Class picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| pgRecordChainingTest[0](false, {1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4c811da4, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@74ce5191], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7e770588], 1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2c87828, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@466039e8, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@40a4aa6c]}) | 0.980s | passed |
| pgRecordChainingTest[1](true, {1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@31d05da5], 1AAXX.3.1=[], 1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@35b832, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@21480b41]}) | 0.980s | passed |
| testBulkFragmentsNoDuplicates[0](.sam) | 1.381s | passed |
| testBulkFragmentsNoDuplicates[1](.bam) | 1.326s | passed |
| testBulkFragmentsNoDuplicates[2](.cram) | 1.769s | passed |
| testBulkFragmentsWithDuplicates[0](.sam) | 1.429s | passed |
| testBulkFragmentsWithDuplicates[1](.bam) | 1.395s | passed |
| testBulkFragmentsWithDuplicates[2](.cram) | 2.313s | passed |
| testBulkPairsNoDuplicates[0](.sam) | 1.582s | passed |
| testBulkPairsNoDuplicates[1](.bam) | 1.504s | passed |
| testBulkPairsNoDuplicates[2](.cram) | 2.344s | passed |
| testBulkPairsWithDuplicates[0](.sam) | 1.047s | passed |
| testBulkPairsWithDuplicates[1](.bam) | 1.084s | passed |
| testBulkPairsWithDuplicates[2](.cram) | 1.602s | passed |
| testDifferentChromosomesInOppositeOrder | 0.899s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 1.013s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.930s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.943s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.939s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.930s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.934s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 1.013s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.909s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.894s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.871s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.945s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.942s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.965s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.962s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.931s | passed |
| testMappedPairWithSamePosition | 0.985s | passed |
| testMappedPairWithSamePositionSameCigar | 0.879s | passed |
| testMatePairFirstUnmapped | 0.904s | passed |
| testMatePairSecondUnmapped | 0.988s | passed |
| testOpticalDuplicateBehaviorNullRegex | 0.901s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.959s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.965s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) | 0.923s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) | 0.916s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) | 0.958s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) | 0.979s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) | 0.932s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) | 1.008s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) | 0.984s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) | 0.934s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) | 0.920s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) | 0.934s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) | 1.015s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) | 0.926s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) | 0.914s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) | 1.001s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.960s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.940s | passed |
| testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) | 0.986s | passed |
| testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) | 0.911s | passed |
| testOpticalDuplicateFinding | 0.938s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.955s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.967s | passed |
| testSingleMappedFragment | 0.984s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.936s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.975s | passed |
| testSingleMappedPair | 0.966s | passed |
| testSingleUnmappedFragment | 1.024s | passed |
| testSingleUnmappedPair | 0.976s | passed |
| testStackOverFlowPairSetSwap | 0.932s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.946s | passed |
| testThreeMappedPairs | 0.926s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.948s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 1.014s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.964s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 1.011s | passed |
| testTwoMappedFragments | 0.913s | passed |
| testTwoMappedPairWithSamePosition | 0.987s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.963s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.998s | passed |
| testTwoMappedPairs | 0.985s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.978s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 1.038s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.982s | passed |
| testTwoMappedPairsMatesSoftClipped | 1.011s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.994s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 1.017s | passed |
| testTwoMappedPairsWithSoftClipping | 0.919s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 1.016s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 0.985s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.972s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.945s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.997s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.964s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.995s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.910s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.925s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.920s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.909s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.994s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.957s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.998s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.858s | passed |
| testTwoUnmappedFragments | 0.935s | passed |
| testWithBarcodeComplex | 0.967s | passed |
| testWithBarcodeDuplicate | 0.993s | passed |
| testWithBarcodeFragmentDuplicate | 0.904s | passed |
| testWithIndividualReadBarcodes | 0.914s | passed |
| testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) | 0.913s | passed |
| testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) | 0.998s | passed |
| testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) | 0.901s | passed |
| testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) | 0.969s | passed |
Standard error
[Thu Apr 24 13:07:55 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5481467333553287128/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5481467333553287128/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5481467333553287128/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:07:55 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 13:07:55 MarkDuplicates Start of doWork freeMemory: 979512792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:55 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:07:55 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 13:07:55 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:07:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 915870376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:55 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 974220000; totalMemory: 1607467008; maxMemory: 2147483648 INFO 2025-04-24 13:07:55 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:55 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:55 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:56 MarkDuplicates Before output close freeMemory: 883897040; totalMemory: 1247805440; maxMemory: 2147483648 INFO 2025-04-24 13:07:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:56 MarkDuplicates After output close freeMemory: 867265056; totalMemory: 1231028224; maxMemory: 2147483648 [Thu Apr 24 13:07:56 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1231028224 [Thu Apr 24 13:07:56 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8929347887835854540/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8929347887835854540/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8929347887835854540/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:07:56 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 13:07:56 MarkDuplicates Start of doWork freeMemory: 979511872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:56 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:07:56 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 13:07:56 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:07:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 915869216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:57 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 807534936; totalMemory: 1440743424; maxMemory: 2147483648 INFO 2025-04-24 13:07:57 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:57 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:57 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:57 MarkDuplicates Before output close freeMemory: 870308992; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2025-04-24 13:07:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:57 MarkDuplicates After output close freeMemory: 870449008; totalMemory: 1234173952; maxMemory: 2147483648 [Thu Apr 24 13:07:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1234173952 [Thu Apr 24 13:07:58 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16888988286845136402/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16888988286845136402/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16888988286845136402/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester16756770547194881902/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 13:07:58 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 13:07:58 MarkDuplicates Start of doWork freeMemory: 979476656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:58 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:07:58 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 13:07:58 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:07:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 915830152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:07:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:07:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:07:58 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:07:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 643923496; totalMemory: 1277165568; maxMemory: 2147483648 INFO 2025-04-24 13:07:58 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:07:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:07:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:07:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:07:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:07:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:07:59 MarkDuplicates Before output close freeMemory: 883904720; totalMemory: 1247805440; maxMemory: 2147483648 INFO 2025-04-24 13:07:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:07:59 MarkDuplicates After output close freeMemory: 867267144; totalMemory: 1231028224; maxMemory: 2147483648 [Thu Apr 24 13:07:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1231028224 [Thu Apr 24 13:07:59 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3714147344466254214/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3714147344466254214/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3714147344466254214/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:07:59 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 13:07:59 MarkDuplicates Start of doWork freeMemory: 971271616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:07:59 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:07:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:07:59 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 13:07:59 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:08:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 906839104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:00 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 701765744; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:00 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:08:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:00 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:00 MarkDuplicates Before output close freeMemory: 893512416; totalMemory: 1265631232; maxMemory: 2147483648 INFO 2025-04-24 13:08:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:00 MarkDuplicates After output close freeMemory: 880023472; totalMemory: 1251999744; maxMemory: 2147483648 [Thu Apr 24 13:08:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1251999744 [Thu Apr 24 13:08:01 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11942722907712590768/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11942722907712590768/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11942722907712590768/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:01 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 13:08:01 MarkDuplicates Start of doWork freeMemory: 971314112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:01 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:08:01 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 13:08:01 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:08:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 906878968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:01 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 701774616; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:01 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:08:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:01 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:01 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:01 MarkDuplicates Before output close freeMemory: 893517992; totalMemory: 1265631232; maxMemory: 2147483648 INFO 2025-04-24 13:08:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:02 MarkDuplicates After output close freeMemory: 886323512; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:08:02 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:08:02 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8360177342990201682/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8360177342990201682/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8360177342990201682/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester3580336404388857721/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 13:08:02 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 13:08:03 MarkDuplicates Start of doWork freeMemory: 970965256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:03 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:08:03 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 13:08:03 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:08:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 906535336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:03 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 805284504; totalMemory: 1447034880; maxMemory: 2147483648 INFO 2025-04-24 13:08:03 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:08:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:04 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:04 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:04 MarkDuplicates Before output close freeMemory: 903710784; totalMemory: 1276116992; maxMemory: 2147483648 INFO 2025-04-24 13:08:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:04 MarkDuplicates After output close freeMemory: 896513272; totalMemory: 1268776960; maxMemory: 2147483648 [Thu Apr 24 13:08:04 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1268776960 [Thu Apr 24 13:08:04 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18346412040104898316/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18346412040104898316/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18346412040104898316/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:04 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 13:08:04 MarkDuplicates Start of doWork freeMemory: 970796136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:04 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:08:04 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 13:08:05 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:08:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 905689080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:05 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 969739320; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:05 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:05 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:05 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:05 MarkDuplicates Before output close freeMemory: 889905552; totalMemory: 1262485504; maxMemory: 2147483648 INFO 2025-04-24 13:08:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:05 MarkDuplicates After output close freeMemory: 890047576; totalMemory: 1262485504; maxMemory: 2147483648 [Thu Apr 24 13:08:05 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1262485504 [Thu Apr 24 13:08:06 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5590074112122291420/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5590074112122291420/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5590074112122291420/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:06 