulkFragmentsNoDuplicates[2](.cram) | 1.847s | passed |
| testBulkFragmentsWithDuplicates[0](.sam) | 1.430s | passed |
| testBulkFragmentsWithDuplicates[1](.bam) | 1.437s | passed |
| testBulkFragmentsWithDuplicates[2](.cram) | 2.318s | passed |
| testBulkPairsNoDuplicates[0](.sam) | 1.454s | passed |
| testBulkPairsNoDuplicates[1](.bam) | 1.489s | passed |
| testBulkPairsNoDuplicates[2](.cram) | 2.518s | passed |
| testBulkPairsWithDuplicates[0](.sam) | 1.076s | passed |
| testBulkPairsWithDuplicates[1](.bam) | 1.044s | passed |
| testBulkPairsWithDuplicates[2](.cram) | 1.474s | passed |
| testDifferentChromosomesInOppositeOrder | 0.914s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 1.002s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.979s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.932s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.926s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.928s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.939s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.902s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.944s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.907s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.904s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.887s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.816s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.909s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.910s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.894s | passed |
| testMappedPairWithSamePosition | 0.943s | passed |
| testMappedPairWithSamePositionSameCigar | 1.001s | passed |
| testMatePairFirstUnmapped | 0.939s | passed |
| testMatePairSecondUnmapped | 0.937s | passed |
| testOpticalDuplicateBehaviorNullRegex | 0.946s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.926s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.929s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) | 0.930s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) | 0.995s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) | 0.907s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) | 0.939s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) | 0.928s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) | 0.930s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) | 0.966s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) | 0.991s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) | 0.913s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) | 0.928s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) | 0.944s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) | 0.960s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) | 1.007s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) | 0.920s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.955s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.880s | passed |
| testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) | 1.017s | passed |
| testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) | 0.912s | passed |
| testOpticalDuplicateFinding | 0.924s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.936s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.931s | passed |
| testSingleMappedFragment | 0.928s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.956s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.955s | passed |
| testSingleMappedPair | 1.057s | passed |
| testSingleUnmappedFragment | 0.968s | passed |
| testSingleUnmappedPair | 0.934s | passed |
| testStackOverFlowPairSetSwap | 0.952s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 1.025s | passed |
| testThreeMappedPairs | 0.995s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.994s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 1.002s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.981s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.969s | passed |
| testTwoMappedFragments | 0.938s | passed |
| testTwoMappedPairWithSamePosition | 0.930s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 1.007s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.908s | passed |
| testTwoMappedPairs | 0.909s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.901s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.947s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.889s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.987s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.900s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.875s | passed |
| testTwoMappedPairsWithSoftClipping | 0.907s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.919s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 0.837s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.950s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.934s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.936s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 1.014s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.923s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.937s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 1.014s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.929s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.937s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.896s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.924s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.924s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.957s | passed |
| testTwoUnmappedFragments | 0.962s | passed |
| testWithBarcodeComplex | 0.930s | passed |
| testWithBarcodeDuplicate | 0.913s | passed |
| testWithBarcodeFragmentDuplicate | 0.981s | passed |
| testWithIndividualReadBarcodes | 0.904s | passed |
| testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) | 0.935s | passed |
| testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) | 1.032s | passed |
| testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) | 0.923s | passed |
| testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) | 0.996s | passed |
Standard error
[Thu Apr 24 13:06:06 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16325043609966900219/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16325043609966900219/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16325043609966900219/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 13:06:06 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 13:06:06 MarkDuplicates Start of doWork freeMemory: 979613704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:06 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:06 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 13:06:06 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:06:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 915968584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:07 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 978557432; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:06:07 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:07 MarkDuplicates Before output close freeMemory: 873557880; totalMemory: 1237319680; maxMemory: 2147483648 INFO 2025-04-24 13:06:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:07 MarkDuplicates After output close freeMemory: 867408408; totalMemory: 1231028224; maxMemory: 2147483648 [Thu Apr 24 13:06:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1231028224 [Thu Apr 24 13:06:08 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16685584174860832197/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16685584174860832197/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16685584174860832197/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 13:06:08 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 13:06:08 MarkDuplicates Start of doWork freeMemory: 979612776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:08 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:08 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 13:06:08 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:06:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 915967304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:08 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 976459288; totalMemory: 1609564160; maxMemory: 2147483648 INFO 2025-04-24 13:06:08 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:08 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:08 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:09 MarkDuplicates Before output close freeMemory: 880892840; totalMemory: 1244659712; maxMemory: 2147483648 INFO 2025-04-24 13:06:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:09 MarkDuplicates After output close freeMemory: 870552624; totalMemory: 1234173952; maxMemory: 2147483648 [Thu Apr 24 13:06:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1234173952 [Thu Apr 24 13:06:09 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14853628134849033278/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14853628134849033278/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14853628134849033278/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester16328455264208033909/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 13:06:09 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 13:06:10 MarkDuplicates Start of doWork freeMemory: 979575392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:10 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:10 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 13:06:10 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:06:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 915932784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:10 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 795018424; totalMemory: 1428160512; maxMemory: 2147483648 INFO 2025-04-24 13:06:10 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:11 MarkDuplicates Before output close freeMemory: 873518944; totalMemory: 1237319680; maxMemory: 2147483648 INFO 2025-04-24 13:06:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:11 MarkDuplicates After output close freeMemory: 870512824; totalMemory: 1234173952; maxMemory: 2147483648 [Thu Apr 24 13:06:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1234173952 [Thu Apr 24 13:06:11 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3492993139928552259/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3492993139928552259/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3492993139928552259/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 13:06:11 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 13:06:11 MarkDuplicates Start of doWork freeMemory: 971383760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:11 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:11 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 13:06:11 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:06:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 906951664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:12 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 964000528; totalMemory: 1605369856; maxMemory: 2147483648 INFO 2025-04-24 13:06:12 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:06:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:12 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:12 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:12 MarkDuplicates Before output close freeMemory: 893600456; totalMemory: 1265631232; maxMemory: 2147483648 INFO 2025-04-24 13:06:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:12 MarkDuplicates After output close freeMemory: 886402840; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:06:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:06:12 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10567766835962572910/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10567766835962572910/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10567766835962572910/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 13:06:12 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 13:06:12 MarkDuplicates Start of doWork freeMemory: 971413256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:12 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:12 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 13:06:13 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:06:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 906980760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:13 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 1121354184; totalMemory: 1762656256; maxMemory: 2147483648 INFO 2025-04-24 13:06:13 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:06:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:13 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:13 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:13 MarkDuplicates Before output close freeMemory: 896812856; totalMemory: 1268776960; maxMemory: 2147483648 INFO 2025-04-24 13:06:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:13 MarkDuplicates After output close freeMemory: 886472680; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:06:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:06:14 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17972635733176296546/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17972635733176296546/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17972635733176296546/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester7557963135319121516/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 13:06:14 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 13:06:14 MarkDuplicates Start of doWork freeMemory: 971072584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:14 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:15 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 13:06:15 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:06:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 906638328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:15 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 862016096; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:06:15 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:06:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:15 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:15 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:16 MarkDuplicates Before output close freeMemory: 903813752; totalMemory: 1276116992; maxMemory: 2147483648 INFO 2025-04-24 13:06:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:16 MarkDuplicates After output close freeMemory: 886130280; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:06:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:06:16 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9475654164304430880/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9475654164304430880/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9475654164304430880/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 13:06:16 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 13:06:16 MarkDuplicates Start of doWork freeMemory: 970898240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:16 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:16 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 13:06:16 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:06:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 905790976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:17 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 946769928; totalMemory: 1588592640; maxMemory: 2147483648 INFO 2025-04-24 13:06:17 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:17 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:17 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:17 MarkDuplicates Before output close freeMemory: 882667440; totalMemory: 1255145472; maxMemory: 2147483648 INFO 2025-04-24 13:06:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:17 MarkDuplicates After output close freeMemory: 882809240; totalMemory: 1255145472; maxMemory: 2147483648 [Thu Apr 24 13:06:17 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1255145472 [Thu Apr 24 13:06:18 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2069853313024125581/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2069853313024125581/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2069853313024125581/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 13:06:18 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 13:06:18 MarkDuplicates Start of doWork freeMemory: 970894112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:18 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:18 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 13:06:18 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:06:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 905789800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:18 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 694064864; totalMemory: 1335885824; maxMemory: 2147483648 INFO 2025-04-24 13:06:18 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:18 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:18 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:19 MarkDuplicates Before output close freeMemory: 893150800; totalMemory: 1265631232; maxMemory: 2147483648 INFO 2025-04-24 13:06:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:19 MarkDuplicates After output close freeMemory: 893290944; totalMemory: 1265631232; maxMemory: 2147483648 [Thu Apr 24 13:06:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1265631232 [Thu Apr 24 13:06:20 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2023447080491521474/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2023447080491521474/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2023447080491521474/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester466478329415842157/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 13:06:20 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 13:06:20 MarkDuplicates Start of doWork