Class picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| TestSingleSet | 0.951s | passed |
| testBulkFragmentsNoDuplicates[0](.sam) | 1.297s | passed |
| testBulkFragmentsNoDuplicates[1](.bam) | 1.357s | passed |
| testBulkFragmentsNoDuplicates[2](.cram) | 1.873s | passed |
| testBulkFragmentsWithDuplicates[0](.sam) | 1.454s | passed |
| testBulkFragmentsWithDuplicates[1](.bam) | 1.458s | passed |
| testBulkFragmentsWithDuplicates[2](.cram) | 2.288s | passed |
| testBulkPairsNoDuplicates[0](.sam) | 1.659s | passed |
| testBulkPairsNoDuplicates[1](.bam) | 1.513s | passed |
| testBulkPairsNoDuplicates[2](.cram) | 2.489s | passed |
| testBulkPairsWithDuplicates[0](.sam) | 1.050s | passed |
| testBulkPairsWithDuplicates[1](.bam) | 1.029s | passed |
| testBulkPairsWithDuplicates[2](.cram) | 1.433s | passed |
| testDifferentChromosomesInOppositeOrder | 0.981s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.946s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.968s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.954s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.932s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.957s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.960s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.974s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.954s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 1.045s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.982s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.959s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.958s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.939s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.943s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.955s | passed |
| testMappedPairWithSamePosition | 0.945s | passed |
| testMappedPairWithSamePositionSameCigar | 1.025s | passed |
| testMatePairFirstUnmapped | 0.968s | passed |
| testMatePairSecondUnmapped | 0.959s | passed |
| testMultiRepresentativeReadTags | 0.908s | passed |
| testOpticalAndNonOpticalSet | 0.940s | passed |
| testOpticalDuplicateBehaviorNullRegex | 0.936s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 1.022s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.922s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) | 0.984s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) | 0.918s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) | 0.950s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) | 0.998s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) | 0.948s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) | 0.922s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) | 1.014s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) | 0.941s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) | 0.959s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) | 0.960s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) | 0.946s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) | 0.964s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) | 1.007s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) | 1.016s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.958s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.954s | passed |
| testOpticalDuplicateFinding | 1.016s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.986s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 1.022s | passed |
| testSingleMappedFragment | 0.965s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.933s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.991s | passed |
| testSingleMappedPair | 0.948s | passed |
| testSingleUnmappedFragment | 0.964s | passed |
| testSingleUnmappedPair | 0.951s | passed |
| testSingleton | 0.945s | passed |
| testStackOverFlowPairSetSwap | 0.962s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.957s | passed |
| testThreeMappedPairs | 0.951s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.954s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.930s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.957s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 1.024s | passed |
| testTwoMappedFragments | 0.911s | passed |
| testTwoMappedPairWithSamePosition | 1.028s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.924s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.951s | passed |
| testTwoMappedPairs | 0.950s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.949s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.952s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.964s | passed |
| testTwoMappedPairsMatesSoftClipped | 1.025s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.978s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 1.032s | passed |
| testTwoMappedPairsWithSoftClipping | 0.979s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.969s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 1.035s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.977s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.962s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.943s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 1.000s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.922s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.939s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.932s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.949s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.947s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.946s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.970s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.930s | passed |
| testTwoUnmappedFragments | 0.950s | passed |
Standard error
[Thu Apr 24 13:09:44 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5285736672300024277/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5285736672300024277/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5285736672300024277/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:44 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 13:09:44 MarkDuplicates Start of doWork freeMemory: 979409608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:44 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:44 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 13:09:44 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:09:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 915764520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:45 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 708869520; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:09:45 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:45 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:45 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:45 MarkDuplicates Before output close freeMemory: 877547728; totalMemory: 1241513984; maxMemory: 2147483648 INFO 2025-04-24 13:09:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:45 MarkDuplicates After output close freeMemory: 863007176; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:09:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:09:45 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3581751843841792964/input.bam --OUTPUT /tmp/MarkDuplicatesTester.tmp3581751843841792964/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3581751843841792964/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:45 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 13:09:46 MarkDuplicates Start of doWork freeMemory: 979409008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:46 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 13:09:46 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:09:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 915763712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:46 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 955281304; totalMemory: 1588592640; maxMemory: 2147483648 INFO 2025-04-24 13:09:46 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:46 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:46 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:46 MarkDuplicates Before output close freeMemory: 870203504; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2025-04-24 13:09:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:47 MarkDuplicates After output close freeMemory: 863006136; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:09:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:09:47 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5068486850048227212/input.cram --OUTPUT /tmp/MarkDuplicatesTester.tmp5068486850048227212/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5068486850048227212/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester6555411190527788199/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 13:09:47 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 13:09:47 MarkDuplicates Start of doWork freeMemory: 979373968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:48 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 13:09:48 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2025-04-24 13:09:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 915728728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:48 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 548401624; totalMemory: 1181745152; maxMemory: 2147483648 INFO 2025-04-24 13:09:48 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:48 MarkDuplicates Before output close freeMemory: 880654912; totalMemory: 1244659712; maxMemory: 2147483648 INFO 2025-04-24 13:09:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:48 MarkDuplicates After output close freeMemory: 870311440; totalMemory: 1234173952; maxMemory: 2147483648 [Thu Apr 24 13:09:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1234173952 [Thu Apr 24 13:09:49 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10085661157414567106/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10085661157414567106/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10085661157414567106/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:49 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 13:09:49 MarkDuplicates Start of doWork freeMemory: 971183632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:49 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:49 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 13:09:49 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:09:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 906748872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:49 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 970129744; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:09:50 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:09:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:50 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:50 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:50 MarkDuplicates Before output close freeMemory: 886100976; totalMemory: 1258291200; maxMemory: 2147483648 INFO 2025-04-24 13:09:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:50 MarkDuplicates After output close freeMemory: 886240744; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:09:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:09:50 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12055607022369917524/input.bam --OUTPUT /tmp/MarkDuplicatesTester.tmp12055607022369917524/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12055607022369917524/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:50 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 13:09:50 MarkDuplicates Start of doWork freeMemory: 971210616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:50 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 13:09:51 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:09:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 906772872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:51 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 945941816; totalMemory: 1587544064; maxMemory: 2147483648 INFO 2025-04-24 13:09:51 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:09:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:51 MarkDuplicates Before output close freeMemory: 890221416; totalMemory: 1262485504; maxMemory: 2147483648 INFO 2025-04-24 13:09:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:51 MarkDuplicates After output close freeMemory: 883024120; totalMemory: 1255145472; maxMemory: 2147483648 [Thu Apr 24 13:09:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1255145472 [Thu Apr 24 13:09:52 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp16418703784493646902/input.cram --OUTPUT /tmp/MarkDuplicatesTester.tmp16418703784493646902/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16418703784493646902/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester456332474207730144/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 13:09:52 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 13:09:52 MarkDuplicates Start of doWork freeMemory: 970814184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:52 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:52 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 13:09:53 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2025-04-24 13:09:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 906381480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:53 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 944596664; totalMemory: 1586495488; maxMemory: 2147483648 INFO 2025-04-24 13:09:53 MarkDuplicates Marking 20000 records as duplicates. INFO 2025-04-24 13:09:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:53 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:53 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:54 MarkDuplicates Before output close freeMemory: 903559688; totalMemory: 1276116992; maxMemory: 2147483648 INFO 2025-04-24 13:09:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:54 MarkDuplicates After output close freeMemory: 