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 13:08:06 MarkDuplicates Start of doWork freeMemory: 970795216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:06 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:08:06 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 13:08:06 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:08:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 905687792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:07 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 855443352; totalMemory: 1497366528; maxMemory: 2147483648 INFO 2025-04-24 13:08:07 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:07 MarkDuplicates Before output close freeMemory: 885706120; totalMemory: 1258291200; maxMemory: 2147483648 INFO 2025-04-24 13:08:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:07 MarkDuplicates After output close freeMemory: 882705808; totalMemory: 1255145472; maxMemory: 2147483648 [Thu Apr 24 13:08:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1255145472 [Thu Apr 24 13:08:08 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7611935979334311784/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7611935979334311784/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7611935979334311784/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester7322018174841583435/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 13:08:08 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 13:08:08 MarkDuplicates Start of doWork freeMemory: 970460424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:08 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:08:08 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 13:08:08 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:08:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 905360648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:09 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 697827328; totalMemory: 1340080128; maxMemory: 2147483648 INFO 2025-04-24 13:08:09 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:09 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:09 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:09 MarkDuplicates Before output close freeMemory: 889573952; totalMemory: 1262485504; maxMemory: 2147483648 INFO 2025-04-24 13:08:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:09 MarkDuplicates After output close freeMemory: 885522248; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:08:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:08:10 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8928134311932680305/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8928134311932680305/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8928134311932680305/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:10 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 13:08:10 MarkDuplicates Start of doWork freeMemory: 981312720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:10 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:08:10 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 13:08:10 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:08:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 917650896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:10 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 847087160; totalMemory: 1478492160; maxMemory: 2147483648 INFO 2025-04-24 13:08:10 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:08:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:10 MarkDuplicates Before output close freeMemory: 868961696; totalMemory: 1231028224; maxMemory: 2147483648 INFO 2025-04-24 13:08:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:11 MarkDuplicates After output close freeMemory: 861767032; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:08:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:08:11 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11995119071986725441/input.bam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11995119071986725441/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11995119071986725441/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:11 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 13:08:11 MarkDuplicates Start of doWork freeMemory: 981311760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:11 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:08:11 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 13:08:11 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:08:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 917649784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:11 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 859669032; totalMemory: 1491075072; maxMemory: 2147483648 INFO 2025-04-24 13:08:11 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:08:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:11 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:11 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:11 MarkDuplicates Before output close freeMemory: 872105792; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2025-04-24 13:08:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:12 MarkDuplicates After output close freeMemory: 861765696; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:08:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:08:12 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14100676126667900393/input.cram --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14100676126667900393/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14100676126667900393/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester7246575518277967496/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 13:08:12 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 13:08:12 MarkDuplicates Start of doWork freeMemory: 981177936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:12 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:08:12 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 13:08:12 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:08:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 917518736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:13 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 1099661976; totalMemory: 1731198976; maxMemory: 2147483648 INFO 2025-04-24 13:08:13 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:08:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:13 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:13 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:13 MarkDuplicates Before output close freeMemory: 879318208; totalMemory: 1241513984; maxMemory: 2147483648 INFO 2025-04-24 13:08:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:13 MarkDuplicates After output close freeMemory: 864779896; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:08:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:08:13 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9324922962316024223/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9324922962316024223/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9324922962316024223/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:13 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 13:08:13 MarkDuplicates Start of doWork freeMemory: 986430816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:13 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 931896520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:14 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 637243704; totalMemory: 1263534080; maxMemory: 2147483648 INFO 2025-04-24 13:08:14 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:14 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:08:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:14 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:14 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:14 MarkDuplicates Before output close freeMemory: 863597080; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:14 MarkDuplicates After output close freeMemory: 859544448; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:14 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:14 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7030529894365763514/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7030529894365763514/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7030529894365763514/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:14 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 13:08:14 MarkDuplicates Start of doWork freeMemory: 986423920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:14 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:14 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:08:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 931888904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:15 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 985367352; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:15 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:08:15 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:08:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:15 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:15 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:15 MarkDuplicates Before output close freeMemory: 863590216; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:15 MarkDuplicates After output close freeMemory: 859534936; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:15 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:15 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9396579837304390776/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9396579837304390776/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9396579837304390776/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:15 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 13:08:15 MarkDuplicates Start of doWork freeMemory: 986423192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:15 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:15 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:08:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 931887992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:16 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 573276256; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:08:16 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:08:16 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:08:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:16 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:16 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:16 MarkDuplicates Before output close freeMemory: 842617968; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:08:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:16 MarkDuplicates After output close freeMemory: 842756992; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:08:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:08:16 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3804172836279348945/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3804172836279348945/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3804172836279348945/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:16 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 13:08:16 MarkDuplicates Start of doWork freeMemory: 986422480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:16 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:16 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:08:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 931887464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:17 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 716930456; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:17 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:08:17 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:08:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:17 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:17 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:17 MarkDuplicates Before output close freeMemory: 856248744; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:17 MarkDuplicates After output close freeMemory: 853242040; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:17 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:17 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12001830646072506665/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12001830646072506665/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12001830646072506665/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:17 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 13:08:17 MarkDuplicates Start of doWork freeMemory: 986420568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:17 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:17 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:08:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 931885568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:18 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 716928560; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:18 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:08:18 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:08:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:18 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:18 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:18 MarkDuplicates Before output close freeMemory: 859392568; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:18 MarkDuplicates After output close freeMemory: 859531592; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:18 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:18 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10735513040651867839/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10735513040651867839/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10735513040651867839/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:18 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 13:08:18 MarkDuplicates Start of doWork freeMemory: 986419872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:18 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:18 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:08:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 931884872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:18 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 716927864; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:19 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:08:19 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:08:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:19 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:19 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:19 MarkDuplicates Before output close freeMemory: 866731904; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:08:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:19 MarkDuplicates After output close freeMemory: 859530896; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:19 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13634418987726228287/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13634418987726228287/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13634418987726228287/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:19 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 13:08:19 MarkDuplicates Start of doWork freeMemory: 986419168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:19 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:19 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:08:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 931884168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:19 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 716927160; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:20 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:08:20 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:08:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:20 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:20 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:20 MarkDuplicates Before output close freeMemory: 856245440; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:20 MarkDuplicates After output close freeMemory: 856384464; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:20 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:20 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15320569440418304825/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15320569440418304825/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15320569440418304825/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:20 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 13:08:20 MarkDuplicates Start of doWork freeMemory: 986425056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:20 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 13:08:20 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:08:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 931891360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:20 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 985365704; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:21 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:21 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:21 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:21 MarkDuplicates Before output close freeMemory: 859394464; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:21 MarkDuplicates After output close freeMemory: 853248248; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:21 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp449205261353950717/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp449205261353950717/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp449205261353950717/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:21 