freeMemory: 970605928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:20 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 13:06:20 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:06:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 905501872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:21 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 601499560; totalMemory: 1243611136; maxMemory: 2147483648 INFO 2025-04-24 13:06:21 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:21 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:21 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:21 MarkDuplicates Before output close freeMemory: 870840800; totalMemory: 1243611136; maxMemory: 2147483648 INFO 2025-04-24 13:06:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:21 MarkDuplicates After output close freeMemory: 870980520; totalMemory: 1243611136; maxMemory: 2147483648 [Thu Apr 24 13:06:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1243611136 [Thu Apr 24 13:06:21 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15351790565938876586/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15351790565938876586/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15351790565938876586/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 13:06:21 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 13:06:22 MarkDuplicates Start of doWork freeMemory: 981414664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:22 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:22 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 13:06:22 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:06:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 917755448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:22 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 800002936; totalMemory: 1431306240; maxMemory: 2147483648 INFO 2025-04-24 13:06:22 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:06:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:22 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:22 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:22 MarkDuplicates Before output close freeMemory: 864869064; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2025-04-24 13:06:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:22 MarkDuplicates After output close freeMemory: 865014392; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:06:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:06:23 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11157678899611852554/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11157678899611852554/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11157678899611852554/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 13:06:23 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 13:06:23 MarkDuplicates Start of doWork freeMemory: 981413464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:23 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:23 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 13:06:23 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:06:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 917753920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:23 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 787418800; totalMemory: 1418723328; maxMemory: 2147483648 INFO 2025-04-24 13:06:23 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:06:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:23 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:23 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:23 MarkDuplicates Before output close freeMemory: 864867248; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2025-04-24 13:06:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:23 MarkDuplicates After output close freeMemory: 865012944; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:06:23 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:06:24 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7388857064402123958/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7388857064402123958/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7388857064402123958/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester6410272833722072909/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 13:06:24 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 13:06:24 MarkDuplicates Start of doWork freeMemory: 981280072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:06:24 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 13:06:24 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:06:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 917625376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 980228328; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:06:25 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:06:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:25 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:25 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:25 MarkDuplicates Before output close freeMemory: 879422224; totalMemory: 1241513984; maxMemory: 2147483648 INFO 2025-04-24 13:06:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:25 MarkDuplicates After output close freeMemory: 869078184; totalMemory: 1231028224; maxMemory: 2147483648 [Thu Apr 24 13:06:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1231028224 [Thu Apr 24 13:06:25 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16150578473218259462/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16150578473218259462/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16150578473218259462/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 13:06:25 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 13:06:25 MarkDuplicates Start of doWork freeMemory: 986532496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:25 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 931998184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:25 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 717040000; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:26 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:26 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:06:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:26 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:26 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:26 MarkDuplicates Before output close freeMemory: 863698752; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:26 MarkDuplicates After output close freeMemory: 859646112; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:06:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:06:26 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3222664738303881527/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3222664738303881527/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3222664738303881527/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 13:06:26 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 13:06:26 MarkDuplicates Start of doWork freeMemory: 986525592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:26 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:26 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:06:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 931990592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:26 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 985469040; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:06:27 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:06:27 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:06:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:27 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:27 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:27 MarkDuplicates Before output close freeMemory: 856351864; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:06:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:27 MarkDuplicates After output close freeMemory: 856490856; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:27 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:27 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15336108812233228243/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15336108812233228243/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15336108812233228243/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 13:06:27 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 13:06:27 MarkDuplicates Start of doWork freeMemory: 986524848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:27 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:27 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:06:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 931989664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:27 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 986516448; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:06:28 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:06:28 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:06:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:28 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:28 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:28 MarkDuplicates Before output close freeMemory: 859496848; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:06:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:28 MarkDuplicates After output close freeMemory: 859638488; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:06:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:06:28 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13157533344300565136/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13157533344300565136/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13157533344300565136/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 13:06:28 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 13:06:28 MarkDuplicates Start of doWork freeMemory: 986524144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:28 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:28 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:06:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 931986296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:28 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 647825680; totalMemory: 1274019840; maxMemory: 2147483648 INFO 2025-04-24 13:06:29 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:06:29 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:06:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:29 MarkDuplicates Before output close freeMemory: 866836168; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:06:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:29 MarkDuplicates After output close freeMemory: 866977808; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:06:29 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:06:29 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11510317323543894538/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11510317323543894538/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11510317323543894538/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 13:06:29 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 13:06:29 MarkDuplicates Start of doWork freeMemory: 986523448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:29 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:29 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:29 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:06:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 931985576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:29 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 717028096; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:29 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:06:29 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:06:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:30 MarkDuplicates Before output close freeMemory: 863686472; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:30 MarkDuplicates After output close freeMemory: 859634704; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:06:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:06:30 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9641305022511426142/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9641305022511426142/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9641305022511426142/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 13:06:30 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 13:06:30 MarkDuplicates Start of doWork freeMemory: 986522752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:30 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:30 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:06:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 931987736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:30 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 717027384; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:30 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:06:30 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:06:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:30 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:30 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:31 MarkDuplicates Before output close freeMemory: 859494744; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:06:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:31 MarkDuplicates After output close freeMemory: 856487936; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:31 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:31 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15743423888181195923/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15743423888181195923/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15743423888181195923/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 13:06:31 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 13:06:31 MarkDuplicates Start of doWork freeMemory: 986522040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:31 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:31 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:06:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 931984192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:31 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 717026912; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:31 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:06:31 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:06:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:31 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:31 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:31 MarkDuplicates Before output close freeMemory: 853202576; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:06:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:32 MarkDuplicates After output close freeMemory: 853341568; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:06:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:06:32 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17348033521258897439/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17348033521258897439/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17348033521258897439/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 13:06:32 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 13:06:32 MarkDuplicates Start of doWork freeMemory: 986527920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:32 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:32 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 13:06:32 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:06:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 931994224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:32 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 775756680; totalMemory: 1401946112; maxMemory: 2147483648 INFO 2025-04-24 13:06:32 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:32 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:32 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:32 MarkDuplicates Before output close freeMemory: 863694912; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:32 MarkDuplicates After output close freeMemory: 859639696; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:06:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:06:33 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6597020584945248868/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6597020584945248868/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6597020584945248868/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 13:06:33 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 13:06:33 MarkDuplicates Start of doWork freeMemory: 986526920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:33 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:33 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 13:06:33 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:06:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 931993128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:33 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 717032064; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:33 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:06:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:33 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:33 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:33 MarkDuplicates Before output close freeMemory: 859499704; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:06:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:33 MarkDuplicates After output close freeMemory: 856492688; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:33 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12594114986506490981/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12594114986506490981/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12594114986506490981/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 