Class picard.sam.markduplicates.MarkDuplicatesTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| pgRecordChainingTest[0](false, {1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1685e349, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@405b2944], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@118191a4], 1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6838c67e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@511eff9b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4816fdf5]}) | 1.041s | passed |
| pgRecordChainingTest[1](true, {1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7298d843], 1AAXX.3.1=[], 1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2f2dd6d4, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f1996a1]}) | 1.015s | passed |
| testBulkFragmentsNoDuplicates[0](.sam) | 1.240s | passed |
| testBulkFragmentsNoDuplicates[1](.bam) | 1.318s | passed |
| testBulkFragmentsNoDuplicates[2](.cram) | 1.752s | passed |
| testBulkFragmentsWithDuplicates[0](.sam) | 1.454s | passed |
| testBulkFragmentsWithDuplicates[1](.bam) | 1.446s | passed |
| testBulkFragmentsWithDuplicates[2](.cram) | 2.295s | passed |
| testBulkPairsNoDuplicates[0](.sam) | 1.475s | passed |
| testBulkPairsNoDuplicates[1](.bam) | 1.416s | passed |
| testBulkPairsNoDuplicates[2](.cram) | 2.407s | passed |
| testBulkPairsWithDuplicates[0](.sam) | 1.065s | passed |
| testBulkPairsWithDuplicates[1](.bam) | 1.064s | passed |
| testBulkPairsWithDuplicates[2](.cram) | 1.516s | passed |
| testDifferentChromosomesInOppositeOrder | 0.920s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.964s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.977s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.945s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.953s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.933s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 1.047s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 1.042s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 1.055s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.964s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 1.047s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.988s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.948s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.948s | passed |
| testMappedPairAndMatePairSecondUnmapped | 1.043s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.976s | passed |
| testMappedPairWithSamePosition | 1.037s | passed |
| testMappedPairWithSamePositionSameCigar | 0.927s | passed |
| testMatePairFirstUnmapped | 0.981s | passed |
| testMatePairSecondUnmapped | 1.009s | passed |
| testOpticalDuplicateBehaviorNullRegex | 0.976s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.971s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 1.029s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) | 1.038s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) | 1.039s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) | 0.934s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) | 0.977s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) | 0.941s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) | 0.940s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) | 0.989s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) | 1.006s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) | 1.046s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) | 0.925s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) | 0.974s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) | 0.962s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) | 0.979s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) | 0.940s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.924s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.956s | passed |
| testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) | 1.035s | passed |
| testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) | 1.007s | passed |
| testOpticalDuplicateFinding | 0.943s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.909s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 1.008s | passed |
| testSingleMappedFragment | 0.947s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.949s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.966s | passed |
| testSingleMappedPair | 0.951s | passed |
| testSingleUnmappedFragment | 0.970s | passed |
| testSingleUnmappedPair | 1.002s | passed |
| testStackOverFlowPairSetSwap | 1.008s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.944s | passed |
| testThreeMappedPairs | 0.963s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.949s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 1.028s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.922s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 1.041s | passed |
| testTwoMappedFragments | 0.961s | passed |
| testTwoMappedPairWithSamePosition | 0.978s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 1.003s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.957s | passed |
| testTwoMappedPairs | 0.952s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.971s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.958s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.978s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.966s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.965s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.957s | passed |
| testTwoMappedPairsWithSoftClipping | 0.962s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 1.021s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 0.967s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.912s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.949s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.982s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 1.005s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.920s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 1.003s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.987s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.964s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.997s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.961s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.965s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 1.081s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.963s | passed |
| testTwoUnmappedFragments | 0.970s | passed |
| testWithBarcodeComplex | 0.958s | passed |
| testWithBarcodeDuplicate | 1.009s | passed |
| testWithBarcodeFragmentDuplicate | 0.974s | passed |
| testWithIndividualReadBarcodes | 0.951s | passed |
| testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) | 0.978s | passed |
| testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) | 0.971s | passed |
| testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) | 0.942s | passed |
| testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) | 1.026s | passed |
Standard error
[Thu Apr 24 13:13:23 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6203947642421131575/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6203947642421131575/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6203947642421131575/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:23 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 13:13:23 MarkDuplicates Start of doWork freeMemory: 979231592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:23 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:23 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 13:13:23 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:13:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 915586592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:23 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 546162128; totalMemory: 1179648000; maxMemory: 2147483648 INFO 2025-04-24 13:13:23 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:23 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:23 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:23 MarkDuplicates Before output close freeMemory: 815500936; totalMemory: 1179648000; maxMemory: 2147483648 INFO 2025-04-24 13:13:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:24 MarkDuplicates After output close freeMemory: 815646096; totalMemory: 1179648000; maxMemory: 2147483648 [Thu Apr 24 13:13:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1179648000 [Thu Apr 24 13:13:24 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12521142054825457340/input.bam --OUTPUT /tmp/MarkDuplicatesTester.tmp12521142054825457340/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12521142054825457340/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:24 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 13:13:24 MarkDuplicates Start of doWork freeMemory: 979230872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:24 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 13:13:24 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:13:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 915585416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 978126384; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:13:25 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:25 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:25 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:25 MarkDuplicates Before output close freeMemory: 873126240; totalMemory: 1237319680; maxMemory: 2147483648 INFO 2025-04-24 13:13:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:25 MarkDuplicates After output close freeMemory: 870122776; totalMemory: 1234173952; maxMemory: 2147483648 [Thu Apr 24 13:13:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1234173952 [Thu Apr 24 13:13:26 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12221871459913697854/input.cram --OUTPUT /tmp/MarkDuplicatesTester.tmp12221871459913697854/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12221871459913697854/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester14022662691664318578/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 13:13:26 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 13:13:26 MarkDuplicates Start of doWork freeMemory: 979004224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:26 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:26 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 13:13:26 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:13:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 915363496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:26 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 678059952; totalMemory: 1311768576; maxMemory: 2147483648 INFO 2025-04-24 13:13:26 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:26 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:26 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:27 MarkDuplicates Before output close freeMemory: 883438192; totalMemory: 1247805440; maxMemory: 2147483648 INFO 2025-04-24 13:13:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:27 MarkDuplicates After output close freeMemory: 877285568; totalMemory: 1241513984; maxMemory: 2147483648 [Thu Apr 24 13:13:27 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1241513984 [Thu Apr 24 13:13:27 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp16517268114090849647/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp16517268114090849647/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16517268114090849647/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:27 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 13:13:27 MarkDuplicates Start of doWork freeMemory: 970965256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:27 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:27 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 13:13:27 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:13:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 906530440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:28 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 969911312; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:13:28 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:13:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:28 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:28 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:28 MarkDuplicates Before output close freeMemory: 890076904; totalMemory: 1262485504; maxMemory: 2147483648 INFO 2025-04-24 13:13:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:28 MarkDuplicates After output close freeMemory: 886022400; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:13:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:13:28 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17040571320050433565/input.bam --OUTPUT /tmp/MarkDuplicatesTester.tmp17040571320050433565/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17040571320050433565/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:28 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 13:13:29 MarkDuplicates Start of doWork freeMemory: 971028592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:29 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:29 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 13:13:29 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:13:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 906596144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:29 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 942711464; totalMemory: 1584398336; maxMemory: 2147483648 INFO 2025-04-24 13:13:29 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:13:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:29 MarkDuplicates Before output close freeMemory: 890136824; totalMemory: 1262485504; maxMemory: 2147483648 INFO 2025-04-24 13:13:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:30 MarkDuplicates After output close freeMemory: 886085224; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:13:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:13:30 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp4608482053598132567/input.cram --OUTPUT /tmp/MarkDuplicatesTester.tmp4608482053598132567/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4608482053598132567/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester14895303433656623521/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 13:13:30 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 13:13:30 MarkDuplicates Start of doWork freeMemory: 970767784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:30 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:31 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 13:13:31 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:13:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 906333000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:31 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 861708112; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:13:31 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:13:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:32 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:32 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:32 MarkDuplicates Before output close freeMemory: 893022696; totalMemory: 1265631232; maxMemory: 2147483648 INFO 2025-04-24 13:13:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:32 MarkDuplicates After output close freeMemory: 890019488; totalMemory: 1262485504; maxMemory: 2147483648 [Thu Apr 24 13:13:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1262485504 [Thu Apr 24 13:13:32 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2073725794353334572/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2073725794353334572/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2073725794353334572/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:32 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 13:13:32 MarkDuplicates Start of doWork freeMemory: 970509480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:32 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:32 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:13:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 905407176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:33 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 1137177416; totalMemory: 1779433472; maxMemory: 2147483648 INFO 2025-04-24 13:13:33 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:33 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:33 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:33 MarkDuplicates Before output close freeMemory: 900056568; totalMemory: 1272971264; maxMemory: 2147483648 INFO 2025-04-24 13:13:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:33 MarkDuplicates After output close freeMemory: 889716152; totalMemory: 1262485504; maxMemory: 2147483648 [Thu Apr 24 13:13:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1262485504 [Thu Apr 24 13:13:34 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2253731816731982142/input.bam --OUTPUT /tmp/MarkDuplicatesTester.tmp2253731816731982142/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2253731816731982142/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:34 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 13:13:34 MarkDuplicates Start of doWork freeMemory: 970508584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:34 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:34 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:13:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 905403736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:34 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 914928152; totalMemory: 1557135360; maxMemory: 2147483648 INFO 2025-04-24 13:13:34 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:34 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:34 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:35 MarkDuplicates Before output close freeMemory: 889616400; totalMemory: 1262485504; maxMemory: 2147483648 INFO 2025-04-24 13:13:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:35 MarkDuplicates After output