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 13:08:21 MarkDuplicates Start of doWork freeMemory: 986424088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:21 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:21 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 13:08:21 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:08:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 931889744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:21 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 579565824; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:08:21 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:08:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:21 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:21 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:22 MarkDuplicates Before output close freeMemory: 848911120; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:08:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:22 MarkDuplicates After output close freeMemory: 849049784; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:08:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:08:22 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11369736899051025154/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11369736899051025154/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11369736899051025154/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:22 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 13:08:22 MarkDuplicates Start of doWork freeMemory: 986423464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:22 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:22 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 13:08:22 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:08:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 931889688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:22 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 716931304; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:22 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:08:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:22 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:22 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:23 MarkDuplicates Before output close freeMemory: 859396256; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:23 MarkDuplicates After output close freeMemory: 856391920; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:23 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:23 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp258927288325212618/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp258927288325212618/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp258927288325212618/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:23 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 13:08:23 MarkDuplicates Start of doWork freeMemory: 986421352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:23 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:23 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:23 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 13:08:23 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:08:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 931887200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:23 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 768309768; totalMemory: 1394606080; maxMemory: 2147483648 INFO 2025-04-24 13:08:23 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:23 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:23 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:23 MarkDuplicates Before output close freeMemory: 859393624; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:24 MarkDuplicates After output close freeMemory: 859535696; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:24 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13569608149373689269/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13569608149373689269/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13569608149373689269/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:24 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 13:08:24 MarkDuplicates Start of doWork freeMemory: 986420416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:24 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 13:08:24 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:08:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 931886264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 716927944; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:24 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:24 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:24 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:24 MarkDuplicates Before output close freeMemory: 859392688; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:24 MarkDuplicates After output close freeMemory: 859531544; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:24 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14097206746426828160/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14097206746426828160/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14097206746426828160/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:24 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 13:08:25 MarkDuplicates Start of doWork freeMemory: 986418520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:25 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:25 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 13:08:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 931885984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:25 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 772502776; totalMemory: 1398800384; maxMemory: 2147483648 INFO 2025-04-24 13:08:25 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:25 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:25 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:25 MarkDuplicates Before output close freeMemory: 863586584; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:25 MarkDuplicates After output close freeMemory: 853239728; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:25 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9681381682690682517/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9681381682690682517/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9681381682690682517/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:25 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 13:08:26 MarkDuplicates Start of doWork freeMemory: 986419400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:26 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:26 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 13:08:26 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 931885328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:26 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 716924280; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:26 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:08:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:26 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:26 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:26 MarkDuplicates Before output close freeMemory: 856245944; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:26 MarkDuplicates After output close freeMemory: 856384904; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:26 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9489763447041919403/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9489763447041919403/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9489763447041919403/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:26 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 13:08:27 MarkDuplicates Start of doWork freeMemory: 986418624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:27 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:27 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 13:08:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 931884552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:27 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 772501344; totalMemory: 1398800384; maxMemory: 2147483648 INFO 2025-04-24 13:08:27 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:08:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:27 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:27 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:27 MarkDuplicates Before output close freeMemory: 863585200; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:27 MarkDuplicates After output close freeMemory: 853238400; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:27 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:27 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7026546718035491930/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7026546718035491930/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7026546718035491930/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:27 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 13:08:28 MarkDuplicates Start of doWork freeMemory: 986417608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:28 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:28 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 13:08:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 931883392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:28 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 716925152; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:28 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:28 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:28 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:28 MarkDuplicates Before output close freeMemory: 856244160; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:28 MarkDuplicates After output close freeMemory: 853239936; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:28 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6749639140194759263/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6749639140194759263/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6749639140194759263/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:28 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 13:08:28 MarkDuplicates Start of doWork freeMemory: 986418176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:28 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:28 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 13:08:28 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:08:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 931884184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:29 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 1048273072; totalMemory: 1674575872; maxMemory: 2147483648 INFO 2025-04-24 13:08:29 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:29 MarkDuplicates Before output close freeMemory: 863584752; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:29 MarkDuplicates After output close freeMemory: 859531952; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:29 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:29 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3160844236163930696/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3160844236163930696/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3160844236163930696/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:29 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 13:08:29 MarkDuplicates Start of doWork freeMemory: 986417360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:29 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:29 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:29 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 13:08:29 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:08:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 931883368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:30 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 573269976; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:08:30 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:30 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:30 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:30 MarkDuplicates Before output close freeMemory: 842612416; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:08:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:30 MarkDuplicates After output close freeMemory: 842754000; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:08:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:08:30 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12750933595861138058/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12750933595861138058/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12750933595861138058/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:30 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 13:08:30 MarkDuplicates Start of doWork freeMemory: 986416704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:30 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:08:30 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:08:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 931883008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:31 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 768305432; totalMemory: 1394606080; maxMemory: 2147483648 INFO 2025-04-24 13:08:31 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:31 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:31 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:31 MarkDuplicates Before output close freeMemory: 856243664; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:31 MarkDuplicates After output close freeMemory: 856385160; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:31 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:31 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12736582999658350894/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12736582999658350894/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12736582999658350894/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:31 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 13:08:31 MarkDuplicates Start of doWork freeMemory: 986416008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:31 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:08:31 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:08:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 931882296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:32 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 985359288; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:32 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:32 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:32 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:32 MarkDuplicates Before output close freeMemory: 859388808; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:32 MarkDuplicates After output close freeMemory: 859530080; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:32 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15096771828780905825/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15096771828780905825/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15096771828780905825/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_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 13:08:32 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 13:08:32 MarkDuplicates Start of doWork freeMemory: 986413904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:32 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 931876856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:33 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 877354416; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:08:33 MarkDuplicates Marking 2 records as duplicates. WARNING 2025-04-24 13:08:33 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! INFO 2025-04-24 13:08:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:33 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:33 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:33 MarkDuplicates Before output close freeMemory: 853094920; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:08:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:33 MarkDuplicates After output close freeMemory: 853233880; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:33 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp352526031701149793/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp352526031701149793/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp352526031701149793/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:33 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 13:08:33 MarkDuplicates Start of doWork freeMemory: 986412736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:33 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 931875608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:33 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 716917400; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:34 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:34 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:08:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:34 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:34 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:34 MarkDuplicates Before output close freeMemory: 856238976; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:34 MarkDuplicates After output close freeMemory: 856377920; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:34 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10155372180682249956/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10155372180682249956/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10155372180682249956/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:34 