893216256; totalMemory: 1265631232; maxMemory: 2147483648 [Thu Apr 24 13:09:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1265631232 [Thu Apr 24 13:09:54 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5291052781774027278/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5291052781774027278/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5291052781774027278/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:54 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 13:09:54 MarkDuplicates Start of doWork freeMemory: 970561040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:54 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:54 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 13:09:54 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:09:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 905456744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:55 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 936998504; totalMemory: 1579155456; maxMemory: 2147483648 INFO 2025-04-24 13:09:55 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:55 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:55 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:55 MarkDuplicates Before output close freeMemory: 885476272; totalMemory: 1258291200; maxMemory: 2147483648 INFO 2025-04-24 13:09:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:55 MarkDuplicates After output close freeMemory: 885618296; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:09:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:09:56 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12472625003977766102/input.bam --OUTPUT /tmp/MarkDuplicatesTester.tmp12472625003977766102/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12472625003977766102/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:09:56 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 13:09:56 MarkDuplicates Start of doWork freeMemory: 970691824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:56 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:56 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 13:09:56 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:09:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 905587040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:56 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 957049136; totalMemory: 1599078400; maxMemory: 2147483648 INFO 2025-04-24 13:09:56 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:57 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:57 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:57 MarkDuplicates Before output close freeMemory: 896088480; totalMemory: 1268776960; maxMemory: 2147483648 INFO 2025-04-24 13:09:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:57 MarkDuplicates After output close freeMemory: 885745512; totalMemory: 1258291200; maxMemory: 2147483648 [Thu Apr 24 13:09:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1258291200 [Thu Apr 24 13:09:58 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3020193939505115126/input.cram --OUTPUT /tmp/MarkDuplicatesTester.tmp3020193939505115126/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3020193939505115126/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester17657522484404985599/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 13:09:58 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 13:09:58 MarkDuplicates Start of doWork freeMemory: 970489000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:58 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:09:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:09:58 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 13:09:58 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2025-04-24 13:09:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 905384912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:09:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:09:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:09:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:09:59 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:09:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 927486992; totalMemory: 1569718272; maxMemory: 2147483648 INFO 2025-04-24 13:09:59 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:09:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:09:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:09:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:09:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:09:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:09:59 MarkDuplicates Before output close freeMemory: 903229760; totalMemory: 1276116992; maxMemory: 2147483648 INFO 2025-04-24 13:09:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:09:59 MarkDuplicates After output close freeMemory: 896029480; totalMemory: 1268776960; maxMemory: 2147483648 [Thu Apr 24 13:09:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1268776960 [Thu Apr 24 13:10:00 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12568441800641395894/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12568441800641395894/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12568441800641395894/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:00 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 13:10:00 MarkDuplicates Start of doWork freeMemory: 981210104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:00 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:00 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 13:10:00 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:10:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 917548280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:00 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 967570784; totalMemory: 1599078400; maxMemory: 2147483648 INFO 2025-04-24 13:10:00 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:10:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:00 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:00 MarkDuplicates Before output close freeMemory: 872004824; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2025-04-24 13:10:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:00 MarkDuplicates After output close freeMemory: 864810160; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:10:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:10:01 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14418723939541274706/input.bam --OUTPUT /tmp/MarkDuplicatesTester.tmp14418723939541274706/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14418723939541274706/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:01 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 13:10:01 MarkDuplicates Start of doWork freeMemory: 981209160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:01 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:01 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:10:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 917549792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:01 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 711717200; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:01 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:10:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:01 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:01 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:01 MarkDuplicates Before output close freeMemory: 864665784; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2025-04-24 13:10:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:01 MarkDuplicates After output close freeMemory: 864805984; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:10:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:10:02 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp16409276956430658647/input.cram --OUTPUT /tmp/MarkDuplicatesTester.tmp16409276956430658647/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16409276956430658647/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester15625207701148134090/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 13:10:02 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 13:10:02 MarkDuplicates Start of doWork freeMemory: 981080152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:02 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:02 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2025-04-24 13:10:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 917422744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:02 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 711592864; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:03 MarkDuplicates Marking 6200 records as duplicates. INFO 2025-04-24 13:10:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:03 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:03 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:03 MarkDuplicates Before output close freeMemory: 879219584; totalMemory: 1241513984; maxMemory: 2147483648 INFO 2025-04-24 13:10:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:03 MarkDuplicates After output close freeMemory: 861536216; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:10:03 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:10:03 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp4703994580071351503/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp4703994580071351503/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4703994580071351503/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:03 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 13:10:03 MarkDuplicates Start of doWork freeMemory: 986323840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:03 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 923402720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:04 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 985268768; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:04 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:04 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:10:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:04 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:04 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:04 MarkDuplicates Before output close freeMemory: 859300392; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:04 MarkDuplicates After output close freeMemory: 856293608; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:04 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:04 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9107363088827545504/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9107363088827545504/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9107363088827545504/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:04 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 13:10:04 MarkDuplicates Start of doWork freeMemory: 986321544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:04 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:04 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:10:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 923397872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:04 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 716829536; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:05 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:10:05 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:10:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:05 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:05 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:05 MarkDuplicates Before output close freeMemory: 863487864; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:05 MarkDuplicates After output close freeMemory: 859432584; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:05 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:05 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15730021546671086220/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15730021546671086220/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15730021546671086220/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:05 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 13:10:05 MarkDuplicates Start of doWork freeMemory: 986320784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:05 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:05 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:10:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 923397280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:05 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 716828760; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:06 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:10:06 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:10:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:06 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:06 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:06 MarkDuplicates Before output close freeMemory: 859292792; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:06 MarkDuplicates After output close freeMemory: 859434464; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:06 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3058541673331847194/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3058541673331847194/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3058541673331847194/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:06 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 13:10:06 MarkDuplicates Start of doWork freeMemory: 986320104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:06 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:06 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:10:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 923393776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:06 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 