close freeMemory: 885564888; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:13:35 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:13:36 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp13697187769874281953/input.cram --OUTPUT /tmp/MarkDuplicatesTester.tmp13697187769874281953/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13697187769874281953/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester3902485592479293148/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 13:13:36 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 13:13:36 MarkDuplicates Start of doWork freeMemory: 970340056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:36 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:36 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 13:13:36 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:13:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 905236080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:36 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 804657272; totalMemory: 1447034880; maxMemory: 2147483648 INFO 2025-04-24 13:13:36 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:37 MarkDuplicates Before output close freeMemory: 895743480; totalMemory: 1268776960; maxMemory: 2147483648 INFO 2025-04-24 13:13:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:37 MarkDuplicates After output close freeMemory: 892737504; totalMemory: 1265631232; maxMemory: 2147483648 [Thu Apr 24 13:13:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1265631232 [Thu Apr 24 13:13:37 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2455310166884745923/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2455310166884745923/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2455310166884745923/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:37 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 13:13:37 MarkDuplicates Start of doWork freeMemory: 981027584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:38 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:13:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 917367648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:38 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 817443808; totalMemory: 1449132032; maxMemory: 2147483648 INFO 2025-04-24 13:13:38 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:13:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:38 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:38 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:38 MarkDuplicates Before output close freeMemory: 871827064; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2025-04-24 13:13:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:38 MarkDuplicates After output close freeMemory: 864629296; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:13:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:13:38 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1808510202785234279/input.bam --OUTPUT /tmp/MarkDuplicatesTester.tmp1808510202785234279/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1808510202785234279/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:38 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 13:13:39 MarkDuplicates Start of doWork freeMemory: 981028568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:39 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:39 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 13:13:39 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:13:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 917369424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:39 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 871968736; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:13:39 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:13:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:39 MarkDuplicates Before output close freeMemory: 868676880; totalMemory: 1231028224; maxMemory: 2147483648 INFO 2025-04-24 13:13:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:39 MarkDuplicates After output close freeMemory: 868819696; totalMemory: 1231028224; maxMemory: 2147483648 [Thu Apr 24 13:13:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1231028224 [Thu Apr 24 13:13:40 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp288002089550941083/input.cram --OUTPUT /tmp/MarkDuplicatesTester.tmp288002089550941083/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp288002089550941083/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester13555463940788891734/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 13:13:40 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 13:13:40 MarkDuplicates Start of doWork freeMemory: 980899696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:40 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:13:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 917237640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:40 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 980891792; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:13:40 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:13:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:41 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:41 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:41 MarkDuplicates Before output close freeMemory: 885325936; totalMemory: 1247805440; maxMemory: 2147483648 INFO 2025-04-24 13:13:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:41 MarkDuplicates After output close freeMemory: 868691144; totalMemory: 1231028224; maxMemory: 2147483648 [Thu Apr 24 13:13:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1231028224 [Thu Apr 24 13:13:41 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15479711263216436342/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15479711263216436342/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15479711263216436342/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:41 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 13:13:41 MarkDuplicates Start of doWork freeMemory: 986147856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:41 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:13:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:13:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 923224872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:41 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 636963928; totalMemory: 1263534080; maxMemory: 2147483648 INFO 2025-04-24 13:13:42 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:13:42 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:13:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:42 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:42 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:42 MarkDuplicates Before output close freeMemory: 852828256; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:13:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:42 MarkDuplicates After output close freeMemory: 848775544; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:13:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:13:42 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3685028233879510917/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3685028233879510917/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3685028233879510917/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:42 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 13:13:42 MarkDuplicates Start of doWork freeMemory: 986139656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:42 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:13:42 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:13:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 923213328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:42 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 803679456; totalMemory: 1430257664; maxMemory: 2147483648 INFO 2025-04-24 13:13:43 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:13:43 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:13:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:43 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:43 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:43 MarkDuplicates Before output close freeMemory: 863305976; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:13:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:43 MarkDuplicates After output close freeMemory: 852959240; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:13:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:13:43 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8901156383459939574/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8901156383459939574/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8901156383459939574/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:43 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 13:13:43 MarkDuplicates Start of doWork freeMemory: 986138936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:43 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:13:43 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:13:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 923215448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:43 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 715598352; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:13:43 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:13:43 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:13:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:43 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:43 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:44 MarkDuplicates Before output close freeMemory: 866450984; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:13:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:44 MarkDuplicates After output close freeMemory: 859250240; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:13:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:13:44 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp16812821117839072859/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp16812821117839072859/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16812821117839072859/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:44 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 13:13:44 MarkDuplicates Start of doWork freeMemory: 986138240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:44 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:13:44 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:13:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 923214752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:44 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 877078360; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:13:44 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:13:44 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:13:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:44 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:44 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:45 MarkDuplicates Before output close freeMemory: 859110256; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:13:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:45 MarkDuplicates After output close freeMemory: 856103448; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:13:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:13:45 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12791711064211052557/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12791711064211052557/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12791711064211052557/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:45 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 13:13:45 MarkDuplicates Start of doWork freeMemory: 986137568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:13:45 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:13:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 923213896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:45 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 716645560; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:13:45 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:13:45 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:13:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:45 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:45 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:46 MarkDuplicates Before output close freeMemory: 859109584; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:13:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:46 MarkDuplicates After output close freeMemory: 859248608; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:13:46 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:13:46 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17876656075794111648/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17876656075794111648/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17876656075794111648/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:46 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 13:13:46 MarkDuplicates Start of doWork freeMemory: 986136888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:13:46 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:13:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 923213384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:46 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 877076992; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:13:46 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:13:46 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:13:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:46 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:46 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:46 MarkDuplicates Before output close freeMemory: 859108896; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:13:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:47 MarkDuplicates After output close freeMemory: 856102192; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:13:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:13:47 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15520797228617274693/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15520797228617274693/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15520797228617274693/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:47 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 13:13:47 MarkDuplicates Start of doWork freeMemory: 986136192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:13:47 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:13:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 923212504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:47 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 985079624; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:13:47 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:13:47 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:13:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:47 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:47 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:48 MarkDuplicates Before output close freeMemory: 855962472; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:13:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:48 MarkDuplicates After output close freeMemory: 856101496; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:13:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:13:48 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8783919874088529904/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8783919874088529904/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8783919874088529904/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:48 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 13:13:48 MarkDuplicates Start of doWork freeMemory: 986142104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:48 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:48 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:13:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 923219240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:48 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 1068968832; totalMemory: 1695547392; maxMemory: 2147483648 INFO 2025-04-24 13:13:48 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:49 MarkDuplicates Before output close freeMemory: 855966048; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:13:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:49 MarkDuplicates After output close freeMemory: 856107928; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:13:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:13:49 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9559969672343571807/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9559969672343571807/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9559969672343571807/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:49 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 13:13:49 MarkDuplicates Start of doWork freeMemory: 986141128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:49 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:49 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:13:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 923218760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:49 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 986133664; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:13:49 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:13:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:49 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:49 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:50 MarkDuplicates Before output close freeMemory: 866453968; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:13:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:50 MarkDuplicates After output close freeMemory: 859252680; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:13:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:13:50 