13:06:33 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 13:06:34 MarkDuplicates Start of doWork freeMemory: 986526296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:34 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:34 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 13:06:34 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:06:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 931992504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:34 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 768415008; totalMemory: 1394606080; maxMemory: 2147483648 INFO 2025-04-24 13:06:34 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:06:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:34 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:34 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:34 MarkDuplicates Before output close freeMemory: 856353352; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:06:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:34 MarkDuplicates After output close freeMemory: 856492064; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:34 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10178455363994788658/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10178455363994788658/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10178455363994788658/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 13:06:34 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 13:06:34 MarkDuplicates Start of doWork freeMemory: 986524168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:34 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:35 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 13:06:35 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:06:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 931990032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:35 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 717029032; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:35 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:35 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:35 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:35 MarkDuplicates Before output close freeMemory: 853204992; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:06:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:35 MarkDuplicates After output close freeMemory: 853343920; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:06:35 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:06:35 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10153265019634310271/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10153265019634310271/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10153265019634310271/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 13:06:35 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 13:06:35 MarkDuplicates Start of doWork freeMemory: 986523248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:35 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:35 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 13:06:35 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:06:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 931989096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:36 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 1037892352; totalMemory: 1664090112; maxMemory: 2147483648 INFO 2025-04-24 13:06:36 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:36 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:36 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:36 MarkDuplicates Before output close freeMemory: 853204064; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:06:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:36 MarkDuplicates After output close freeMemory: 853342992; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:06:36 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:06:36 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18154460813906359582/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18154460813906359582/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18154460813906359582/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 13:06:36 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 13:06:36 MarkDuplicates Start of doWork freeMemory: 986522888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:36 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:36 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 13:06:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 931988832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:37 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 579666944; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:06:37 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:37 MarkDuplicates Before output close freeMemory: 849009360; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:06:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:37 MarkDuplicates After output close freeMemory: 849150984; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:06:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:06:37 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18209764918184362031/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18209764918184362031/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18209764918184362031/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 13:06:37 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 13:06:37 MarkDuplicates Start of doWork freeMemory: 986522240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:37 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 13:06:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 931988184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:37 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 772604976; totalMemory: 1398800384; maxMemory: 2147483648 INFO 2025-04-24 13:06:38 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:06:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:38 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:38 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:38 MarkDuplicates Before output close freeMemory: 856348792; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:06:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:38 MarkDuplicates After output close freeMemory: 849147688; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:06:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:06:38 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8603270027704588680/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8603270027704588680/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8603270027704588680/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 13:06:38 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 13:06:38 MarkDuplicates Start of doWork freeMemory: 986521448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:38 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:38 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 13:06:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 931987376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:38 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 717026296; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:39 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:06:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:39 MarkDuplicates Before output close freeMemory: 859493720; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:06:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:39 MarkDuplicates After output close freeMemory: 853341192; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:06:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:06:39 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16651708659168967498/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16651708659168967498/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16651708659168967498/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 13:06:39 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 13:06:39 MarkDuplicates Start of doWork freeMemory: 986520432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:39 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:39 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 13:06:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 931986216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:39 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 877460768; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:06:39 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:40 MarkDuplicates Before output close freeMemory: 863687016; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:40 MarkDuplicates After output close freeMemory: 856485912; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:40 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11852452428821801362/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11852452428821801362/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11852452428821801362/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 13:06:40 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 13:06:40 MarkDuplicates Start of doWork freeMemory: 986521000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:40 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 13:06:40 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:06:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 931987008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:40 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 717026088; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:40 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:40 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:40 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:40 MarkDuplicates Before output close freeMemory: 856347544; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:06:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:41 MarkDuplicates After output close freeMemory: 856486472; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:41 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6535477952068458313/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6535477952068458313/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6535477952068458313/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 13:06:41 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 13:06:41 MarkDuplicates Start of doWork freeMemory: 986520184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:41 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:41 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 13:06:41 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:06:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 931986208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:41 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 985460504; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:06:41 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:41 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:41 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:41 MarkDuplicates Before output close freeMemory: 863686768; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:42 MarkDuplicates After output close freeMemory: 853339936; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:06:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:06:42 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10089573694412858850/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10089573694412858850/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10089573694412858850/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 13:06:42 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 13:06:42 MarkDuplicates Start of doWork freeMemory: 986519536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:42 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:42 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 13:06:42 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:06:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 931985256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:42 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 579661224; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:06:42 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:42 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:42 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:42 MarkDuplicates Before output close freeMemory: 849006456; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:06:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:43 MarkDuplicates After output close freeMemory: 849147920; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:06:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:06:43 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2287866848558257012/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2287866848558257012/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2287866848558257012/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 13:06:43 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 13:06:43 MarkDuplicates Start of doWork freeMemory: 986518832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:43 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:06:43 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 13:06:43 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:06:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 931985136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:43 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 717023992; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:43 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:06:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:43 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:43 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:43 MarkDuplicates Before output close freeMemory: 856345912; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:06:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:43 MarkDuplicates After output close freeMemory: 856484608; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:44 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17684789179230212067/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17684789179230212067/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17684789179230212067/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 13:06:44 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 13:06:44 MarkDuplicates Start of doWork freeMemory: 986516760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:44 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 931982544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:44 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 717021800; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:44 MarkDuplicates Marking 2 records as duplicates. WARNING 2025-04-24 13:06:44 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! INFO 2025-04-24 13:06:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:44 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:44 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:44 MarkDuplicates Before output close freeMemory: 859489232; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:06:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:44 MarkDuplicates After output close freeMemory: 859630744; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:06:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:06:44 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17447526565129579721/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17447526565129579721/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17447526565129579721/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 13:06:44 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 13:06:45 MarkDuplicates Start of doWork freeMemory: 986515584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 931981304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:45 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 717020232; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:45 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:45 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:06:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:45 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:45 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:45 MarkDuplicates Before output close freeMemory: 853196104; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:06:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:45 MarkDuplicates After output close freeMemory: 853337696; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:06:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:06:45 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14137553791179690933/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14137553791179690933/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14137553791179690933/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 13:06:45 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 13:06:46 MarkDuplicates Start of doWork freeMemory: 986513696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 931976544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:46 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 717021840; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:46 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:46 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:46 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:46 MarkDuplicates Before output close freeMemory: 859485472; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:06:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:46 MarkDuplicates After output close freeMemory: 856482256; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:46 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:46 