716828096; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:07 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:10:07 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:10:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:07 MarkDuplicates Before output close freeMemory: 859292120; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:07 MarkDuplicates After output close freeMemory: 859431144; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:07 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5028928256320671209/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5028928256320671209/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5028928256320671209/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:07 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 13:10:07 MarkDuplicates Start of doWork freeMemory: 986319440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:07 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:07 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:10:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 923395936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:07 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 716827416; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:07 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:10:07 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:10:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:08 MarkDuplicates Before output close freeMemory: 859291448; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:08 MarkDuplicates After output close freeMemory: 859430472; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:08 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:08 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7303354440932987799/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7303354440932987799/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7303354440932987799/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:08 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 13:10:08 MarkDuplicates Start of doWork freeMemory: 986318760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:08 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:08 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:10:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 923395256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:08 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 716826736; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:08 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:10:08 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:10:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:08 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:08 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:09 MarkDuplicates Before output close freeMemory: 859290768; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:09 MarkDuplicates After output close freeMemory: 856283984; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:09 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1617372086285067825/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1617372086285067825/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1617372086285067825/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:09 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 13:10:09 MarkDuplicates Start of doWork freeMemory: 986318072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:09 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:09 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2025-04-24 13:10:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 923391744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:09 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 716826064; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:09 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:10:09 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:10:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:09 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:09 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:10 MarkDuplicates Before output close freeMemory: 859290088; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:10 MarkDuplicates After output close freeMemory: 856283384; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:10 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:10 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10336035037063566057/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10336035037063566057/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10336035037063566057/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:10 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 13:10:10 MarkDuplicates Start of doWork freeMemory: 986323968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:10 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:10 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:10:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 923401672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:10 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 716832472; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:10 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:11 MarkDuplicates Before output close freeMemory: 866636704; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:10:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:11 MarkDuplicates After output close freeMemory: 856289784; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:11 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp938967929785612059/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp938967929785612059/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp938967929785612059/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:11 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 13:10:11 MarkDuplicates Start of doWork freeMemory: 986323040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:11 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:11 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:10:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 923400656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:11 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 715782952; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:11 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:10:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:11 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:11 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:11 MarkDuplicates Before output close freeMemory: 863487112; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:12 MarkDuplicates After output close freeMemory: 856291968; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:12 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2249346262866353000/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2249346262866353000/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2249346262866353000/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:12 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 13:10:12 MarkDuplicates Start of doWork freeMemory: 986322424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:12 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:12 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:10:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 923400040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:12 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 986314944; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:10:12 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:10:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:12 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:12 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:13 MarkDuplicates Before output close freeMemory: 856149496; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:13 MarkDuplicates After output close freeMemory: 853142512; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:13 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp4181437457213984460/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp4181437457213984460/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4181437457213984460/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:13 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 13:10:13 MarkDuplicates Start of doWork freeMemory: 986320320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:13 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:13 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:10:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 923397616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:13 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 716828528; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:13 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:13 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:13 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:13 MarkDuplicates Before output close freeMemory: 856146888; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:14 MarkDuplicates After output close freeMemory: 856285816; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:14 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:14 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp391327122718100548/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp391327122718100548/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp391327122718100548/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:14 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 13:10:14 MarkDuplicates Start of doWork freeMemory: 986319440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:14 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:14 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:10:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 923396736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:14 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 716824336; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:14 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:14 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:14 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:14 MarkDuplicates Before output close freeMemory: 863486040; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:15 MarkDuplicates After output close freeMemory: 856284968; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:15 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:15 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1938651642124377237/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1938651642124377237/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1938651642124377237/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:15 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 13:10:15 MarkDuplicates Start of doWork freeMemory: 986319096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:15 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 923396448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:15 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 716823976; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:15 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:15 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:15 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:15 MarkDuplicates Before output close freeMemory: 866631368; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:10:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:16 MarkDuplicates After output close freeMemory: 859432960; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:16 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9624124988197900613/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9624124988197900613/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9624124988197900613/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:16 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 13:10:16 MarkDuplicates Start of doWork freeMemory: 986318464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:16 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 923395832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:16 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 715778096; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:16 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:10:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:16 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:16 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:16 MarkDuplicates Before output close freeMemory: 859290760; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:16 MarkDuplicates After output close freeMemory: 859432344; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:17 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14371195706366493865/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14371195706366493865/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14371195706366493865/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:17 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 13:10:17 MarkDuplicates Start of doWork freeMemory: 986317704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:17 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 923395056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:17 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 716822584; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:17 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:10:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:17 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:17 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:17 MarkDuplicates Before output close freeMemory: 863484296; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:17 MarkDuplicates After output close freeMemory: 856285840; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:17 