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14620772253678706817/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14620772253678706817/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14620772253678706817/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:50 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 13:13:50 MarkDuplicates Start of doWork freeMemory: 986140520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:50 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:13:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 923218152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:50 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 877081152; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:13:50 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:13:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:50 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:50 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:51 MarkDuplicates Before output close freeMemory: 855967600; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:13:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:51 MarkDuplicates After output close freeMemory: 856106336; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:13:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:13:51 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17995045422317668632/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17995045422317668632/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17995045422317668632/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:51 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 13:13:51 MarkDuplicates Start of doWork freeMemory: 986138416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:51 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:51 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:13:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 923215696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:51 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 986130640; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:13:51 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:13:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:52 MarkDuplicates Before output close freeMemory: 863305008; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:13:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:52 MarkDuplicates After output close freeMemory: 852961320; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:13:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:13:52 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp16222286708988267950/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp16222286708988267950/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16222286708988267950/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:52 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 13:13:52 MarkDuplicates Start of doWork freeMemory: 986137456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:52 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:52 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 13:13:52 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:13:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 923214736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:52 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 956769552; totalMemory: 1583349760; maxMemory: 2147483648 INFO 2025-04-24 13:13:52 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:13:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:52 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:52 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:53 MarkDuplicates Before output close freeMemory: 859109744; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:13:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:53 MarkDuplicates After output close freeMemory: 856105864; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:13:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:13:53 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11665562530285644772/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11665562530285644772/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11665562530285644772/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:53 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 13:13:53 MarkDuplicates Start of doWork freeMemory: 986137112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:53 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:53 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 13:13:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:13:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 923214464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:53 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 715596728; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:13:53 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:53 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:53 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:54 MarkDuplicates Before output close freeMemory: 866448784; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:13:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:54 MarkDuplicates After output close freeMemory: 863445776; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:13:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:13:54 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15204072499828283041/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15204072499828283041/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15204072499828283041/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:54 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 13:13:54 MarkDuplicates Start of doWork freeMemory: 986136472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:54 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:54 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 13:13:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:13:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 923213840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:54 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 877076808; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:13:54 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:13:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:54 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:54 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:54 MarkDuplicates Before output close freeMemory: 863303072; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:13:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:55 MarkDuplicates After output close freeMemory: 859247656; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:13:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:13:55 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3786041331989070899/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3786041331989070899/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3786041331989070899/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:55 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 13:13:55 MarkDuplicates Start of doWork freeMemory: 986135736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:55 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:55 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 13:13:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:13:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 923213088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:55 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 986127960; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:13:55 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:13:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:55 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:55 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:56 MarkDuplicates Before output close freeMemory: 855962296; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:13:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:56 MarkDuplicates After output close freeMemory: 856101152; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:13:56 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:13:56 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9379453347622737669/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9379453347622737669/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9379453347622737669/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:56 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 13:13:56 MarkDuplicates Start of doWork freeMemory: 986134744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:56 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:56 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 13:13:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:13:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 923211968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:56 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 954669704; totalMemory: 1581252608; maxMemory: 2147483648 INFO 2025-04-24 13:13:56 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:56 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:56 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:57 MarkDuplicates Before output close freeMemory: 859103792; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:13:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:57 MarkDuplicates After output close freeMemory: 859249040; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:13:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:13:57 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10161831178296743193/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10161831178296743193/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10161831178296743193/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:57 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 13:13:57 MarkDuplicates Start of doWork freeMemory: 986135320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:57 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:13:57 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:13:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 923212760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:57 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 986127560; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:13:57 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:57 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:57 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:58 MarkDuplicates Before output close freeMemory: 855961888; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:13:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:58 MarkDuplicates After output close freeMemory: 852957736; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:13:58 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:13:58 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp27825814087179844/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp27825814087179844/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp27825814087179844/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:58 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 13:13:58 MarkDuplicates Start of doWork freeMemory: 986134528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:58 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:58 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 13:13:58 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:13:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 923211968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:58 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 877074864; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:13:58 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:58 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:58 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:58 MarkDuplicates Before output close freeMemory: 859106824; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:13:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:13:59 MarkDuplicates After output close freeMemory: 856100056; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:13:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:13:59 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3282041286020797612/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3282041286020797612/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3282041286020797612/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:13:59 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 13:13:59 MarkDuplicates Start of doWork freeMemory: 986133872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:59 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:13:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:13:59 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 13:13:59 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:13:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 923211560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:13:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:13:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:13:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:13:59 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:13:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 715593784; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:13:59 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:13:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:13:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:13:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:13:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:13:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:13:59 MarkDuplicates Before output close freeMemory: 859106568; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:13:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:00 MarkDuplicates After output close freeMemory: 856099688; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:00 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10506979425834578296/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10506979425834578296/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10506979425834578296/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:00 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 13:14:00 MarkDuplicates Start of doWork freeMemory: 986133176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:00 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:00 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 13:14:00 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:14:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 923210880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:00 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 1038554512; totalMemory: 1665138688; maxMemory: 2147483648 INFO 2025-04-24 13:14:00 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:14:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:00 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:00 MarkDuplicates Before output close freeMemory: 859106000; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:01 MarkDuplicates After output close freeMemory: 856101544; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:01 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp737586871090744720/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp737586871090744720/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp737586871090744720/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_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 13:14:01 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 13:14:01 MarkDuplicates Start of doWork freeMemory: 986131128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:01 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:01 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 923208168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:01 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 577175824; totalMemory: 1203765248; maxMemory: 2147483648 INFO 2025-04-24 13:14:01 MarkDuplicates Marking 2 records as duplicates. WARNING 2025-04-24 13:14:01 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! INFO 2025-04-24 13:14:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:01 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:01 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:01 MarkDuplicates Before output close freeMemory: 846520704; totalMemory: 1203765248; maxMemory: 2147483648 INFO 2025-04-24 13:14:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:02 MarkDuplicates After output close freeMemory: 846659560; totalMemory: 1203765248; maxMemory: 2147483648 [Thu Apr 24 13:14:02 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1203765248 [Thu Apr 24 13:14:02 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2274362933674278563/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2274362933674278563/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2274362933674278563/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:02 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 13:14:02 MarkDuplicates Start of doWork freeMemory: 986129960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:02 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 923204264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:02 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 803669744; totalMemory: 1430257664; maxMemory: 2147483648 INFO 2025-04-24 13:14:02 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:02 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:02 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:02 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:02 MarkDuplicates Before output close freeMemory: 859101944; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:03 MarkDuplicates After output close freeMemory: 859240992; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:03 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:03 