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 13:08:34 MarkDuplicates Start of doWork freeMemory: 986410832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:34 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:34 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 931876552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:34 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 716918312; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:35 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:35 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:35 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:35 MarkDuplicates Before output close freeMemory: 859382984; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:35 MarkDuplicates After output close freeMemory: 856376176; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:35 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:35 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8890483622292019414/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8890483622292019414/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8890483622292019414/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:35 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 13:08:35 MarkDuplicates Start of doWork freeMemory: 986410096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:35 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 931875816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:35 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 985350592; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:36 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:36 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:36 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:36 MarkDuplicates Before output close freeMemory: 863576552; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:36 MarkDuplicates After output close freeMemory: 856375440; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:36 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:36 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14065455767955839383/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14065455767955839383/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14065455767955839383/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:36 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 13:08:36 MarkDuplicates Start of doWork freeMemory: 986409408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:36 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 931872280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:36 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 716917536; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:37 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:37 MarkDuplicates Before output close freeMemory: 859381552; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:37 MarkDuplicates After output close freeMemory: 856374848; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:37 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18170792383826146211/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18170792383826146211/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18170792383826146211/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:37 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 13:08:37 MarkDuplicates Start of doWork freeMemory: 986408712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 931874416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:37 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 716913528; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:37 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:38 MarkDuplicates Before output close freeMemory: 859380856; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:38 MarkDuplicates After output close freeMemory: 856376728; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:38 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3534897533345801395/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3534897533345801395/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3534897533345801395/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:38 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 13:08:38 MarkDuplicates Start of doWork freeMemory: 986408016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:38 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 931873720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:38 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 716915480; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:38 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:38 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:38 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:39 MarkDuplicates Before output close freeMemory: 859380160; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:39 MarkDuplicates After output close freeMemory: 856373424; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:39 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7540064501950789537/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7540064501950789537/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7540064501950789537/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:39 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 13:08:39 MarkDuplicates Start of doWork freeMemory: 986407320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:39 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 931873024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:39 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 716914784; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:39 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:39 MarkDuplicates Before output close freeMemory: 856233736; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:40 MarkDuplicates After output close freeMemory: 856372656; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:40 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1422114896867086112/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1422114896867086112/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1422114896867086112/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:40 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 13:08:40 MarkDuplicates Start of doWork freeMemory: 986403632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:40 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 931872344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:40 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 985349560; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:40 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:40 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:40 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:40 MarkDuplicates Before output close freeMemory: 856233048; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:41 MarkDuplicates After output close freeMemory: 856371968; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:41 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6490775141665477340/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6490775141665477340/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp6490775141665477340/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:41 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 13:08:41 MarkDuplicates Start of doWork freeMemory: 986405936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:41 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 931868824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:41 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 576401584; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:08:41 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:41 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:41 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:41 MarkDuplicates Before output close freeMemory: 845746600; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:08:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:42 MarkDuplicates After output close freeMemory: 845885592; totalMemory: 1202716672; maxMemory: 2147483648 [Thu Apr 24 13:08:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1202716672 [Thu Apr 24 13:08:42 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14259499122097473775/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14259499122097473775/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14259499122097473775/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:42 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 13:08:42 MarkDuplicates Start of doWork freeMemory: 986405104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:42 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 931870808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:42 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 716909920; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:42 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:42 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:42 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:42 MarkDuplicates Before output close freeMemory: 863571552; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:42 MarkDuplicates After output close freeMemory: 859518848; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:42 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12427658599729703157/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12427658599729703157/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12427658599729703157/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:42 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 13:08:43 MarkDuplicates Start of doWork freeMemory: 986404408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:43 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 931870128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:43 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 985347344; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:43 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:43 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:43 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:43 MarkDuplicates Before output close freeMemory: 863570864; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:43 MarkDuplicates After output close freeMemory: 856372400; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:43 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1297496052975047585/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1297496052975047585/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1297496052975047585/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:43 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 13:08:44 MarkDuplicates Start of doWork freeMemory: 986403696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:44 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 931866568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:44 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 716911824; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:44 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:44 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:44 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:44 MarkDuplicates Before output close freeMemory: 856230112; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:44 MarkDuplicates After output close freeMemory: 856371680; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:44 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp319000574201762289/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp319000574201762289/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp319000574201762289/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:44 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 13:08:45 MarkDuplicates Start of doWork freeMemory: 986402984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 931868704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:45 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 775631384; totalMemory: 1401946112; maxMemory: 2147483648 INFO 2025-04-24 13:08:45 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:45 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:45 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:45 MarkDuplicates Before output close freeMemory: 863569440; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:45 MarkDuplicates After output close freeMemory: 853225320; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:45 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15814802460358622546/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15814802460358622546/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15814802460358622546/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:45 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 13:08:45 MarkDuplicates Start of doWork freeMemory: 986402288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 931867808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:46 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 716907104; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:46 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:46 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:46 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:46 MarkDuplicates Before output close freeMemory: 863568736; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:46 MarkDuplicates After output close freeMemory: 863707688; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:08:46 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:08:46 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9615955247844804467/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9615955247844804467/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9615955247844804467/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:46 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 13:08:46 MarkDuplicates Start of doWork freeMemory: 986401592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 931867312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:47 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 772484264; totalMemory: 1398800384; maxMemory: 2147483648 INFO 2025-04-24 13:08:47 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:47 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:47 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:47 MarkDuplicates Before output close freeMemory: 856228016; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:47 MarkDuplicates After output close freeMemory: 856367040; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:47 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13944849432611672422/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13944849432611672422/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13944849432611672422/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:47 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 13:08:47 MarkDuplicates Start of doWork freeMemory: 986400928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:47 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 931866648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:48 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 716908408; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:48 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:48 MarkDuplicates Before output close freeMemory: 859373080; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:48 MarkDuplicates After output close freeMemory: 856366376; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:48 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp493382163869448887/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp493382163869448887/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp493382163869448887/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:48 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 13:08:48 MarkDuplicates Start of doWork freeMemory: 986400664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:48 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 931866368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:49 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 775628896; totalMemory: 1401946112; maxMemory: 2147483648 INFO 2025-04-24 13:08:49 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:49 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:08:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:49 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:49 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:49 MarkDuplicates Before output close freeMemory: 856227040; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:49 MarkDuplicates After output close freeMemory: 853222776; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:49 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9040502915057248919/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9040502915057248919/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9040502915057248919/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:49 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 13:08:49 MarkDuplicates Start of doWork freeMemory: 986399680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:49 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 931865384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:50 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 716904344; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:50 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:50 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:08:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:50 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:50 