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:17 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14536540568716749210/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14536540568716749210/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14536540568716749210/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:17 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 13:10:18 MarkDuplicates Start of doWork freeMemory: 986316704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:18 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 923393928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:18 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 716821600; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:18 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:18 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:18 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:18 MarkDuplicates Before output close freeMemory: 859289000; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:18 MarkDuplicates After output close freeMemory: 853136400; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:18 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:18 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1977378988149168545/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1977378988149168545/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1977378988149168545/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:18 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 13:10:19 MarkDuplicates Start of doWork freeMemory: 986317304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:19 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:19 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:10:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 923394744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:19 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 716822200; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:19 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:19 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:19 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:19 MarkDuplicates Before output close freeMemory: 863483904; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:19 MarkDuplicates After output close freeMemory: 859428560; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:19 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3936140081900349999/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3936140081900349999/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3936140081900349999/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:19 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 13:10:20 MarkDuplicates Start of doWork freeMemory: 986316520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:10:20 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:10:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 923393944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:20 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 985257056; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:20 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:20 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:20 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:20 MarkDuplicates Before output close freeMemory: 859288808; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:20 MarkDuplicates After output close freeMemory: 848942008; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:10:20 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:10:20 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7233021988212194893/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7233021988212194893/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7233021988212194893/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:20 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 13:10:21 MarkDuplicates Start of doWork freeMemory: 986315888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:21 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:21 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 13:10:21 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:10:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 923393576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:21 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 716824376; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:21 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:21 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:21 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:21 MarkDuplicates Before output close freeMemory: 863482888; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:21 MarkDuplicates After output close freeMemory: 859427424; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:21 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10008013509689273384/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10008013509689273384/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10008013509689273384/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:21 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 13:10:21 MarkDuplicates Start of doWork freeMemory: 986315192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:21 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:22 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 13:10:22 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:10:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 923392896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:22 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 716820384; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:22 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:22 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:22 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:22 MarkDuplicates Before output close freeMemory: 856142288; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:22 MarkDuplicates After output close freeMemory: 856280984; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:22 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10821318962358696546/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10821318962358696546/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10821318962358696546/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_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 13:10:22 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 13:10:22 MarkDuplicates Start of doWork freeMemory: 986313064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:22 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:22 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 923387432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:23 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 716818120; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:23 MarkDuplicates Marking 2 records as duplicates. WARNING 2025-04-24 13:10:23 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! INFO 2025-04-24 13:10:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:23 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:23 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:23 MarkDuplicates Before output close freeMemory: 859285544; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:23 MarkDuplicates After output close freeMemory: 859424504; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:23 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:23 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17072417769948403023/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17072417769948403023/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17072417769948403023/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:23 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 13:10:23 MarkDuplicates Start of doWork freeMemory: 986311896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:23 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 923389040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 985255328; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:24 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:10:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:24 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:24 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:24 MarkDuplicates Before output close freeMemory: 863478184; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:24 MarkDuplicates After output close freeMemory: 853131472; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:24 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp13334661132733068088/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp13334661132733068088/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13334661132733068088/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:24 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 13:10:24 MarkDuplicates Start of doWork freeMemory: 986310016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:24 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 923386992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:25 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 716818160; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:25 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:25 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:25 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:25 MarkDuplicates Before output close freeMemory: 856136456; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:25 MarkDuplicates After output close freeMemory: 856275480; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:25 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11987016678722545906/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11987016678722545906/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11987016678722545906/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:25 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 13:10:25 MarkDuplicates Start of doWork freeMemory: 986309296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:25 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 923383600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:26 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 716817424; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:26 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:26 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:26 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:26 MarkDuplicates Before output close freeMemory: 859281456; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:26 MarkDuplicates After output close freeMemory: 853131600; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:26 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11919935063114317694/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11919935063114317694/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11919935063114317694/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:26 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 13:10:26 MarkDuplicates Start of doWork freeMemory: 986308648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:26 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:26 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 923385792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:27 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 985252232; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:27 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:27 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:27 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:27 MarkDuplicates Before output close freeMemory: 856135080; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:27 MarkDuplicates After output close freeMemory: 853128376; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:27 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:27 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5822290851221969972/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5822290851221969972/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5822290851221969972/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:27 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 13:10:27 MarkDuplicates Start of doWork freeMemory: 986307984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:27 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 923384944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:28 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 579452656; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:10:28 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:28 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:28 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:28 MarkDuplicates Before output close freeMemory: 848794384; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2025-04-24 13:10:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:28 MarkDuplicates After output close freeMemory: 848933376; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:10:28 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:10:28 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6861686138934624314/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6861686138934624314/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6861686138934624314/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:28 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 13:10:28 MarkDuplicates Start of doWork freeMemory: 986307360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:28 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 923384504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:29 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 716815488; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:29 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:29 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:29 