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12268237175053111072/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12268237175053111072/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12268237175053111072/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:03 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 13:14:03 MarkDuplicates Start of doWork freeMemory: 986128072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:03 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 923205216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:03 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 986120232; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:14:03 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:03 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:03 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:03 MarkDuplicates Before output close freeMemory: 866440264; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:14:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:04 MarkDuplicates After output close freeMemory: 863433488; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:14:04 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:14:04 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1469387539174101710/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1469387539174101710/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1469387539174101710/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:04 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 13:14:04 MarkDuplicates Start of doWork freeMemory: 986127456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:04 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 923204432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:04 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 809958864; totalMemory: 1436549120; maxMemory: 2147483648 INFO 2025-04-24 13:14:04 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:04 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:04 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:04 MarkDuplicates Before output close freeMemory: 855953896; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:05 MarkDuplicates After output close freeMemory: 852947192; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:05 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:05 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8926412171100708164/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8926412171100708164/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8926412171100708164/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:05 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 13:14:05 MarkDuplicates Start of doWork freeMemory: 986126792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:05 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 923201112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:05 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 716634936; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:05 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:05 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:05 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:05 MarkDuplicates Before output close freeMemory: 859098960; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:06 MarkDuplicates After output close freeMemory: 859240560; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:06 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2724697834358068451/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2724697834358068451/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2724697834358068451/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:06 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 13:14:06 MarkDuplicates Start of doWork freeMemory: 986126128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:06 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 923203272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:06 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 799471760; totalMemory: 1426063360; maxMemory: 2147483648 INFO 2025-04-24 13:14:06 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:06 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:06 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:06 MarkDuplicates Before output close freeMemory: 863292592; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:07 MarkDuplicates After output close freeMemory: 859237312; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:07 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp266077868259170028/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp266077868259170028/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp266077868259170028/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:07 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 13:14:07 MarkDuplicates Start of doWork freeMemory: 986125472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:07 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 923202448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:07 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 985069072; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:14:07 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:07 MarkDuplicates Before output close freeMemory: 863291944; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:08 MarkDuplicates After output close freeMemory: 856093552; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:08 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:08 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5064990236283685626/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5064990236283685626/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5064990236283685626/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:08 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 13:14:08 MarkDuplicates Start of doWork freeMemory: 986124792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:08 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:08 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 923201752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:08 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 799470424; totalMemory: 1426063360; maxMemory: 2147483648 INFO 2025-04-24 13:14:08 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:08 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:08 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:08 MarkDuplicates Before output close freeMemory: 859096952; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:09 MarkDuplicates After output close freeMemory: 852944520; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:09 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11056691082567464663/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11056691082567464663/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11056691082567464663/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:09 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 13:14:09 MarkDuplicates Start of doWork freeMemory: 986124104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:09 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 923198424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:09 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 716632248; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:09 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:09 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:09 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:09 MarkDuplicates Before output close freeMemory: 855950544; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:09 MarkDuplicates After output close freeMemory: 852946392; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:10 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14390297169056645420/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14390297169056645420/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14390297169056645420/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:10 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 13:14:10 MarkDuplicates Start of doWork freeMemory: 986123432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:10 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 923200592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:10 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 877063704; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:10 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:10 MarkDuplicates Before output close freeMemory: 863289904; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:10 MarkDuplicates After output close freeMemory: 859237168; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:10 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:10 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1997694669785031670/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1997694669785031670/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1997694669785031670/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:10 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 13:14:11 MarkDuplicates Start of doWork freeMemory: 986122776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:11 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 923199752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:11 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 716627840; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:11 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:11 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:11 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:11 MarkDuplicates Before output close freeMemory: 866434976; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:14:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:11 MarkDuplicates After output close freeMemory: 856088168; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:11 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3290889469485834878/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3290889469485834878/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3290889469485834878/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:11 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 13:14:12 MarkDuplicates Start of doWork freeMemory: 986122112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:12 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 923199256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:12 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 877062368; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:12 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:12 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:12 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:12 MarkDuplicates Before output close freeMemory: 863288576; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:12 MarkDuplicates After output close freeMemory: 863427600; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:14:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:14:12 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2883859346981890375/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2883859346981890375/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2883859346981890375/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:12 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 13:14:13 MarkDuplicates Start of doWork freeMemory: 986121440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:13 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 923198416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:13 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 985061728; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:14:13 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:13 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:13 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:13 MarkDuplicates Before output close freeMemory: 855947880; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:13 MarkDuplicates After output close freeMemory: 856089480; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:13 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2295388257440001360/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2295388257440001360/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2295388257440001360/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:13 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 13:14:14 MarkDuplicates Start of doWork freeMemory: 986120752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:14 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 923195080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:14 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 877061024; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:14 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:14 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:14 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:14 MarkDuplicates Before output close freeMemory: 863287224; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:14 MarkDuplicates After output close freeMemory: 859231944; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:14 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:14 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5793906278732764874/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5793906278732764874/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5793906278732764874/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:14 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 13:14:15 MarkDuplicates Start of doWork freeMemory: 986120088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:15 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 923194400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:15 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 715579640; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:14:15 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:15 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:15 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:15 MarkDuplicates Before output close freeMemory: 866432280; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:14:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:15 MarkDuplicates After output close freeMemory: 863425472; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:14:15 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:14:15 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9496942564446805527/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9496942564446805527/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9496942564446805527/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:15 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 13:14:15 MarkDuplicates Start of doWork freeMemory: 986119368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:15 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 923196528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:16 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 877059640; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:16 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:16 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:16 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:16 MarkDuplicates Before output close freeMemory: 863285840; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:16 MarkDuplicates After output close freeMemory: 859233176; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:16 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12434656791348294394/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12434656791348294394/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12434656791348294394/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:16 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 13:14:16 MarkDuplicates Start of doWork freeMemory: 986118712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:16 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 923193040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:17 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 986110888; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:14:17 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:17 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:17 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:17 MarkDuplicates Before output close freeMemory: 859090880; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:17 MarkDuplicates After output close freeMemory: 856086720; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:17 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:17 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5185399657229866314/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5185399657229866314/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5185399657229866314/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:17 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 13:14:17 MarkDuplicates Start of doWork freeMemory: 986118472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:17 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 923192800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:18 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 877058592; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:18 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:18 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:18 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:18 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:18 MarkDuplicates Before output close freeMemory: 855944872; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:18 MarkDuplicates After output close freeMemory: 856083752; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:18 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:18 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12348390058088555607/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12348390058088555607/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12348390058088555607/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:18 