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:50 MarkDuplicates Before output close freeMemory: 853080256; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:08:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:50 MarkDuplicates After output close freeMemory: 853219240; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:50 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7798443068418915804/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7798443068418915804/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7798443068418915804/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:50 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 13:08:50 MarkDuplicates Start of doWork freeMemory: 986397872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:50 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:08:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 931863344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:51 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 775626112; totalMemory: 1401946112; maxMemory: 2147483648 INFO 2025-04-24 13:08:51 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:08:51 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:08:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:51 MarkDuplicates Before output close freeMemory: 856224248; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:51 MarkDuplicates After output close freeMemory: 856363064; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:51 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13227458533803489018/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13227458533803489018/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13227458533803489018/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:51 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 13:08:51 MarkDuplicates Start of doWork freeMemory: 986398040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:51 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 931863576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:52 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 716902720; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:52 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:52 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:08:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:52 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:52 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:52 MarkDuplicates Before output close freeMemory: 853078648; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:08:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:52 MarkDuplicates After output close freeMemory: 853217504; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:52 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11990536521368156104/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11990536521368156104/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11990536521368156104/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:52 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 13:08:52 MarkDuplicates Start of doWork freeMemory: 986398504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:52 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:08:52 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:08:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 931864528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:53 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 1145774296; totalMemory: 1772093440; maxMemory: 2147483648 INFO 2025-04-24 13:08:53 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:53 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:53 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:53 MarkDuplicates Before output close freeMemory: 863565104; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:53 MarkDuplicates After output close freeMemory: 859509744; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:08:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:08:53 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11067512060442711099/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11067512060442711099/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11067512060442711099/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:53 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 13:08:53 MarkDuplicates Start of doWork freeMemory: 986398456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:53 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:53 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 13:08:53 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2025-04-24 13:08:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 931864760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:54 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 843783992; totalMemory: 1470103552; maxMemory: 2147483648 INFO 2025-04-24 13:08:54 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:54 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:54 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:54 MarkDuplicates Before output close freeMemory: 859371216; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:54 MarkDuplicates After output close freeMemory: 856364264; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:54 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4796762847568584299/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4796762847568584299/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4796762847568584299/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:54 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 13:08:54 MarkDuplicates Start of doWork freeMemory: 986396832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:54 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:54 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 13:08:54 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:08:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 931862776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:54 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 716901728; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:55 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:08:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:55 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:55 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:55 MarkDuplicates Before output close freeMemory: 863563488; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:55 MarkDuplicates After output close freeMemory: 853216512; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:08:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:08:55 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7457830242262382974/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7457830242262382974/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7457830242262382974/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:55 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 13:08:55 MarkDuplicates Start of doWork freeMemory: 986394648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:55 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:55 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 13:08:55 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:08:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 931860352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:55 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 985337648; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:56 MarkDuplicates Marking 3 records as duplicates. INFO 2025-04-24 13:08:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:56 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:56 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:56 MarkDuplicates Before output close freeMemory: 869852760; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2025-04-24 13:08:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:56 MarkDuplicates After output close freeMemory: 856360056; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:56 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:56 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15298915637729038885/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15298915637729038885/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp15298915637729038885/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:56 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 13:08:56 MarkDuplicates Start of doWork freeMemory: 986395808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:56 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:08:56 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 13:08:56 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:08:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 931861816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:56 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 716904000; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:57 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:57 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:57 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:57 MarkDuplicates Before output close freeMemory: 863562456; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:08:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:57 MarkDuplicates After output close freeMemory: 856361208; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:57 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1745411222275937489/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1745411222275937489/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1745411222275937489/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:57 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 13:08:57 MarkDuplicates Start of doWork freeMemory: 986395824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:57 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:57 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:08:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 931862304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:57 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 985339216; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:08:58 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:58 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:58 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:58 MarkDuplicates Before output close freeMemory: 856223168; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:08:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:58 MarkDuplicates After output close freeMemory: 856364288; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:58 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:58 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12585302446761892078/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12585302446761892078/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12585302446761892078/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:58 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 13:08:58 MarkDuplicates Start of doWork freeMemory: 986394696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:58 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:58 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:08:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 931858360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:58 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 716902648; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:08:59 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:08:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:08:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:08:59 MarkDuplicates Before output close freeMemory: 859367776; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:08:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:08:59 MarkDuplicates After output close freeMemory: 856360512; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:08:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:08:59 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14219860337436466725/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14219860337436466725/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14219860337436466725/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:08:59 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 13:08:59 MarkDuplicates Start of doWork freeMemory: 986281872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:59 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:08:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:08:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:08:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 931718584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:08:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:08:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:08:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:08:59 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:08:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 772335384; totalMemory: 1398800384; maxMemory: 2147483648 INFO 2025-04-24 13:08:59 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:08:59 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:08:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:08:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:08:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:08:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:00 MarkDuplicates Before output close freeMemory: 863390040; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:00 MarkDuplicates After output close freeMemory: 853074976; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:00 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7594197637382675902/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7594197637382675902/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7594197637382675902/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:00 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 13:09:00 MarkDuplicates Start of doWork freeMemory: 986381840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:00 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:09:00 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2025-04-24 13:09:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 931845704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:00 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 716889144; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:00 MarkDuplicates Marking 12 records as duplicates. INFO 2025-04-24 13:09:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:00 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:01 MarkDuplicates Before output close freeMemory: 866693984; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:09:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:01 MarkDuplicates After output close freeMemory: 853201384; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:01 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8127241577762634370/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8127241577762634370/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8127241577762634370/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:01 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 13:09:01 MarkDuplicates Start of doWork freeMemory: 986389024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:01 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:01 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:01 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 13:09:01 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:09:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 931854568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:01 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 768277456; totalMemory: 1394606080; maxMemory: 2147483648 INFO 2025-04-24 13:09:01 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:09:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:01 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:01 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:01 MarkDuplicates Before output close freeMemory: 863555680; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:02 MarkDuplicates After output close freeMemory: 863694496; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:09:02 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:09:02 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10094549579763419636/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10094549579763419636/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10094549579763419636/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:02 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 13:09:02 MarkDuplicates Start of doWork freeMemory: 986388064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:02 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:02 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 13:09:02 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:09:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 931853592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:02 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 716892768; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:02 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:02 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:02 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:02 MarkDuplicates Before output close freeMemory: 856214432; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:03 MarkDuplicates After output close freeMemory: 856353392; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:03 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:03 