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:29 MarkDuplicates Before output close freeMemory: 863473824; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:29 MarkDuplicates After output close freeMemory: 859421192; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:29 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:29 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp380903262709638977/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp380903262709638977/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp380903262709638977/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:29 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 13:10:29 MarkDuplicates Start of doWork freeMemory: 986306704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:29 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:29 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 923383864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:30 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 716814848; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:30 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:30 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:30 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:30 MarkDuplicates Before output close freeMemory: 859278872; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:30 MarkDuplicates After output close freeMemory: 859417792; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:30 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:30 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6631274159082787706/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6631274159082787706/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6631274159082787706/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:30 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 13:10:30 MarkDuplicates Start of doWork freeMemory: 986306024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:30 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 923382984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:31 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 716811048; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:31 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:31 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:31 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:31 MarkDuplicates Before output close freeMemory: 856132456; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:31 MarkDuplicates After output close freeMemory: 853125648; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:31 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:31 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7117115214412733070/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7117115214412733070/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7117115214412733070/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:31 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 13:10:31 MarkDuplicates Start of doWork freeMemory: 986305352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:31 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:31 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 923379656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:32 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 715764904; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:32 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:32 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:32 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:32 MarkDuplicates Before output close freeMemory: 863468568; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:32 MarkDuplicates After output close freeMemory: 856273920; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:32 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:32 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11196808799170722284/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11196808799170722284/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11196808799170722284/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:32 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 13:10:32 MarkDuplicates Start of doWork freeMemory: 986304664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:32 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 923381808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:33 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 985248248; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:33 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:33 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:33 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:33 MarkDuplicates Before output close freeMemory: 859276824; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:33 MarkDuplicates After output close freeMemory: 856270120; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:33 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:33 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6537511075206855239/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6537511075206855239/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6537511075206855239/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:33 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 13:10:33 MarkDuplicates Start of doWork freeMemory: 986304000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:33 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 923380960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:34 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 845786976; totalMemory: 1472200704; maxMemory: 2147483648 INFO 2025-04-24 13:10:34 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:34 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:34 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:34 MarkDuplicates Before output close freeMemory: 859276160; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:34 MarkDuplicates After output close freeMemory: 856269456; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:34 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:34 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10728131383703604945/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10728131383703604945/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10728131383703604945/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:34 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 13:10:34 MarkDuplicates Start of doWork freeMemory: 986303312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:34 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:34 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 923380456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:34 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 716811440; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:35 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:35 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:35 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:35 MarkDuplicates Before output close freeMemory: 852984016; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:10:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:35 MarkDuplicates After output close freeMemory: 853123040; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:35 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:35 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2099187220507365294/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2099187220507365294/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2099187220507365294/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:35 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 13:10:35 MarkDuplicates Start of doWork freeMemory: 986302256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:35 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 923376560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:35 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 716810384; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:36 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:36 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:36 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:36 MarkDuplicates Before output close freeMemory: 852982960; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:10:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:36 MarkDuplicates After output close freeMemory: 848927576; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:10:36 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:10:36 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp4093259665876889504/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp4093259665876889504/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4093259665876889504/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:36 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 13:10:36 MarkDuplicates Start of doWork freeMemory: 986301584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:36 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 923378544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:36 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 985242096; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:37 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:37 MarkDuplicates Before output close freeMemory: 859273744; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:37 MarkDuplicates After output close freeMemory: 859415344; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:37 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15687278040583055354/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15687278040583055354/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15687278040583055354/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:37 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 13:10:37 MarkDuplicates Start of doWork freeMemory: 986300896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 923377872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:37 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 573151048; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:10:37 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:38 MarkDuplicates Before output close freeMemory: 842495848; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:10:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:38 MarkDuplicates After output close freeMemory: 842637416; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:10:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:10:38 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9293874729589489620/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9293874729589489620/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9293874729589489620/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:38 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 13:10:38 MarkDuplicates Start of doWork freeMemory: 986300264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:38 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 923377408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:38 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 715759816; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:38 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:38 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:38 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:39 MarkDuplicates Before output close freeMemory: 863466728; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:39 MarkDuplicates After output close freeMemory: 863605648; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:10:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:10:39 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp12008580964604531244/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp12008580964604531244/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp12008580964604531244/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:39 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 13:10:39 MarkDuplicates Start of doWork freeMemory: 986299992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:39 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 923374296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:39 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 716807968; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:39 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:39 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:10:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:40 MarkDuplicates Before output close freeMemory: 856126384; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:40 MarkDuplicates After output close freeMemory: 856267848; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:40 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7432158676160760109/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7432158676160760109/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7432158676160760109/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:40 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 13:10:40 MarkDuplicates Start of doWork freeMemory: 986299024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:40 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 923373328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:40 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 716807000; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:40 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:40 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:10:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:40 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:40 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:40 MarkDuplicates Before output close freeMemory: 863465376; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:41 MarkDuplicates After output close freeMemory: 