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13894643979134125269/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13894643979134125269/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13894643979134125269/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 13:06:46 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 13:06:46 MarkDuplicates Start of doWork freeMemory: 986511776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 931974608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:47 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 717016832; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:47 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:47 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:47 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:47 MarkDuplicates Before output close freeMemory: 863678224; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:47 MarkDuplicates After output close freeMemory: 856477112; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:47 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10816055573604335689/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10816055573604335689/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10816055573604335689/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 13:06:47 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 13:06:47 MarkDuplicates Start of doWork freeMemory: 986511080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:47 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 931976800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:48 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 717016112; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:48 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:48 MarkDuplicates Before output close freeMemory: 859483232; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:06:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:48 MarkDuplicates After output close freeMemory: 856479080; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:48 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1895588843204707023/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1895588843204707023/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1895588843204707023/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 13:06:48 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 13:06:48 MarkDuplicates Start of doWork freeMemory: 986510392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:48 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 931973488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:49 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 985453296; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:06:49 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:49 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:49 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:49 MarkDuplicates Before output close freeMemory: 863676848; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:49 MarkDuplicates After output close freeMemory: 853330008; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:06:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:06:49 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15930591320752990451/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15930591320752990451/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15930591320752990451/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 13:06:49 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 13:06:49 MarkDuplicates Start of doWork freeMemory: 986509376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:49 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 931974912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:50 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 579650720; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:06:50 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:50 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:50 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:50 MarkDuplicates Before output close freeMemory: 848995768; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:06:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:50 MarkDuplicates After output close freeMemory: 849134688; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:06:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:06:50 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9844274821460508263/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9844274821460508263/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9844274821460508263/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 13:06:50 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 13:06:50 MarkDuplicates Start of doWork freeMemory: 986508688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 931974208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:51 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 717013472; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:51 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:51 MarkDuplicates Before output close freeMemory: 863675136; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:51 MarkDuplicates After output close freeMemory: 856476680; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:51 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14319881987959963540/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14319881987959963540/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14319881987959963540/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 13:06:51 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 13:06:51 MarkDuplicates Start of doWork freeMemory: 986507992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:51 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 931973696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:52 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 778882104; totalMemory: 1405091840; maxMemory: 2147483648 INFO 2025-04-24 13:06:52 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:52 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:52 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:52 MarkDuplicates Before output close freeMemory: 859480136; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:06:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:52 MarkDuplicates After output close freeMemory: 856473400; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:52 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9734063391791081543/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9734063391791081543/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9734063391791081543/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 13:06:52 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 13:06:52 MarkDuplicates Start of doWork freeMemory: 986507296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:52 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:52 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 931973016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:52 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 717012096; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:53 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:53 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:53 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:53 MarkDuplicates Before output close freeMemory: 863673752; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:53 MarkDuplicates After output close freeMemory: 859618368; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:06:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:06:53 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11232776534394858590/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11232776534394858590/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11232776534394858590/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 13:06:53 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 13:06:53 MarkDuplicates Start of doWork freeMemory: 986506608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:53 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 931972312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:54 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 1045215704; totalMemory: 1671430144; maxMemory: 2147483648 INFO 2025-04-24 13:06:54 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:54 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:54 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:54 MarkDuplicates Before output close freeMemory: 863673056; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:54 MarkDuplicates After output close freeMemory: 863812048; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:06:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:06:54 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13181976140933187148/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13181976140933187148/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13181976140933187148/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 13:06:54 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 13:06:54 MarkDuplicates Start of doWork freeMemory: 986505912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:54 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 931971432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:54 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 569161480; totalMemory: 1195376640; maxMemory: 2147483648 INFO 2025-04-24 13:06:55 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:55 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:55 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:55 MarkDuplicates Before output close freeMemory: 838506536; totalMemory: 1195376640; maxMemory: 2147483648 INFO 2025-04-24 13:06:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:55 MarkDuplicates After output close freeMemory: 838645528; totalMemory: 1195376640; maxMemory: 2147483648 [Thu Apr 24 13:06:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1195376640 [Thu Apr 24 13:06:55 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15857000106298748717/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15857000106298748717/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15857000106298748717/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 13:06:55 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 13:06:55 MarkDuplicates Start of doWork freeMemory: 986505312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:55 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 931971016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:55 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 1042072000; totalMemory: 1668284416; maxMemory: 2147483648 INFO 2025-04-24 13:06:56 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:56 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:56 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:56 MarkDuplicates Before output close freeMemory: 856331728; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:06:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:56 MarkDuplicates After output close freeMemory: 853324992; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:06:56 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:06:56 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4782764535471222129/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4782764535471222129/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4782764535471222129/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 13:06:56 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 13:06:56 MarkDuplicates Start of doWork freeMemory: 986504592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:56 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 931970128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:56 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 579645936; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:06:56 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:56 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:56 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:57 MarkDuplicates Before output close freeMemory: 848990984; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:06:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:57 MarkDuplicates After output close freeMemory: 849129904; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:06:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:06:57 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12429632372927147072/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12429632372927147072/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12429632372927147072/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 13:06:57 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 13:06:57 MarkDuplicates Start of doWork freeMemory: 986503904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:57 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:57 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 931966752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:57 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 775732304; totalMemory: 1401946112; maxMemory: 2147483648 INFO 2025-04-24 13:06:57 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:57 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:57 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:58 MarkDuplicates Before output close freeMemory: 863670360; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:06:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:58 MarkDuplicates After output close freeMemory: 859614976; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:06:58 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:06:58 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10788158750866472195/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10788158750866472195/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10788158750866472195/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 13:06:58 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 13:06:58 MarkDuplicates Start of doWork freeMemory: 986503216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:58 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 931966064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:58 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 717008016; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:06:58 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:58 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:58 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:58 MarkDuplicates Before output close freeMemory: 856329640; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:06:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:06:59 MarkDuplicates After output close freeMemory: 856468632; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:06:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:06:59 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8283052091231226324/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8283052091231226324/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8283052091231226324/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 13:06:59 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 13:06:59 MarkDuplicates Start of doWork freeMemory: 986502552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:59 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:06:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:06:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:06:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 931968256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:06:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:06:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:06:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:06:59 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:06:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 778876664; totalMemory: 1405091840; maxMemory: 2147483648 INFO 2025-04-24 13:06:59 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:06:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:06:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:06:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:06:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:06:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:06:59 MarkDuplicates Before output close freeMemory: 866814728; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:06:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:00 MarkDuplicates After output close freeMemory: 863807992; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:07:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:07:00 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5503086851262808415/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5503086851262808415/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5503086851262808415/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 13:07:00 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 13:07:00 MarkDuplicates Start of doWork freeMemory: 986502272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:00 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 931965120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:00 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 717007192; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:00 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:00 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:00 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:00 MarkDuplicates Before output close freeMemory: 859471104; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:01 MarkDuplicates After output close freeMemory: 853324952; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:01 