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7333942791740246535/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7333942791740246535/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7333942791740246535/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:03 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 13:09:03 MarkDuplicates Start of doWork freeMemory: 986383288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:03 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:03 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 13:09:03 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2025-04-24 13:09:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 931847992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:03 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 1041946624; totalMemory: 1668284416; maxMemory: 2147483648 INFO 2025-04-24 13:09:03 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:09:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:03 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:03 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:03 MarkDuplicates Before output close freeMemory: 859355520; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:04 MarkDuplicates After output close freeMemory: 856351328; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:04 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:04 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16236642349812342401/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16236642349812342401/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16236642349812342401/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:04 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 13:09:04 MarkDuplicates Start of doWork freeMemory: 986387952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:04 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:04 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 13:09:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 931854016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:04 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 845867992; totalMemory: 1472200704; maxMemory: 2147483648 INFO 2025-04-24 13:09:04 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:04 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:04 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:04 MarkDuplicates Before output close freeMemory: 856214984; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:05 MarkDuplicates After output close freeMemory: 853210608; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:05 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:05 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12404688097128242020/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12404688097128242020/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12404688097128242020/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:05 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 13:09:05 MarkDuplicates Start of doWork freeMemory: 986384424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:05 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:05 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 13:09:05 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2025-04-24 13:09:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 931849608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:05 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 1052436832; totalMemory: 1678770176; maxMemory: 2147483648 INFO 2025-04-24 13:09:05 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:09:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:05 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:05 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:05 MarkDuplicates Before output close freeMemory: 859356656; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:06 MarkDuplicates After output close freeMemory: 856352392; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:06 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17048440689524544280/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17048440689524544280/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17048440689524544280/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:06 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 13:09:06 MarkDuplicates Start of doWork freeMemory: 986387584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:06 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:06 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 13:09:06 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:09:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 931853808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:06 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 576386904; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:09:06 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:09:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:06 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:06 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:06 MarkDuplicates Before output close freeMemory: 845725608; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:09:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:06 MarkDuplicates After output close freeMemory: 845870744; totalMemory: 1202716672; maxMemory: 2147483648 [Thu Apr 24 13:09:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1202716672 [Thu Apr 24 13:09:07 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4491607315870876966/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4491607315870876966/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp4491607315870876966/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:07 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 13:09:07 MarkDuplicates Start of doWork freeMemory: 986385384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:07 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:07 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 13:09:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 931851168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:07 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 1048243608; totalMemory: 1674575872; maxMemory: 2147483648 INFO 2025-04-24 13:09:07 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:07 MarkDuplicates Before output close freeMemory: 863551968; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:07 MarkDuplicates After output close freeMemory: 859496624; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:09:07 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3469749989214452117/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3469749989214452117/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3469749989214452117/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:07 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 13:09:08 MarkDuplicates Start of doWork freeMemory: 986384768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:08 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:08 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 13:09:08 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 931850536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:08 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 573238048; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:09:08 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:08 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:08 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:08 MarkDuplicates Before output close freeMemory: 842579896; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:09:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:08 MarkDuplicates After output close freeMemory: 842718784; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:09:08 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:09:08 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14673373225315150767/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14673373225315150767/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14673373225315150767/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:08 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 13:09:09 MarkDuplicates Start of doWork freeMemory: 986384000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:09 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:09 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 13:09:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 931849768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:09 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 1037756448; totalMemory: 1664090112; maxMemory: 2147483648 INFO 2025-04-24 13:09:09 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:09 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:09 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:09 MarkDuplicates Before output close freeMemory: 856210616; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:09 MarkDuplicates After output close freeMemory: 849009472; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:09:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:09:09 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp695230505765387151/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp695230505765387151/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp695230505765387151/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:09 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 13:09:10 MarkDuplicates Start of doWork freeMemory: 986383000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:10 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:10 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 13:09:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 931848768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:10 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 853206072; totalMemory: 1479540736; maxMemory: 2147483648 INFO 2025-04-24 13:09:10 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:10 MarkDuplicates Before output close freeMemory: 856209616; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:10 MarkDuplicates After output close freeMemory: 856348504; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:10 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:10 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5802535829710952073/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5802535829710952073/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5802535829710952073/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:10 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 13:09:11 MarkDuplicates Start of doWork freeMemory: 986381544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:11 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:11 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 13:09:11 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 931847328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:11 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 772464280; totalMemory: 1398800384; maxMemory: 2147483648 INFO 2025-04-24 13:09:11 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:11 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:11 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:11 MarkDuplicates Before output close freeMemory: 859354008; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:11 MarkDuplicates After output close freeMemory: 853204440; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:11 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18275690093563693762/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18275690093563693762/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18275690093563693762/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:11 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 13:09:12 MarkDuplicates Start of doWork freeMemory: 986380872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:12 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:12 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 13:09:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 931846640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:12 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 985324520; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:12 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:12 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:12 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:12 MarkDuplicates Before output close freeMemory: 859353536; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:12 MarkDuplicates After output close freeMemory: 859492368; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:09:12 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3220063026229956598/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3220063026229956598/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3220063026229956598/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:12 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 13:09:13 MarkDuplicates Start of doWork freeMemory: 986379608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:13 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:13 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 13:09:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 931845376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:13 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 782948088; totalMemory: 1409286144; maxMemory: 2147483648 INFO 2025-04-24 13:09:13 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:13 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:13 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:13 MarkDuplicates Before output close freeMemory: 863546576; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:13 MarkDuplicates After output close freeMemory: 856348224; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:13 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12307727972505917727/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12307727972505917727/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp12307727972505917727/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:13 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 13:09:14 MarkDuplicates Start of doWork freeMemory: 986379688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:14 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:14 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 13:09:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 931845472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:14 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 985320040; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:14 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:14 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:14 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:14 MarkDuplicates Before output close freeMemory: 859351968; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:14 MarkDuplicates After output close freeMemory: 853199472; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:14 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:14 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7391381766550222377/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7391381766550222377/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7391381766550222377/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:14 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 13:09:15 MarkDuplicates Start of doWork freeMemory: 986378736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:15 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:15 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 13:09:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 931844504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:15 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 849007504; totalMemory: 1475346432; maxMemory: 2147483648 INFO 2025-04-24 13:09:15 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:15 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:15 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:15 MarkDuplicates Before output close freeMemory: 863545312; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:15 MarkDuplicates After output close freeMemory: 856347352; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:15 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:15 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18425540768022901827/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18425540768022901827/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp18425540768022901827/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:15 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 13:09:16 MarkDuplicates Start of doWork freeMemory: 986377912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:16 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:16 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 13:09:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 931843696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:16 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 716882808; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:16 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:16 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:16 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:16 MarkDuplicates Before output close freeMemory: 863544496; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:16 MarkDuplicates After output close freeMemory: 849006504; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:09:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:09:16 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1311123267974309773/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1311123267974309773/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1311123267974309773/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:16 