856264328; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:41 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8678104999072378201/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8678104999072378201/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8678104999072378201/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:41 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 13:10:41 MarkDuplicates Start of doWork freeMemory: 986297240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:41 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:41 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:10:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 923371352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:41 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 985240696; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:41 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:10:41 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:10:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:41 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:41 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:41 MarkDuplicates Before output close freeMemory: 863463672; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:42 MarkDuplicates After output close freeMemory: 859408184; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:42 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11913957241636979214/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11913957241636979214/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11913957241636979214/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:42 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 13:10:42 MarkDuplicates Start of doWork freeMemory: 986297424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:42 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 923374400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:42 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 716805416; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:42 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:42 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:10:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:42 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:42 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:42 MarkDuplicates Before output close freeMemory: 856123776; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:43 MarkDuplicates After output close freeMemory: 853116904; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:43 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6492003472203401122/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6492003472203401122/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6492003472203401122/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:43 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 13:10:43 MarkDuplicates Start of doWork freeMemory: 986297920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:43 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:43 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 13:10:43 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:10:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 923375344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:43 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 986290144; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:10:43 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:43 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:43 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:43 MarkDuplicates Before output close freeMemory: 863464528; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:44 MarkDuplicates After output close freeMemory: 853117712; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:44 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8952179133490686954/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8952179133490686954/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8952179133490686954/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:44 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 13:10:44 MarkDuplicates Start of doWork freeMemory: 986294896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:44 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:44 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 13:10:44 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2025-04-24 13:10:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 923372376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:44 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 986287344; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:10:44 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:44 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:44 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:44 MarkDuplicates Before output close freeMemory: 859270664; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:45 MarkDuplicates After output close freeMemory: 853117984; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:45 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp18235133753398979767/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp18235133753398979767/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp18235133753398979767/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:45 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 13:10:45 MarkDuplicates Start of doWork freeMemory: 986295936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:45 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 13:10:45 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:10:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 923373304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:45 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 653889584; totalMemory: 1280311296; maxMemory: 2147483648 INFO 2025-04-24 13:10:45 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:10:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:45 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:45 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:45 MarkDuplicates Before output close freeMemory: 866608336; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:10:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:46 MarkDuplicates After output close freeMemory: 856261360; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:46 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:46 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7601652054431882257/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7601652054431882257/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7601652054431882257/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:46 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 13:10:46 MarkDuplicates Start of doWork freeMemory: 986293784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:46 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 13:10:46 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:10:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 923370936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:46 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 716801992; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:46 MarkDuplicates Marking 3 records as duplicates. INFO 2025-04-24 13:10:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:46 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:46 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:46 MarkDuplicates Before output close freeMemory: 863460456; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:10:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:47 MarkDuplicates After output close freeMemory: 863599240; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:10:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:10:47 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17775017809700099637/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17775017809700099637/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17775017809700099637/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:47 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 13:10:47 MarkDuplicates Start of doWork freeMemory: 986294952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:47 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 13:10:47 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:10:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 923372392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:47 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 715754584; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:47 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:47 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:47 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:47 MarkDuplicates Before output close freeMemory: 852975864; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:10:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:47 MarkDuplicates After output close freeMemory: 848920448; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:10:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:10:47 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7494237366845238318/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7494237366845238318/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7494237366845238318/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:47 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 13:10:48 MarkDuplicates Start of doWork freeMemory: 986295008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:48 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:48 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:10:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 923370056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:48 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 716800552; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:48 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:48 MarkDuplicates Before output close freeMemory: 856122376; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:48 MarkDuplicates After output close freeMemory: 856260840; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:48 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17613213092769127339/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17613213092769127339/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17613213092769127339/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:48 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 13:10:49 MarkDuplicates Start of doWork freeMemory: 986293896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:49 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:49 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:10:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 923371784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:49 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 715753936; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:49 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:10:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:49 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:49 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:49 MarkDuplicates Before output close freeMemory: 859266992; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:49 MarkDuplicates After output close freeMemory: 856259832; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:49 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3432924288394296447/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3432924288394296447/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3432924288394296447/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:49 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 13:10:50 MarkDuplicates Start of doWork freeMemory: 986181104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:10:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 923226416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:50 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 716660088; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:10:50 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:50 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:10:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:50 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:50 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:50 MarkDuplicates Before output close freeMemory: 852803528; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:10:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:50 MarkDuplicates After output close freeMemory: 852971608; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:50 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6079964051637709440/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6079964051637709440/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6079964051637709440/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:50 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 13:10:51 MarkDuplicates Start of doWork freeMemory: 986281096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:51 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:51 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 13:10:51 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2025-04-24 13:10:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 923356568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:51 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 715740488; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:51 MarkDuplicates Marking 12 records as duplicates. INFO 2025-04-24 13:10:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:51 MarkDuplicates Before output close freeMemory: 856107496; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:10:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:51 