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12567205757057420477/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12567205757057420477/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12567205757057420477/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 13:07:01 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 13:07:01 MarkDuplicates Start of doWork freeMemory: 986501256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:01 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:01 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:01 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 931966976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:01 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 877441376; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:07:01 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:01 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:01 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:01 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:01 MarkDuplicates Before output close freeMemory: 856327568; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:01 MarkDuplicates After output close freeMemory: 849126488; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:07:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:07:01 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17046300370906455266/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17046300370906455266/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17046300370906455266/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 13:07:01 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 13:07:02 MarkDuplicates Start of doWork freeMemory: 986499456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:02 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:02 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:07:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 931964760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:02 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 717004112; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:02 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:07:02 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:02 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:02 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:02 MarkDuplicates Before output close freeMemory: 863665464; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:07:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:02 MarkDuplicates After output close freeMemory: 859613136; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:02 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:02 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9641684993550605268/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9641684993550605268/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9641684993550605268/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 13:07:02 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 13:07:02 MarkDuplicates Start of doWork freeMemory: 986499632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:02 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 931965336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:03 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 717007608; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:03 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:03 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:03 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:03 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:03 MarkDuplicates Before output close freeMemory: 859468440; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:03 MarkDuplicates After output close freeMemory: 859613760; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:03 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:03 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15929553919117146909/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15929553919117146909/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15929553919117146909/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 13:07:03 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 13:07:03 MarkDuplicates Start of doWork freeMemory: 986500088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:03 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:03 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 13:07:03 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:07:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 931966096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:04 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 717008280; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:04 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:04 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:04 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:04 MarkDuplicates Before output close freeMemory: 856326648; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:04 MarkDuplicates After output close freeMemory: 856465488; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:04 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:04 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1308607160686713582/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1308607160686713582/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1308607160686713582/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 13:07:04 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 13:07:04 MarkDuplicates Start of doWork freeMemory: 986500032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:04 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:04 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 13:07:04 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2025-04-24 13:07:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 931966320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:05 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 717005208; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:05 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:05 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:05 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:05 MarkDuplicates Before output close freeMemory: 863667088; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:07:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:05 MarkDuplicates After output close freeMemory: 853320104; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:05 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:05 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7070012212131045480/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7070012212131045480/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7070012212131045480/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 13:07:05 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 13:07:05 MarkDuplicates Start of doWork freeMemory: 986498064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:05 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:05 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 13:07:05 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:07:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 931963992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:06 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 717002944; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:06 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:07:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:06 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:06 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:06 MarkDuplicates Before output close freeMemory: 859470408; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:06 MarkDuplicates After output close freeMemory: 859609288; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:06 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1754924551980680996/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1754924551980680996/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1754924551980680996/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 13:07:06 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 13:07:06 MarkDuplicates Start of doWork freeMemory: 986495896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:06 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:06 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 13:07:06 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 931961600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:07 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 717004104; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:07 MarkDuplicates Marking 3 records as duplicates. INFO 2025-04-24 13:07:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:07 MarkDuplicates Before output close freeMemory: 856322520; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:07 MarkDuplicates After output close freeMemory: 853315680; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:07 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1721332112783162603/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1721332112783162603/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1721332112783162603/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 13:07:07 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 13:07:07 MarkDuplicates Start of doWork freeMemory: 986497056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:07 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:07 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 13:07:07 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:07:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 931963064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:08 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 985437392; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:07:08 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:08 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:08 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:08 MarkDuplicates Before output close freeMemory: 856323672; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:08 MarkDuplicates After output close freeMemory: 849122496; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:07:08 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:07:08 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13602276749217728188/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13602276749217728188/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13602276749217728188/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 13:07:08 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 13:07:08 MarkDuplicates Start of doWork freeMemory: 986497072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:08 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:08 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:07:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 931963384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:09 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 717005688; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:09 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:09 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:09 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:09 MarkDuplicates Before output close freeMemory: 859470152; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:09 MarkDuplicates After output close freeMemory: 853319808; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:09 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2991968032162220830/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2991968032162220830/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2991968032162220830/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 13:07:09 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 13:07:09 MarkDuplicates Start of doWork freeMemory: 986495952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:09 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:09 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:07:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 931962448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:10 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 717001256; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:10 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:10 MarkDuplicates Before output close freeMemory: 859469032; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:10 MarkDuplicates After output close freeMemory: 859607600; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:10 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:10 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18073850457019633559/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18073850457019633559/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18073850457019633559/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 13:07:10 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 13:07:10 MarkDuplicates Start of doWork freeMemory: 986383128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:10 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 931819840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:11 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 716862112; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:11 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:11 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:11 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:11 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:11 MarkDuplicates Before output close freeMemory: 863491296; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:07:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:11 MarkDuplicates After output close freeMemory: 859465144; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:11 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11148553830943695446/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11148553830943695446/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11148553830943695446/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 13:07:11 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 13:07:11 MarkDuplicates Start of doWork freeMemory: 986483096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:11 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:11 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 13:07:11 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2025-04-24 13:07:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 931946960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:12 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 985426520; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:07:12 MarkDuplicates Marking 12 records as duplicates. INFO 2025-04-24 13:07:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:12 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:12 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:12 MarkDuplicates Before output close freeMemory: 863649512; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:07:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:12 MarkDuplicates After output close freeMemory: 859594096; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:12 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11111311841560532420/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11111311841560532420/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11111311841560532420/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 13:07:12 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 13:07:12 MarkDuplicates Start of doWork freeMemory: 986490280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:12 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:12 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 13:07:12 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:07:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 931955808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:13 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 716998472; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:13 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:07:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:13 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:13 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:13 MarkDuplicates Before output close freeMemory: 856316896; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:13 MarkDuplicates After output close freeMemory: 856458432; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:13 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12974037945395064293/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12974037945395064293/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12974037945395064293/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 13:07:13 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 13:07:13 MarkDuplicates Start of doWork freeMemory: 986489312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:13 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:13 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 13:07:13 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:07:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 931954856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:14 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 1038910176; totalMemory: 1665138688; maxMemory: 2147483648 INFO 2025-04-24 13:07:14 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:14 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:14 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:14 MarkDuplicates Before output close freeMemory: 853169960; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:07:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:14 MarkDuplicates After output close freeMemory: 853311568; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:14 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:14 