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 13:09:17 MarkDuplicates Start of doWork freeMemory: 986377048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:17 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:17 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 13:09:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 931842832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:17 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 877317384; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:09:17 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:17 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:17 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:17 MarkDuplicates Before output close freeMemory: 856203600; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:17 MarkDuplicates After output close freeMemory: 856342560; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:17 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:17 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16751688594711414675/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16751688594711414675/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp16751688594711414675/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:17 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 13:09:18 MarkDuplicates Start of doWork freeMemory: 986376232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:18 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:18 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 13:09:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 931842016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:18 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 986367808; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:09:18 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:18 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:18 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:18 MarkDuplicates Before output close freeMemory: 859348512; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:18 MarkDuplicates After output close freeMemory: 856344392; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:18 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:18 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9121167247026328065/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9121167247026328065/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9121167247026328065/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:18 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 13:09:19 MarkDuplicates Start of doWork freeMemory: 986376584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:19 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:19 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 13:09:19 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2025-04-24 13:09:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 931842688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:19 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 985317112; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:19 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:19 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:19 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:19 MarkDuplicates Before output close freeMemory: 863543392; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:19 MarkDuplicates After output close freeMemory: 859488000; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:09:19 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13412065698307091612/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13412065698307091612/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp13412065698307091612/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:19 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 13:09:20 MarkDuplicates Start of doWork freeMemory: 986373256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:20 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 931838776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:20 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 573226320; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:09:20 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:20 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:20 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:20 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:20 MarkDuplicates Before output close freeMemory: 842568072; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:09:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:20 MarkDuplicates After output close freeMemory: 842709704; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:09:20 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:09:20 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10278485530667199098/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10278485530667199098/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10278485530667199098/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:20 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 13:09:20 MarkDuplicates Start of doWork freeMemory: 986372464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:20 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 931835328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:21 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 716880440; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:21 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:21 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:21 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:21 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:21 MarkDuplicates Before output close freeMemory: 859344496; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:21 MarkDuplicates After output close freeMemory: 859483480; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:09:21 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9638238469072574841/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9638238469072574841/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9638238469072574841/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:21 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 13:09:21 MarkDuplicates Start of doWork freeMemory: 986371760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:21 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:21 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 931834624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:22 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 986363768; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:09:22 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:22 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:22 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:22 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:22 MarkDuplicates Before output close freeMemory: 856198064; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:22 MarkDuplicates After output close freeMemory: 856337040; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:22 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10336880914401952171/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10336880914401952171/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp10336880914401952171/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:22 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 13:09:22 MarkDuplicates Start of doWork freeMemory: 986369840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:22 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:22 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 931832728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:23 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 716877832; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:23 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:23 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:23 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:23 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:23 MarkDuplicates Before output close freeMemory: 856196152; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:23 MarkDuplicates After output close freeMemory: 853192032; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:23 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:23 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17024496340128684614/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17024496340128684614/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17024496340128684614/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:23 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 13:09:23 MarkDuplicates Start of doWork freeMemory: 986369144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:23 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:23 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:23 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 931834848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 985309496; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:24 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:24 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:24 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:24 MarkDuplicates Before output close freeMemory: 859341176; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:24 MarkDuplicates After output close freeMemory: 859480160; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:09:24 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9610535999969822732/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9610535999969822732/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9610535999969822732/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:24 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 13:09:24 MarkDuplicates Start of doWork freeMemory: 986368472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:24 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 931834008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:25 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 716876464; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:25 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:25 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:25 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:25 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:25 MarkDuplicates Before output close freeMemory: 863534816; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:25 MarkDuplicates After output close freeMemory: 856336384; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:25 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9766583139280801633/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9766583139280801633/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp9766583139280801633/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:25 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 13:09:25 MarkDuplicates Start of doWork freeMemory: 986366824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:25 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:25 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 931832560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:26 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 715826224; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:09:26 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:26 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:26 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:26 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:26 MarkDuplicates Before output close freeMemory: 856192656; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:26 MarkDuplicates After output close freeMemory: 856335224; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:26 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17104978313783850794/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17104978313783850794/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17104978313783850794/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:26 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 13:09:26 MarkDuplicates Start of doWork freeMemory: 986366112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:26 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:26 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 931831832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:27 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 986358136; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:09:27 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:27 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:27 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:27 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:27 MarkDuplicates Before output close freeMemory: 856192584; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:27 MarkDuplicates After output close freeMemory: 856331408; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:27 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:27 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2769546251805775256/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2769546251805775256/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp2769546251805775256/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:27 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 13:09:27 MarkDuplicates Start of doWork freeMemory: 986365416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:27 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:27 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 931830936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:27 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 846893712; totalMemory: 1473249280; maxMemory: 2147483648 INFO 2025-04-24 13:09:28 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:28 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:28 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:28 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:28 MarkDuplicates Before output close freeMemory: 863531912; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:28 MarkDuplicates After output close freeMemory: 859476328; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:09:28 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5791893594632010773/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5791893594632010773/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5791893594632010773/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:28 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 13:09:28 MarkDuplicates Start of doWork freeMemory: 986363528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:28 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:28 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 931829048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:28 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 985306536; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:29 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:29 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:29 MarkDuplicates Before output close freeMemory: 859335720; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:29 MarkDuplicates After output close freeMemory: 856331360; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:29 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:29 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp879860358696988908/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp879860358696988908/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp879860358696988908/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:29 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 13:09:29 MarkDuplicates Start of doWork freeMemory: 986360840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:29 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:29 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:29 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 931828352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:29 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 575313048; totalMemory: 1201668096; maxMemory: 2147483648 INFO 2025-04-24 13:09:30 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:30 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:30 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:30 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:30 MarkDuplicates Before output close freeMemory: 844654960; totalMemory: 1201668096; maxMemory: 2147483648 INFO 2025-04-24 13:09:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:30 MarkDuplicates After output close freeMemory: 844796432; totalMemory: 1201668096; maxMemory: 2147483648 [Thu Apr 24 13:09:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1201668096 [Thu Apr 24 13:09:30 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp723377549346635154/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp723377549346635154/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp723377549346635154/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:30 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 13:09:30 MarkDuplicates Start of doWork freeMemory: 986362128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:30 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:30 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:09:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 931827896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:30 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 715821592; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:09:30 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:30 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:30 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:30 