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 13:14:18 MarkDuplicates Start of doWork freeMemory: 986117488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:18 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 923191800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:19 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 715576888; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:14:19 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:19 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:19 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:19 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:19 MarkDuplicates Before output close freeMemory: 859089536; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:19 MarkDuplicates After output close freeMemory: 859228416; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:19 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp569550471974998675/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp569550471974998675/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp569550471974998675/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:19 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 13:14:19 MarkDuplicates Start of doWork freeMemory: 986115728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:19 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:19 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:14:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 923192664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:20 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 877055840; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:20 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:14:20 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:20 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:20 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:20 MarkDuplicates Before output close freeMemory: 863282152; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:20 MarkDuplicates After output close freeMemory: 859226768; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:20 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:20 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3707068701340670428/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3707068701340670428/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3707068701340670428/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:20 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 13:14:20 MarkDuplicates Start of doWork freeMemory: 986115904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 923190216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:21 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 716620568; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:21 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:21 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:21 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:21 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:21 MarkDuplicates Before output close freeMemory: 859087976; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:21 MarkDuplicates After output close freeMemory: 856081208; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:21 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp67324160649623210/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp67324160649623210/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp67324160649623210/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:21 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 13:14:21 MarkDuplicates Start of doWork freeMemory: 986116464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:21 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:21 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 13:14:21 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:14:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 923193888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:22 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 1068945528; totalMemory: 1695547392; maxMemory: 2147483648 INFO 2025-04-24 13:14:22 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:14:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:22 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:22 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:22 MarkDuplicates Before output close freeMemory: 859088768; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:22 MarkDuplicates After output close freeMemory: 859227608; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:22 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6810738267352268156/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6810738267352268156/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6810738267352268156/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:22 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 13:14:22 MarkDuplicates Start of doWork freeMemory: 986116400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:22 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:22 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 13:14:22 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2025-04-24 13:14:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 923190872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:23 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 572966664; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:14:23 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:14:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:23 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:23 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:23 MarkDuplicates Before output close freeMemory: 842311952; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:14:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:23 MarkDuplicates After output close freeMemory: 842453272; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:14:23 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:14:23 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11889604441838150226/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11889604441838150226/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11889604441838150226/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:23 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 13:14:23 MarkDuplicates Start of doWork freeMemory: 986114440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:23 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:23 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 13:14:23 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:14:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 923191792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 877054760; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:24 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:14:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:24 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:24 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:24 MarkDuplicates Before output close freeMemory: 863281104; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:24 MarkDuplicates After output close freeMemory: 863422640; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:14:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:14:24 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp13677952383801247839/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp13677952383801247839/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13677952383801247839/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:24 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 13:14:24 MarkDuplicates Start of doWork freeMemory: 986112264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:24 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 13:14:24 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 923189400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 716620456; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:25 MarkDuplicates Marking 3 records as duplicates. INFO 2025-04-24 13:14:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:25 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:25 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:25 MarkDuplicates Before output close freeMemory: 859084624; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:25 MarkDuplicates After output close freeMemory: 852931952; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:25 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17490136921117999443/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17490136921117999443/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17490136921117999443/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:25 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 13:14:25 MarkDuplicates Start of doWork freeMemory: 986113432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:25 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:25 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 13:14:25 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:14:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 923190872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:25 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 877053768; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:26 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:14:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:26 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:26 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:26 MarkDuplicates Before output close freeMemory: 855940072; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:26 MarkDuplicates After output close freeMemory: 856078856; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:26 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12553282927182508671/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12553282927182508671/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12553282927182508671/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:26 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 13:14:26 MarkDuplicates Start of doWork freeMemory: 986113472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:26 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:26 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:14:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 923188512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:26 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 715573496; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:14:27 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:14:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:27 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:27 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:27 MarkDuplicates Before output close freeMemory: 859086560; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:27 MarkDuplicates After output close freeMemory: 852933568; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:27 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:27 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1285527866904582579/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1285527866904582579/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1285527866904582579/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:27 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 13:14:27 MarkDuplicates Start of doWork freeMemory: 986112328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:27 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:27 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:14:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 923190200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:27 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 1038533760; totalMemory: 1665138688; maxMemory: 2147483648 INFO 2025-04-24 13:14:28 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:14:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:28 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:28 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:28 MarkDuplicates Before output close freeMemory: 855939688; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:28 MarkDuplicates After output close freeMemory: 856078152; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:28 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp582697226271588999/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp582697226271588999/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp582697226271588999/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:28 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 13:14:28 MarkDuplicates Start of doWork freeMemory: 985999536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:28 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 923044856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:28 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 845453368; totalMemory: 1472200704; maxMemory: 2147483648 INFO 2025-04-24 13:14:29 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:29 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:29 MarkDuplicates Before output close freeMemory: 863107720; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:29 MarkDuplicates After output close freeMemory: 859081488; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:29 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:29 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp869086140881882429/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp869086140881882429/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp869086140881882429/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:29 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 13:14:29 MarkDuplicates Start of doWork freeMemory: 986099528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:29 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:29 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 13:14:29 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2025-04-24 13:14:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 923174984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:29 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 877039608; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:29 MarkDuplicates Marking 12 records as duplicates. INFO 2025-04-24 13:14:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:30 MarkDuplicates Before output close freeMemory: 859071648; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:30 MarkDuplicates After output close freeMemory: 859210536; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:30 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8099742651251147855/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8099742651251147855/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8099742651251147855/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:30 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 13:14:30 MarkDuplicates Start of doWork freeMemory: 986106712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:30 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:30 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 13:14:30 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:14:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 923183720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:30 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 716614920; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:30 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:14:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:30 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:30 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:31 MarkDuplicates Before output close freeMemory: 859079080; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:31 MarkDuplicates After output close freeMemory: 859217864; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:31 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:31 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12636016791899011312/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12636016791899011312/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12636016791899011312/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:31 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 13:14:31 MarkDuplicates Start of doWork freeMemory: 986105760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:31 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:31 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 13:14:31 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:14:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 923182768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:31 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 877045920; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:31 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:31 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:31 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:32 MarkDuplicates Before output close freeMemory: 863272184; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:32 MarkDuplicates After output close freeMemory: 859216840; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:32 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5836280763630447024/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5836280763630447024/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5836280763630447024/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:32 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 13:14:32 MarkDuplicates Start of doWork freeMemory: 986101024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:32 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:32 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2025-04-24 13:14:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 923177264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:32 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 