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1883275778842195595/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1883275778842195595/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1883275778842195595/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 13:07:14 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 13:07:14 MarkDuplicates Start of doWork freeMemory: 986484544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:14 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:14 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 13:07:14 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2025-04-24 13:07:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 931949232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:15 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 850161104; totalMemory: 1476395008; maxMemory: 2147483648 INFO 2025-04-24 13:07:15 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:07:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:15 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:15 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:15 MarkDuplicates Before output close freeMemory: 866796800; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:07:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:15 MarkDuplicates After output close freeMemory: 866935688; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:07:15 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:07:15 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2500542287335673494/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2500542287335673494/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2500542287335673494/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 13:07:15 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 13:07:15 MarkDuplicates Start of doWork freeMemory: 986489200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:15 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:15 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 13:07:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 931955248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:16 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 1038910520; totalMemory: 1665138688; maxMemory: 2147483648 INFO 2025-04-24 13:07:16 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:16 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:16 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:16 MarkDuplicates Before output close freeMemory: 866801984; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:07:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:16 MarkDuplicates After output close freeMemory: 866940680; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:07:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:07:16 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5995479826806159561/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5995479826806159561/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5995479826806159561/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 13:07:16 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 13:07:16 MarkDuplicates Start of doWork freeMemory: 986485664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:16 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:16 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 13:07:16 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2025-04-24 13:07:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 931950832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:16 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 836528088; totalMemory: 1462763520; maxMemory: 2147483648 INFO 2025-04-24 13:07:17 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:07:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:17 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:17 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:17 MarkDuplicates Before output close freeMemory: 863652192; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:07:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:17 MarkDuplicates After output close freeMemory: 863790976; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:07:17 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:07:17 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3702020389778512241/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3702020389778512241/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3702020389778512241/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 13:07:17 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 13:07:17 MarkDuplicates Start of doWork freeMemory: 986488816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:17 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:17 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 13:07:17 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:07:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 931955024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:17 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 772571832; totalMemory: 1398800384; maxMemory: 2147483648 INFO 2025-04-24 13:07:18 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:07:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:18 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:18 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:18 MarkDuplicates Before output close freeMemory: 856315840; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:18 MarkDuplicates After output close freeMemory: 856457192; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:18 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:18 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3395820228151428426/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3395820228151428426/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3395820228151428426/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 13:07:18 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 13:07:18 MarkDuplicates Start of doWork freeMemory: 986486608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:18 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:18 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 13:07:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 931952392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:18 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 716994152; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:19 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:19 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:19 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:19 MarkDuplicates Before output close freeMemory: 859458888; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:19 MarkDuplicates After output close freeMemory: 856452120; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:19 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8131818843604493553/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8131818843604493553/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8131818843604493553/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 13:07:19 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 13:07:19 MarkDuplicates Start of doWork freeMemory: 986485992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:19 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:19 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 13:07:19 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 931951760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:19 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 1045195160; totalMemory: 1671430144; maxMemory: 2147483648 INFO 2025-04-24 13:07:19 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:19 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:19 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:20 MarkDuplicates Before output close freeMemory: 856312608; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:20 MarkDuplicates After output close freeMemory: 856451416; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:20 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:20 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14735705214763924510/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14735705214763924510/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14735705214763924510/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 13:07:20 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 13:07:20 MarkDuplicates Start of doWork freeMemory: 986485224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:20 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 13:07:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 931951008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:20 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 577532160; totalMemory: 1203765248; maxMemory: 2147483648 INFO 2025-04-24 13:07:20 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:20 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:20 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:21 MarkDuplicates Before output close freeMemory: 846874664; totalMemory: 1203765248; maxMemory: 2147483648 INFO 2025-04-24 13:07:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:21 MarkDuplicates After output close freeMemory: 847013552; totalMemory: 1203765248; maxMemory: 2147483648 [Thu Apr 24 13:07:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1203765248 [Thu Apr 24 13:07:21 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17695544818067192767/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17695544818067192767/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17695544818067192767/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 13:07:21 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 13:07:21 MarkDuplicates Start of doWork freeMemory: 986484224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:21 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:21 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 13:07:21 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 931949992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:21 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 775712672; totalMemory: 1401946112; maxMemory: 2147483648 INFO 2025-04-24 13:07:21 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:21 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:21 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:21 MarkDuplicates Before output close freeMemory: 859456568; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:22 MarkDuplicates After output close freeMemory: 853303896; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:22 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15976842594492543319/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15976842594492543319/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15976842594492543319/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 13:07:22 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 13:07:22 MarkDuplicates Start of doWork freeMemory: 986482776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:22 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:22 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 13:07:22 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 931948560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:22 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 716990320; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:22 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:22 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:22 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:22 MarkDuplicates Before output close freeMemory: 859455240; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:22 MarkDuplicates After output close freeMemory: 853305176; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:23 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8302706016910051510/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8302706016910051510/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8302706016910051510/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 13:07:23 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 13:07:23 MarkDuplicates Start of doWork freeMemory: 986482104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:23 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:23 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:23 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 13:07:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 931947872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:23 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 775710552; totalMemory: 1401946112; maxMemory: 2147483648 INFO 2025-04-24 13:07:23 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:23 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:23 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:23 MarkDuplicates Before output close freeMemory: 856309040; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:23 MarkDuplicates After output close freeMemory: 856447608; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:23 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:23 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1076029306498570263/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1076029306498570263/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1076029306498570263/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 13:07:23 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 13:07:24 MarkDuplicates Start of doWork freeMemory: 986480840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:24 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 13:07:24 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 931946608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 523001808; totalMemory: 1149239296; maxMemory: 2147483648 INFO 2025-04-24 13:07:24 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:24 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:24 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:24 MarkDuplicates Before output close freeMemory: 792344640; totalMemory: 1149239296; maxMemory: 2147483648 INFO 2025-04-24 13:07:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:24 MarkDuplicates After output close freeMemory: 792483104; totalMemory: 1149239296; maxMemory: 2147483648 [Thu Apr 24 13:07:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1149239296 [Thu Apr 24 13:07:24 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7895283779651929306/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7895283779651929306/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7895283779651929306/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 13:07:24 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 13:07:24 MarkDuplicates Start of doWork freeMemory: 986480920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:25 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 13:07:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 931946688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:25 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 1048339128; totalMemory: 1674575872; maxMemory: 2147483648 INFO 2025-04-24 13:07:25 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:25 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:25 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:25 MarkDuplicates Before output close freeMemory: 863647496; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:07:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:25 MarkDuplicates After output close freeMemory: 856446320; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:25 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12476952866565088050/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12476952866565088050/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12476952866565088050/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 13:07:25 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 13:07:25 MarkDuplicates Start of doWork freeMemory: 986479960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:25 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:25 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 13:07:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 931945744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:26 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 576478320; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:07:26 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:26 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:26 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:26 MarkDuplicates Before output close freeMemory: 845820752; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:07:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:26 MarkDuplicates After output close freeMemory: 845962256; totalMemory: 1202716672; maxMemory: 2147483648 [Thu Apr 24 13:07:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1202716672 [Thu Apr 24 13:07:26 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15443788955856884979/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15443788955856884979/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15443788955856884979/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 13:07:26 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 13:07:26 MarkDuplicates Start of doWork freeMemory: 986479144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:26 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:26 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 13:07:26 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 931944912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:27 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 877419464; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:07:27 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:27 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:27 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:27 