MarkDuplicates After output close freeMemory: 856246312; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:51 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15127273852998928424/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15127273852998928424/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15127273852998928424/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:51 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 13:10:51 MarkDuplicates Start of doWork freeMemory: 986288288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:51 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:52 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 13:10:52 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:10:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 923365280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:52 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 715747904; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:52 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:10:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:52 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:52 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:52 MarkDuplicates Before output close freeMemory: 852969192; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:10:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:52 MarkDuplicates After output close freeMemory: 853107976; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:10:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:10:52 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7643445441889346146/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7643445441889346146/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7643445441889346146/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:52 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 13:10:52 MarkDuplicates Start of doWork freeMemory: 986287352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:52 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:52 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 13:10:52 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2025-04-24 13:10:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 923364360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:53 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 715746808; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:53 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:53 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:53 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:53 MarkDuplicates Before output close freeMemory: 859259472; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:53 MarkDuplicates After output close freeMemory: 859400976; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:53 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9125730163551554691/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9125730163551554691/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9125730163551554691/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:53 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 13:10:53 MarkDuplicates Start of doWork freeMemory: 986282608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:53 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:53 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 13:10:53 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2025-04-24 13:10:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 923358848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:54 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 715742120; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:54 MarkDuplicates Marking 8 records as duplicates. INFO 2025-04-24 13:10:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:54 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:54 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:54 MarkDuplicates Before output close freeMemory: 859254856; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:54 MarkDuplicates After output close freeMemory: 859393744; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:54 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10298039414504597555/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10298039414504597555/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10298039414504597555/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:54 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 13:10:54 MarkDuplicates Start of doWork freeMemory: 986287280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:54 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:54 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 13:10:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 923364752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:55 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 715747192; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:10:55 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:55 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:55 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:55 MarkDuplicates Before output close freeMemory: 852968592; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:10:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:55 MarkDuplicates After output close freeMemory: 848913064; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:10:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:10:55 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14150596172682565110/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14150596172682565110/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14150596172682565110/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:55 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 13:10:55 MarkDuplicates Start of doWork freeMemory: 986283760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:55 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:55 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 13:10:55 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2025-04-24 13:10:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 923360432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:56 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 985226848; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:56 MarkDuplicates Marking 4 records as duplicates. INFO 2025-04-24 13:10:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:56 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:56 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:56 MarkDuplicates Before output close freeMemory: 866596040; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:10:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:56 MarkDuplicates After output close freeMemory: 859394792; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:10:56 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:10:56 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2681669951013365422/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2681669951013365422/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2681669951013365422/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:56 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 13:10:56 MarkDuplicates Start of doWork freeMemory: 986286952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:56 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:56 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 13:10:56 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:10:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 923364584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:57 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 573137232; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:10:57 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:10:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:57 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:57 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:57 MarkDuplicates Before output close freeMemory: 842482512; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:10:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:57 MarkDuplicates After output close freeMemory: 842623904; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:10:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:10:57 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14246973553754582738/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14246973553754582738/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14246973553754582738/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:57 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 13:10:57 MarkDuplicates Start of doWork freeMemory: 986284664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:57 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:57 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 13:10:57 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 923361888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:58 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 985225016; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:10:58 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:58 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:58 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:58 MarkDuplicates Before output close freeMemory: 859256960; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:10:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:58 MarkDuplicates After output close freeMemory: 856250192; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:10:58 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:10:58 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14406630466097879661/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14406630466097879661/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14406630466097879661/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:58 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 13:10:58 MarkDuplicates Start of doWork freeMemory: 986284064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:58 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:58 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 13:10:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 923361288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:10:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:10:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:10:59 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:10:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 576282424; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:10:59 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:10:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:10:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:10:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:10:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:10:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:10:59 MarkDuplicates Before output close freeMemory: 845624944; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2025-04-24 13:10:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:10:59 MarkDuplicates After output close freeMemory: 845763800; totalMemory: 1202716672; maxMemory: 2147483648 [Thu Apr 24 13:10:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1202716672 [Thu Apr 24 13:10:59 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp14163138988369009719/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp14163138988369009719/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp14163138988369009719/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:10:59 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 13:10:59 MarkDuplicates Start of doWork freeMemory: 986283320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:59 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:10:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:10:59 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 13:10:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:10:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 923360544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:10:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:00 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 716788184; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:00 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:00 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:00 MarkDuplicates Before output close freeMemory: 856109960; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:11:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:00 MarkDuplicates After output close freeMemory: 848911440; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:11:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:11:00 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp15303627893710332640/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp15303627893710332640/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp15303627893710332640/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:00 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 13:11:00 MarkDuplicates Start of doWork freeMemory: 986282336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:00 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:00 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 13:11:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 923359544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:00 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 716787216; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:01 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:01 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:01 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:01 MarkDuplicates Before output close freeMemory: 856108968; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:11:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:01 