986093144; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:14:32 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:14:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:32 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:32 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:33 MarkDuplicates Before output close freeMemory: 866413304; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:14:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:33 MarkDuplicates After output close freeMemory: 856066432; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:33 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17312329465519603468/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17312329465519603468/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17312329465519603468/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:33 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 13:14:33 MarkDuplicates Start of doWork freeMemory: 986105696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:33 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 923183184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:33 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 877046328; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:33 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:33 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:33 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:33 MarkDuplicates Before output close freeMemory: 855932744; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:34 MarkDuplicates After output close freeMemory: 852928904; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:34 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17837235668300209778/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17837235668300209778/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17837235668300209778/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:34 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 13:14:34 MarkDuplicates Start of doWork freeMemory: 986102184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:34 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:34 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2025-04-24 13:14:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 923178856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:34 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 986094304; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:14:34 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:14:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:34 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:34 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:35 MarkDuplicates Before output close freeMemory: 855928704; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:35 MarkDuplicates After output close freeMemory: 856070168; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:35 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:35 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8675829839888540625/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8675829839888540625/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8675829839888540625/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:35 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 13:14:35 MarkDuplicates Start of doWork freeMemory: 986105376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:35 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:35 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:14:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 923183008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:35 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 799451384; totalMemory: 1426063360; maxMemory: 2147483648 INFO 2025-04-24 13:14:35 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:14:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:35 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:35 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:35 MarkDuplicates Before output close freeMemory: 855932424; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:36 MarkDuplicates After output close freeMemory: 856071200; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:36 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:36 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10087367008185143665/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10087367008185143665/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10087367008185143665/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:36 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 13:14:36 MarkDuplicates Start of doWork freeMemory: 986103184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:36 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:36 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 13:14:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 923180408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:36 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 716610936; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:36 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:36 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:36 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:36 MarkDuplicates Before output close freeMemory: 855929752; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:37 MarkDuplicates After output close freeMemory: 856068680; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:37 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11826133379800990486/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11826133379800990486/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11826133379800990486/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:37 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 13:14:37 MarkDuplicates Start of doWork freeMemory: 986102584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 923179808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:37 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 1038523624; totalMemory: 1665138688; maxMemory: 2147483648 INFO 2025-04-24 13:14:37 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:37 MarkDuplicates Before output close freeMemory: 866414984; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:14:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:38 MarkDuplicates After output close freeMemory: 856070760; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:38 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10383657521912454370/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10383657521912454370/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10383657521912454370/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:38 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 13:14:38 MarkDuplicates Start of doWork freeMemory: 986101840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:38 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 923179064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:38 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 577148984; totalMemory: 1203765248; maxMemory: 2147483648 INFO 2025-04-24 13:14:38 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:38 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:38 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:38 MarkDuplicates Before output close freeMemory: 846491296; totalMemory: 1203765248; maxMemory: 2147483648 INFO 2025-04-24 13:14:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:39 MarkDuplicates After output close freeMemory: 846632800; totalMemory: 1203765248; maxMemory: 2147483648 [Thu Apr 24 13:14:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1203765248 [Thu Apr 24 13:14:39 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15562339890623086198/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15562339890623086198/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15562339890623086198/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:39 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 13:14:39 MarkDuplicates Start of doWork freeMemory: 986100880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:39 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:39 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 13:14:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 923178104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:39 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 877041216; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:39 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:39 MarkDuplicates Before output close freeMemory: 863267552; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:40 MarkDuplicates After output close freeMemory: 859212104; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:40 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17138736961038203857/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17138736961038203857/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17138736961038203857/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:40 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 13:14:40 MarkDuplicates Start of doWork freeMemory: 986099456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:40 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 923176664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:40 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 716604336; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:40 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:40 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:40 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:40 MarkDuplicates Before output close freeMemory: 859071928; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:41 MarkDuplicates After output close freeMemory: 859210696; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:41 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3577239073371153038/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3577239073371153038/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3577239073371153038/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:41 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 13:14:41 MarkDuplicates Start of doWork freeMemory: 986098808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:41 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 923176032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:41 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 803638824; totalMemory: 1430257664; maxMemory: 2147483648 INFO 2025-04-24 13:14:41 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:41 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:41 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:41 MarkDuplicates Before output close freeMemory: 859071496; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:41 MarkDuplicates After output close freeMemory: 852921224; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:41 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp16367600346825150744/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp16367600346825150744/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16367600346825150744/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:41 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 13:14:42 MarkDuplicates Start of doWork freeMemory: 986097560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:42 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 923174768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:42 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 716602440; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:42 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:42 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:42 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:42 MarkDuplicates Before output close freeMemory: 859070240; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:42 MarkDuplicates After output close freeMemory: 856062976; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:42 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp4113225876724164939/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp4113225876724164939/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4113225876724164939/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:42 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 13:14:43 MarkDuplicates Start of doWork freeMemory: 986097672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:43 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 923174896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:43 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 877038008; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:14:43 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:14:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:43 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:43 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:43 MarkDuplicates Before output close freeMemory: 855924240; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:43 MarkDuplicates After output close freeMemory: 856065744; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:43 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp18320183134743850189/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp18320183134743850189/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp18320183134743850189/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:43 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 13:14:44 MarkDuplicates Start of doWork freeMemory: 986096728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:44 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 923173936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:44 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 715556344; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:14:44 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:44 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:44 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:44 MarkDuplicates Before output close freeMemory: 863263320; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:44 MarkDuplicates After output close freeMemory: 859210520; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:44 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11679179367414337511/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11679179367414337511/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11679179367414337511/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:44 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 13:14:45 MarkDuplicates Start of doWork freeMemory: 986095944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 923173168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:45 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 803635960; totalMemory: 1430257664; maxMemory: 2147483648 INFO 2025-04-24 13:14:45 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:45 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:45 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:45 MarkDuplicates Before output close freeMemory: 863262544; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:45 MarkDuplicates After output close freeMemory: 856061400; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:45 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8125553662962269816/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8125553662962269816/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8125553662962269816/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:45 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 13:14:45 MarkDuplicates Start of doWork freeMemory: 986095112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 923172320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:46 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 716603304; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:46 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:46 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:46 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:46 MarkDuplicates Before output close freeMemory: 855921672; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:46 MarkDuplicates After output close freeMemory: 856060528; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:46 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:46 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9359955333256240415/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9359955333256240415/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9359955333256240415/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:46 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 13:14:46 MarkDuplicates Start of doWork freeMemory: 986094312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:14:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 923171520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:47 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 1038515336; totalMemory: 1665138688; maxMemory: 2147483648 INFO 2025-04-24 13:14:47 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:47 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:47 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:47 MarkDuplicates Before output close freeMemory: 859066600; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:47 MarkDuplicates After output close freeMemory: 856059832; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:47 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12050808887016927906/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12050808887016927906/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12050808887016927906/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:47 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 13:14:47 MarkDuplicates Start of doWork freeMemory: 986094664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:14:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:14:47 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2025-04-24 