MarkDuplicates Before output close freeMemory: 859451416; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:27 MarkDuplicates After output close freeMemory: 856444648; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:27 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:27 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1556167821605061236/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1556167821605061236/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1556167821605061236/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 13:07:27 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 13:07:27 MarkDuplicates Start of doWork freeMemory: 986478272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:27 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:27 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 13:07:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 931944056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:28 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 715937904; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:07:28 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:28 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:28 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:28 MarkDuplicates Before output close freeMemory: 859450552; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:28 MarkDuplicates After output close freeMemory: 849106296; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:07:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:07:28 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8572983784647605547/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8572983784647605547/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8572983784647605547/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 13:07:28 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 13:07:28 MarkDuplicates Start of doWork freeMemory: 986477456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:28 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:28 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 13:07:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 931943224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:29 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 716985648; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:29 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:29 MarkDuplicates Before output close freeMemory: 859449728; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:29 MarkDuplicates After output close freeMemory: 856445504; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:29 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:29 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5943148796064439869/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5943148796064439869/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5943148796064439869/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 13:07:29 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 13:07:29 MarkDuplicates Start of doWork freeMemory: 986477800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:29 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:29 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:29 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 13:07:29 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2025-04-24 13:07:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 931943904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:29 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 716982872; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:30 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:30 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:30 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:30 MarkDuplicates Before output close freeMemory: 856304576; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:30 MarkDuplicates After output close freeMemory: 856446032; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:30 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15783585453404239123/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15783585453404239123/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15783585453404239123/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 13:07:30 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 13:07:30 MarkDuplicates Start of doWork freeMemory: 986474472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:30 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:30 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 931940176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:30 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 715933872; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:07:31 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:31 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:31 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:31 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:31 MarkDuplicates Before output close freeMemory: 859446504; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:31 MarkDuplicates After output close freeMemory: 859588032; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:31 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:31 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13217274190051768039/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13217274190051768039/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13217274190051768039/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 13:07:31 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 13:07:31 MarkDuplicates Start of doWork freeMemory: 986473680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:31 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:31 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 931939384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:31 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 716978344; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:31 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:31 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:31 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:31 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:32 MarkDuplicates Before output close freeMemory: 859445712; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:32 MarkDuplicates After output close freeMemory: 856438968; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:32 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8090787845612906641/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8090787845612906641/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8090787845612906641/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 13:07:32 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 13:07:32 MarkDuplicates Start of doWork freeMemory: 986472976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:32 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:32 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 931935856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:32 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 716977888; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:32 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:32 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:32 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:32 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:33 MarkDuplicates Before output close freeMemory: 853153560; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:07:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:33 MarkDuplicates After output close freeMemory: 853295160; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:33 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8935190444812856144/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8935190444812856144/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8935190444812856144/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 13:07:33 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 13:07:33 MarkDuplicates Start of doWork freeMemory: 986472280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:33 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:33 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 931938000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:33 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 716979816; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:33 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:33 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:33 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:33 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:33 MarkDuplicates Before output close freeMemory: 856298592; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:34 MarkDuplicates After output close freeMemory: 856440192; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:34 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10693941437869698137/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10693941437869698137/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10693941437869698137/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 13:07:34 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 13:07:34 MarkDuplicates Start of doWork freeMemory: 986471584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:34 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:34 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 931937288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:34 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 716978896; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:34 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:34 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:34 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:34 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:34 MarkDuplicates Before output close freeMemory: 859443616; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:34 MarkDuplicates After output close freeMemory: 856436768; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:34 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6296442580786785869/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6296442580786785869/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6296442580786785869/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 13:07:34 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 13:07:35 MarkDuplicates Start of doWork freeMemory: 986470832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:35 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:35 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 931936536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:35 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 715930232; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:07:35 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:35 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:35 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:35 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:35 MarkDuplicates Before output close freeMemory: 856297136; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:35 MarkDuplicates After output close freeMemory: 853290360; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:35 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:35 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1008645360509511557/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1008645360509511557/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1008645360509511557/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 13:07:35 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 13:07:36 MarkDuplicates Start of doWork freeMemory: 986469176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:36 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:36 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 931934896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:36 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 716977168; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:36 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:36 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:36 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:36 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:36 MarkDuplicates Before output close freeMemory: 863635680; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:07:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:36 MarkDuplicates After output close freeMemory: 863774400; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:07:36 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:07:36 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp796974263954685111/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp796974263954685111/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp796974263954685111/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 13:07:36 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 13:07:37 MarkDuplicates Start of doWork freeMemory: 986468472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:37 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 931934176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:37 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 715927872; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:07:37 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:37 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:37 MarkDuplicates Before output close freeMemory: 856294936; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:37 MarkDuplicates After output close freeMemory: 853290648; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:37 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2511146598462569587/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2511146598462569587/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2511146598462569587/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 13:07:37 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 13:07:37 MarkDuplicates Start of doWork freeMemory: 986467768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:37 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 931933488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:38 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 985407904; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:07:38 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:38 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:38 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:38 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:38 MarkDuplicates Before output close freeMemory: 859436720; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:38 MarkDuplicates After output close freeMemory: 856436176; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:38 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10129502210959911907/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10129502210959911907/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10129502210959911907/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 13:07:38 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 13:07:38 MarkDuplicates Start of doWork freeMemory: 986467072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:38 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:39 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 931932592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:39 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 576465864; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:07:39 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:39 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:39 MarkDuplicates Before output close freeMemory: 845807776; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:07:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:39 MarkDuplicates After output close freeMemory: 845949248; totalMemory: 1202716672; maxMemory: 2147483648 [Thu Apr 24 13:07:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1202716672 [Thu Apr 24 13:07:39 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp655105103835281451/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp655105103835281451/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp655105103835281451/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 13:07:39 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 13:07:39 MarkDuplicates Start of doWork freeMemory: 986466368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:39 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:39 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 931932088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:40 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 716971280; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:40 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:40 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:40 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:40 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:40 MarkDuplicates Before output close freeMemory: 859438568; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:40 MarkDuplicates After output close freeMemory: 856431664; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:40 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9751129249720985585/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9751129249720985585/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9751129249720985585/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 13:07:40 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 13:07:40 MarkDuplicates Start of doWork freeMemory: 986465720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:40 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:07:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 931931440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:41 