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:31 MarkDuplicates Before output close freeMemory: 859334384; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:31 MarkDuplicates After output close freeMemory: 859475752; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:31 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:09:31 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1484648610997972210/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1484648610997972210/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1484648610997972210/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:31 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 13:09:31 MarkDuplicates Start of doWork freeMemory: 986363712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:31 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:31 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:09:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 931827352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:31 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 716869000; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:31 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:31 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:31 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:32 MarkDuplicates Before output close freeMemory: 859336784; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:32 MarkDuplicates After output close freeMemory: 856332176; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:32 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.tmp18103808146088220738/MarkDuplicates.sam --METRICS_FILE /tmp/MarkDuplicates.tmp18103808146088220738/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 13:09:32 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 13:09:32 MarkDuplicates Start of doWork freeMemory: 986369360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:32 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:32 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 13:09:32 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:09:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 923445376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:32 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:32 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 986360184; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:32 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:09:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:32 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:32 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:33 MarkDuplicates Before output close freeMemory: 986216416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:33 MarkDuplicates After output close freeMemory: 986360464; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:09:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:09:33 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.tmp7362180627063559347/MarkDuplicates.sam --METRICS_FILE /tmp/MarkDuplicates.tmp7362180627063559347/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 13:09:33 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 13:09:33 MarkDuplicates Start of doWork freeMemory: 986368448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:33 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:33 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 13:09:33 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:09:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 923444656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:33 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:33 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 986356816; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:33 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:09:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:33 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:33 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:33 MarkDuplicates Before output close freeMemory: 986073208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:34 MarkDuplicates After output close freeMemory: 986070280; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:09:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 INFO 2025-04-24 13:09:34 MarkDuplicates Start of doWork freeMemory: 986387880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:34 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:09:34 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 923466608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:34 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:34 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 985333176; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:09:34 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:34 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:34 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:34 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:34 MarkDuplicates Before output close freeMemory: 986194792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:35 MarkDuplicates After output close freeMemory: 986191752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:35 MarkDuplicates Start of doWork freeMemory: 986386920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:35 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:09:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 923465560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:35 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:35 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 985332128; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:09:35 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:35 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:09:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:35 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:35 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:35 MarkDuplicates Before output close freeMemory: 986193720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:36 MarkDuplicates After output close freeMemory: 986190680; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:09:36 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7992778728628670447/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7992778728628670447/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7992778728628670447/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:36 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 13:09:36 MarkDuplicates Start of doWork freeMemory: 986356112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:36 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:36 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 13:09:36 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2025-04-24 13:09:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 931822128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:36 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 985299200; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:36 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:36 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:36 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:36 MarkDuplicates Before output close freeMemory: 866619064; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:09:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:37 MarkDuplicates After output close freeMemory: 863470296; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:09:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:09:37 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17126461554903302356/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17126461554903302356/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp17126461554903302356/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:37 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 13:09:37 MarkDuplicates Start of doWork freeMemory: 986352616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:37 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:09:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 931817896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:37 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 716860568; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:37 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:37 MarkDuplicates Before output close freeMemory: 863469328; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:37 MarkDuplicates After output close freeMemory: 856126256; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:37 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3860023405603121356/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3860023405603121356/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp3860023405603121356/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:37 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 13:09:38 MarkDuplicates Start of doWork freeMemory: 986353176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:38 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 931818880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:38 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 985296760; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:38 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:38 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:38 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:38 MarkDuplicates Before output close freeMemory: 859275824; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:38 MarkDuplicates After output close freeMemory: 852981328; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:38 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8072417899983236747/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8072417899983236747/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp8072417899983236747/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:38 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 13:09:39 MarkDuplicates Start of doWork freeMemory: 986353936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:39 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:39 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 13:09:39 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:09:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 931820160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:39 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 716859128; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:39 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:09:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:39 MarkDuplicates Before output close freeMemory: 859277400; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:39 MarkDuplicates After output close freeMemory: 852982824; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:39 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_ONE_BARCODE_TAG BX --READ_TWO_BARCODE_TAG BX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7003671929008682524/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7003671929008682524/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp7003671929008682524/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:39 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 13:09:40 MarkDuplicates Start of doWork freeMemory: 986350040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:09:40 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:09:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 931815520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:40 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 716854696; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:40 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:40 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:40 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:40 MarkDuplicates Before output close freeMemory: 856126656; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:40 MarkDuplicates After output close freeMemory: 856123584; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:40 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI false --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11949029722032946961/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11949029722032946961/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp11949029722032946961/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_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 13:09:40 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 13:09:40 MarkDuplicates Start of doWork freeMemory: 986348800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:40 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 13:09:40 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 931814584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:41 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 716853696; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:41 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:41 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:41 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:41 MarkDuplicates Before output close freeMemory: 852980536; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:09:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:41 MarkDuplicates After output close freeMemory: 852977496; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:09:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:09:41 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI false --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1793153855717503250/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1793153855717503250/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp1793153855717503250/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_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 13:09:41 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 13:09:41 MarkDuplicates Start of doWork freeMemory: 986348192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:41 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:41 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 13:09:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 931813976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:42 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 985288544; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:42 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:42 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:42 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:42 MarkDuplicates Before output close freeMemory: 863462440; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:09:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:42 MarkDuplicates After output close freeMemory: 859271456; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:09:42 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI true --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14508993187754882729/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14508993187754882729/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp14508993187754882729/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_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 13:09:42 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 13:09:42 MarkDuplicates Start of doWork freeMemory: 986347480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:42 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:42 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 13:09:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 931813264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:43 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 716855688; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:43 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:09:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:43 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:43 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:43 MarkDuplicates Before output close freeMemory: 856124936; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:09:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:43 MarkDuplicates After output close freeMemory: 856124440; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:09:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:09:43 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI true --INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5071738514061761997/input.sam --OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5071738514061761997/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.tmp5071738514061761997/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_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 13:09:43 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 13:09:43 MarkDuplicates Start of doWork freeMemory: 986346760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:43 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:09:43 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 13:09:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:09:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 931812528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:44 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 716851640; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:09:44 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:44 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:44 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:44 MarkDuplicates Before output close freeMemory: 859269936; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:09:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:44 MarkDuplicates After output close freeMemory: 859266824; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:09:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160