13:14:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 923172160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:48 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 577142424; totalMemory: 1203765248; maxMemory: 2147483648 INFO 2025-04-24 13:14:48 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:14:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:14:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:48 MarkDuplicates Before output close freeMemory: 846484264; totalMemory: 1203765248; maxMemory: 2147483648 INFO 2025-04-24 13:14:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:48 MarkDuplicates After output close freeMemory: 846623176; totalMemory: 1203765248; maxMemory: 2147483648 [Thu Apr 24 13:14:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1203765248 [Thu Apr 24 13:14:48 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5984785655932016825/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5984785655932016825/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5984785655932016825/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:48 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 13:14:48 MarkDuplicates Start of doWork freeMemory: 986091360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:48 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:48 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 923168520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:49 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 806776888; totalMemory: 1433403392; maxMemory: 2147483648 INFO 2025-04-24 13:14:49 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:49 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:49 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:49 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:49 MarkDuplicates Before output close freeMemory: 855917688; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:49 MarkDuplicates After output close freeMemory: 856056672; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:49 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2936654120620811180/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2936654120620811180/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2936654120620811180/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:49 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 13:14:49 MarkDuplicates Start of doWork freeMemory: 986090600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:49 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:49 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 923167744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:50 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 716595264; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:50 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:50 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:50 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:50 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:50 MarkDuplicates Before output close freeMemory: 859062648; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:50 MarkDuplicates After output close freeMemory: 859204208; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:50 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2803881764577523686/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2803881764577523686/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2803881764577523686/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:50 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 13:14:50 MarkDuplicates Start of doWork freeMemory: 986089920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:50 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 923167080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:51 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 799435416; totalMemory: 1426063360; maxMemory: 2147483648 INFO 2025-04-24 13:14:51 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:51 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:51 MarkDuplicates Before output close freeMemory: 859061976; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:51 MarkDuplicates After output close freeMemory: 852909504; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:51 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp4524819884442908517/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp4524819884442908517/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4524819884442908517/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:51 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 13:14:51 MarkDuplicates Start of doWork freeMemory: 986089248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:51 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:51 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 923166408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:52 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 716596576; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:52 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:52 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:52 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:52 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:52 MarkDuplicates Before output close freeMemory: 859061304; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:52 MarkDuplicates After output close freeMemory: 852908728; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:52 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3297873031744945050/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3297873031744945050/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3297873031744945050/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:52 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 13:14:52 MarkDuplicates Start of doWork freeMemory: 986088576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:52 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:52 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 923165720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:53 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 799434056; totalMemory: 1426063360; maxMemory: 2147483648 INFO 2025-04-24 13:14:53 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:53 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:53 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:53 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:53 MarkDuplicates Before output close freeMemory: 863254928; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:14:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:53 MarkDuplicates After output close freeMemory: 856053880; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:14:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:14:53 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15763882740244019136/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15763882740244019136/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15763882740244019136/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:53 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 13:14:53 MarkDuplicates Start of doWork freeMemory: 986087880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:53 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:53 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 923165024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:54 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 716595192; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:54 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:54 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:54 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:54 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:54 MarkDuplicates Before output close freeMemory: 859059928; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:14:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:54 MarkDuplicates After output close freeMemory: 859201456; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:14:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:14:54 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9960459704225326172/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9960459704225326172/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9960459704225326172/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:54 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 13:14:54 MarkDuplicates Start of doWork freeMemory: 986086256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:54 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:54 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 923163416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:55 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 803626056; totalMemory: 1430257664; maxMemory: 2147483648 INFO 2025-04-24 13:14:55 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:55 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:55 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:55 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:55 MarkDuplicates Before output close freeMemory: 866398504; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:14:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:55 MarkDuplicates After output close freeMemory: 863394216; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:14:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:14:55 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp752355918734760981/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp752355918734760981/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp752355918734760981/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:55 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 13:14:55 MarkDuplicates Start of doWork freeMemory: 986085592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:55 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:55 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 923162736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:56 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 716590256; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:14:56 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:56 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:56 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:56 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:56 MarkDuplicates Before output close freeMemory: 855912072; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:14:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:56 MarkDuplicates After output close freeMemory: 852905064; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:56 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:56 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7760801775865021357/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7760801775865021357/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7760801775865021357/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:56 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 13:14:56 MarkDuplicates Start of doWork freeMemory: 986084896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:56 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:56 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 923161856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:57 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 1076254440; totalMemory: 1702887424; maxMemory: 2147483648 INFO 2025-04-24 13:14:57 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:57 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:57 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:57 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:57 MarkDuplicates Before output close freeMemory: 866397136; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:14:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:57 MarkDuplicates After output close freeMemory: 863390232; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:14:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:14:57 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17939245570235536704/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17939245570235536704/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17939245570235536704/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:57 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 13:14:57 MarkDuplicates Start of doWork freeMemory: 986084200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:57 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:57 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 923158528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:58 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 568742520; totalMemory: 1195376640; maxMemory: 2147483648 INFO 2025-04-24 13:14:58 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:58 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:58 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:58 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:58 MarkDuplicates Before output close freeMemory: 838084896; totalMemory: 1195376640; maxMemory: 2147483648 INFO 2025-04-24 13:14:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:58 MarkDuplicates After output close freeMemory: 838226264; totalMemory: 1195376640; maxMemory: 2147483648 [Thu Apr 24 13:14:58 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1195376640 [Thu Apr 24 13:14:58 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5957616995877341984/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5957616995877341984/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5957616995877341984/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:58 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 13:14:58 MarkDuplicates Start of doWork freeMemory: 986083536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:58 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:58 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 923160680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:14:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:14:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:14:59 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:14:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 1068913048; totalMemory: 1695547392; maxMemory: 2147483648 INFO 2025-04-24 13:14:59 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:14:59 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:14:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:14:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:14:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:14:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:14:59 MarkDuplicates Before output close freeMemory: 866395776; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:14:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:14:59 MarkDuplicates After output close freeMemory: 852903008; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:14:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:14:59 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10253050594876711997/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10253050594876711997/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10253050594876711997/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:14:59 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 13:14:59 MarkDuplicates Start of doWork freeMemory: 986082840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:59 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:14:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:14:59 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:14:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 923157168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:14:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:00 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 848710744; totalMemory: 1475346432; maxMemory: 2147483648 INFO 2025-04-24 13:15:00 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:15:00 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:15:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:00 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:00 MarkDuplicates Before output close freeMemory: 855906080; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:15:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:00 MarkDuplicates After output close freeMemory: 856051000; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:15:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:15:00 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9333597710481209508/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9333597710481209508/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9333597710481209508/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:15:00 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 13:15:00 MarkDuplicates Start of doWork freeMemory: 986084408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:00 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:15:00 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:15:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 923162280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:01 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 803624816; totalMemory: 1430257664; maxMemory: 2147483648 INFO 2025-04-24 13:15:01 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:15:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:01 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:01 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:01 MarkDuplicates Before output close freeMemory: 859057496; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:15:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:01 MarkDuplicates After output close freeMemory: 859195960; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:15:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:15:01 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.tmp16283952028402725843/MarkDuplicates.sam --METRICS_FILE /tmp/MarkDuplicates.tmp16283952028402725843/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 13:15:01 