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 985408744; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:07:41 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:41 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:41 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:41 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:41 MarkDuplicates Before output close freeMemory: 859437920; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:41 MarkDuplicates After output close freeMemory: 856431016; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:07:41 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13912736715867518049/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13912736715867518049/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13912736715867518049/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 13:07:41 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 13:07:41 MarkDuplicates Start of doWork freeMemory: 986467256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:41 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:41 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:07:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 931933552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:42 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 716975856; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:42 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:42 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:42 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:42 MarkDuplicates Before output close freeMemory: 866780360; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:07:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:42 MarkDuplicates After output close freeMemory: 859578888; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:42 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.tmp1193127191842922884/MarkDuplicates.sam --METRICS_FILE /tmp/MarkDuplicates.tmp1193127191842922884/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 13:07:42 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 13:07:42 MarkDuplicates Start of doWork freeMemory: 986473296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:42 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:07:42 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 13:07:42 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:07:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 923549328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:42 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:43 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 985416224; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:07:43 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:07:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:43 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:43 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:43 MarkDuplicates Before output close freeMemory: 986320960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:43 MarkDuplicates After output close freeMemory: 986464160; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:07:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:07:43 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.tmp10552609957927632437/MarkDuplicates.sam --METRICS_FILE /tmp/MarkDuplicates.tmp10552609957927632437/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 13:07:43 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 13:07:43 MarkDuplicates Start of doWork freeMemory: 986472376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:43 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:07:43 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 13:07:43 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:07:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 923548584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:43 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:44 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 985415480; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:07:44 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:07:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:44 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:44 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:44 MarkDuplicates Before output close freeMemory: 986177136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:44 MarkDuplicates After output close freeMemory: 986174240; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:07:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 INFO 2025-04-24 13:07:44 MarkDuplicates Start of doWork freeMemory: 986491816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:44 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:07:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 923570544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:44 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:45 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 985437112; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:07:45 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:45 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:45 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:45 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:45 MarkDuplicates Before output close freeMemory: 986298752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:45 MarkDuplicates After output close freeMemory: 986298360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:45 MarkDuplicates Start of doWork freeMemory: 986490856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:07:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 923569496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:45 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:46 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 985436064; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:07:46 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:46 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:07:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:46 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:46 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:46 MarkDuplicates Before output close freeMemory: 986297680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:46 MarkDuplicates After output close freeMemory: 986294640; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:07:46 EDT 2025] MarkDuplicates --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4250605658317631793/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4250605658317631793/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4250605658317631793/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 13:07:46 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 13:07:46 MarkDuplicates Start of doWork freeMemory: 986459664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:46 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 13:07:46 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2025-04-24 13:07:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 931925680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:46 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 716964648; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:47 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:47 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:47 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:47 MarkDuplicates Before output close freeMemory: 859432016; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:47 MarkDuplicates After output close freeMemory: 853279544; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:47 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3773413079803268270/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3773413079803268270/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3773413079803268270/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 13:07:47 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 13:07:47 MarkDuplicates Start of doWork freeMemory: 986456048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:47 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:07:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 931921512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:47 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 716964000; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:48 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:48 MarkDuplicates Before output close freeMemory: 859428008; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:48 MarkDuplicates After output close freeMemory: 853278200; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:48 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12212886970682528063/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12212886970682528063/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12212886970682528063/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 13:07:48 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 13:07:48 MarkDuplicates Start of doWork freeMemory: 986456608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:48 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 931922328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:48 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 716961672; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:48 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:49 MarkDuplicates Before output close freeMemory: 863623056; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:07:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:49 MarkDuplicates After output close freeMemory: 863762088; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:07:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:07:49 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_TWO_BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13078754486832514571/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13078754486832514571/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13078754486832514571/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 13:07:49 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 13:07:49 MarkDuplicates Start of doWork freeMemory: 986457376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:49 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:49 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 13:07:49 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:07:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 931923584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:49 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 985400656; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:07:49 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:07:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:49 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:49 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:50 MarkDuplicates Before output close freeMemory: 859430056; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:50 MarkDuplicates After output close freeMemory: 859571552; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:50 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_ONE_BARCODE_TAG BX --READ_TWO_BARCODE_TAG BX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9946137243644538398/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9946137243644538398/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9946137243644538398/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 13:07:50 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 13:07:50 MarkDuplicates Start of doWork freeMemory: 986453608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:07:50 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:07:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 931918888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:50 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 573303576; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:07:50 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:50 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:50 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:50 MarkDuplicates Before output close freeMemory: 842648280; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:07:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:51 MarkDuplicates After output close freeMemory: 842790000; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:07:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:07:51 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI false --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3157354606635763959/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3157354606635763959/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3157354606635763959/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 13:07:51 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 13:07:51 MarkDuplicates Start of doWork freeMemory: 986452360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:51 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:51 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 13:07:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 931918144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:51 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 716957488; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:51 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:51 MarkDuplicates Before output close freeMemory: 856278992; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:52 MarkDuplicates After output close freeMemory: 853274768; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:07:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:07:52 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI false --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7420028079449523538/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7420028079449523538/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7420028079449523538/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 13:07:52 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 13:07:52 MarkDuplicates Start of doWork freeMemory: 986451728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:52 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:52 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 13:07:52 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 931917496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:52 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 716956608; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:52 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:52 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:52 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:52 MarkDuplicates Before output close freeMemory: 859424080; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:07:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:53 MarkDuplicates After output close freeMemory: 859565512; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:07:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:07:53 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI true --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12970646730275351385/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12970646730275351385/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12970646730275351385/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 13:07:53 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 13:07:53 MarkDuplicates Start of doWork freeMemory: 986451008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:53 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:53 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 13:07:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 931916776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:53 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 716955888; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:07:53 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:07:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:53 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:53 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:53 MarkDuplicates Before output close freeMemory: 853131904; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:07:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:53 MarkDuplicates After output close freeMemory: 849076448; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:07:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:07:53 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI true --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8215780026552297384/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8215780026552297384/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8215780026552297384/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 13:07:53 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 13:07:54 MarkDuplicates Start of doWork freeMemory: 986450280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:54 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:07:54 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 13:07:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:07:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 931916048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:54 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 986442504; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:07:54 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:54 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:54 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:54 MarkDuplicates Before output close freeMemory: 856276904; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:07:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:54 MarkDuplicates After output close freeMemory: 856418432; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:07:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432