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 13:15:01 MarkDuplicates Start of doWork freeMemory: 986088616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:01 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:15:01 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 13:15:01 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:15:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 923164632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:01 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:02 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 985031528; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:15:02 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:15:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:02 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:02 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:02 MarkDuplicates Before output close freeMemory: 985936272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:02 MarkDuplicates After output close freeMemory: 986079224; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:15:02 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:15:02 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.tmp7120366079383750557/MarkDuplicates.sam --METRICS_FILE /tmp/MarkDuplicates.tmp7120366079383750557/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 13:15:02 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 13:15:02 MarkDuplicates Start of doWork freeMemory: 986087608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:02 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:15:02 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 13:15:02 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:15:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 923163800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:02 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:03 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 985030696; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:15:03 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:15:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:03 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:03 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:03 MarkDuplicates Before output close freeMemory: 985936392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:03 MarkDuplicates After output close freeMemory: 986075848; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:15:03 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 INFO 2025-04-24 13:15:03 MarkDuplicates Start of doWork freeMemory: 986107032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:03 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:15:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:15:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 923183096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:03 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:04 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 985052312; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:15:04 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:15:04 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:15:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:04 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:04 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:04 MarkDuplicates Before output close freeMemory: 985958600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:04 MarkDuplicates After output close freeMemory: 986100256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:04 MarkDuplicates Start of doWork freeMemory: 986106064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:04 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:15:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:15:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 923184704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:04 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:05 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 985051272; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:15:05 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:15:05 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:15:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:05 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:05 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:05 MarkDuplicates Before output close freeMemory: 985960160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:05 MarkDuplicates After output close freeMemory: 986096632; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:15:05 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp45713597730215150/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp45713597730215150/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp45713597730215150/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:15:05 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 13:15:05 MarkDuplicates Start of doWork freeMemory: 986075624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:05 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:15:05 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 13:15:05 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2025-04-24 13:15:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 923153064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:06 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 716583512; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:15:06 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:15:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:06 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:06 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:06 MarkDuplicates Before output close freeMemory: 859048000; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:15:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:06 MarkDuplicates After output close freeMemory: 859190096; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:15:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:15:06 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp13301312368762506912/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp13301312368762506912/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13301312368762506912/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:15:06 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 13:15:06 MarkDuplicates Start of doWork freeMemory: 986071992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:06 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:15:06 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:15:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 931537472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:07 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 778445944; totalMemory: 1405091840; maxMemory: 2147483648 INFO 2025-04-24 13:15:07 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:15:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:07 MarkDuplicates Before output close freeMemory: 859043976; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:15:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:07 MarkDuplicates After output close freeMemory: 852891448; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:15:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:15:07 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7409846741634495042/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7409846741634495042/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7409846741634495042/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:15:07 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 13:15:07 MarkDuplicates Start of doWork freeMemory: 986072592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:07 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:15:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:15:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 931538312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:08 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 985015528; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:15:08 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:15:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:08 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:08 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:08 MarkDuplicates Before output close freeMemory: 863239056; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:15:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:08 MarkDuplicates After output close freeMemory: 863380736; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:15:08 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:15:08 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp4124432526033737381/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp4124432526033737381/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4124432526033737381/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:15:08 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 13:15:08 MarkDuplicates Start of doWork freeMemory: 986073480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:08 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:15:08 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 13:15:08 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:15:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 931539704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:09 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 838216800; totalMemory: 1464860672; maxMemory: 2147483648 INFO 2025-04-24 13:15:09 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:15:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:09 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:09 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:09 MarkDuplicates Before output close freeMemory: 855900456; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:15:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:09 MarkDuplicates After output close freeMemory: 856039200; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:15:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:15:09 EDT 2025] MarkDuplicates --BARCODE_TAG BC --READ_ONE_BARCODE_TAG BX --READ_TWO_BARCODE_TAG BX --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1254857366412695379/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1254857366412695379/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1254857366412695379/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:15:09 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 13:15:09 MarkDuplicates Start of doWork freeMemory: 986069608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:09 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2025-04-24 13:15:09 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:15:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 931535088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:10 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 716574264; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:15:10 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:15:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:10 MarkDuplicates Before output close freeMemory: 855895792; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:15:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:10 MarkDuplicates After output close freeMemory: 852889136; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:15:10 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:15:10 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI false --INPUT /tmp/MarkDuplicatesTester.tmp1380391040969011099/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1380391040969011099/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1380391040969011099/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_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 13:15:10 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 13:15:10 MarkDuplicates Start of doWork freeMemory: 986068392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:10 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:15:10 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 13:15:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:15:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 931534160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:11 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 922097480; totalMemory: 1548746752; maxMemory: 2147483648 INFO 2025-04-24 13:15:11 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:15:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:11 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:11 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:11 MarkDuplicates Before output close freeMemory: 863235064; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:15:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:11 MarkDuplicates After output close freeMemory: 859179640; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:15:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:15:11 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI false --INPUT /tmp/MarkDuplicatesTester.tmp13550424374771309681/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp13550424374771309681/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13550424374771309681/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_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 13:15:11 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 13:15:11 MarkDuplicates Start of doWork freeMemory: 986067784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:11 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:15:11 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 13:15:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:15:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 931533552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:11 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 716575976; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:15:12 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:15:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:12 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:12 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:12 MarkDuplicates Before output close freeMemory: 859040152; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:15:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:12 MarkDuplicates After output close freeMemory: 852887576; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:15:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:15:12 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI true --INPUT /tmp/MarkDuplicatesTester.tmp17937861620115844930/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17937861620115844930/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17937861620115844930/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_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 13:15:12 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 13:15:12 MarkDuplicates Start of doWork freeMemory: 986067080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:12 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:15:12 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 13:15:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:15:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 931532848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:12 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 877007400; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:15:13 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:15:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:13 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:13 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:13 MarkDuplicates Before output close freeMemory: 863233752; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:15:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:13 MarkDuplicates After output close freeMemory: 859180976; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:15:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:15:13 EDT 2025] MarkDuplicates --BARCODE_TAG RX --TAGGING_POLICY OpticalOnly --DUPLEX_UMI true --INPUT /tmp/MarkDuplicatesTester.tmp14644604527496182612/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14644604527496182612/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14644604527496182612/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_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 13:15:13 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 13:15:13 MarkDuplicates Start of doWork freeMemory: 986065152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:13 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:15:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:15:13 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 13:15:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:15:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 931530936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:15:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:15:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:15:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:15:13 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:15:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 986057392; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:15:14 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:15:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:15:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:15:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:15:14 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:15:14 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:15:14 MarkDuplicates Before output close freeMemory: 859037528; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:15:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:15:14 MarkDuplicates After output close freeMemory: 859176304; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:15:14 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160