MarkDuplicates After output close freeMemory: 853102128; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:01 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:01 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2916240673025783995/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2916240673025783995/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2916240673025783995/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:01 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 13:11:01 MarkDuplicates Start of doWork freeMemory: 986280920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:01 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:11:01 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 923358128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:01 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 716785800; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:02 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:02 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:02 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:02 MarkDuplicates Before output close freeMemory: 856107664; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:11:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:02 MarkDuplicates After output close freeMemory: 856246336; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:11:02 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:11:02 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6161709556288251951/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6161709556288251951/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6161709556288251951/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:02 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 13:11:02 MarkDuplicates Start of doWork freeMemory: 986280264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:02 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:11:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 923357488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:02 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 716785160; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:03 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:03 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:03 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:03 MarkDuplicates Before output close freeMemory: 852961496; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:11:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:03 MarkDuplicates After output close freeMemory: 853100032; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:03 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:03 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6173681100827804959/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6173681100827804959/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6173681100827804959/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:03 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 13:11:03 MarkDuplicates Start of doWork freeMemory: 986279104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:03 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:11:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 923356312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:03 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 716783984; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:03 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:03 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:03 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:04 MarkDuplicates Before output close freeMemory: 859251784; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:11:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:04 MarkDuplicates After output close freeMemory: 856244520; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:11:04 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:11:04 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp6949422319455134431/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp6949422319455134431/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp6949422319455134431/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:04 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 13:11:04 MarkDuplicates Start of doWork freeMemory: 986279208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:04 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:11:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 923356432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:04 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 985219528; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:11:05 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:11:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:05 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:05 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:05 MarkDuplicates Before output close freeMemory: 863445808; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:11:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:05 MarkDuplicates After output close freeMemory: 863587384; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:11:05 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:11:05 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp13983290065955923938/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp13983290065955923938/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13983290065955923938/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:05 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 13:11:05 MarkDuplicates Start of doWork freeMemory: 986278264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:05 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:05 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 13:11:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 923355488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:05 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 716785776; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:05 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:05 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:05 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:06 MarkDuplicates Before output close freeMemory: 856104832; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:11:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:06 MarkDuplicates After output close freeMemory: 853098032; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:06 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:06 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1056753407864441485/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1056753407864441485/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1056753407864441485/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:06 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 13:11:06 MarkDuplicates Start of doWork freeMemory: 986277480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:06 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:11:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 923354688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:06 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 985217784; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:11:07 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:07 MarkDuplicates Before output close freeMemory: 859249768; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:11:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:07 MarkDuplicates After output close freeMemory: 853097240; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:07 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:07 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp16256633095737776268/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp16256633095737776268/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16256633095737776268/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:07 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 13:11:07 MarkDuplicates Start of doWork freeMemory: 986276616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:07 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:11:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 923353840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:07 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 716784128; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:07 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:07 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:07 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:08 MarkDuplicates Before output close freeMemory: 863443216; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:11:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:08 MarkDuplicates After output close freeMemory: 859387840; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:11:08 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:11:08 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp10618945668891057035/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10618945668891057035/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10618945668891057035/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:08 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 13:11:08 MarkDuplicates Start of doWork freeMemory: 986275816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:08 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:08 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 13:11:08 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 923353040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:08 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 716780712; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:08 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:08 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:08 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:09 MarkDuplicates Before output close freeMemory: 859248112; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:11:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:09 MarkDuplicates After output close freeMemory: 848903856; totalMemory: 1205862400; maxMemory: 2147483648 [Thu Apr 24 13:11:09 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1205862400 [Thu Apr 24 13:11:09 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp3377424434413334784/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp3377424434413334784/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp3377424434413334784/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:09 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 13:11:09 MarkDuplicates Start of doWork freeMemory: 986276200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:09 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:11:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:11:09 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2025-04-24 13:11:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 923353696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:09 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 985216712; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:11:10 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:11:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:10 MarkDuplicates Before output close freeMemory: 859248712; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:11:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:10 MarkDuplicates After output close freeMemory: 859387520; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:11:10 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:11:10 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp240615570212414315/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp240615570212414315/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp240615570212414315/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:10 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 13:11:10 MarkDuplicates Start of doWork freeMemory: 986272904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:10 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:10 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 923349864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:10 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 573125968; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:11:10 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:10 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:10 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:10 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:11 MarkDuplicates Before output close freeMemory: 842467736; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2025-04-24 13:11:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:11 MarkDuplicates After output close freeMemory: 842609272; totalMemory: 1199570944; maxMemory: 2147483648 [Thu Apr 24 13:11:11 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1199570944 [Thu Apr 24 13:11:11 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9573146774619296036/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9573146774619296036/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9573146774619296036/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:11 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 13:11:11 MarkDuplicates Start of doWork freeMemory: 986272120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:11 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:11 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 923346440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:11 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 716776800; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:11 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:11 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:11 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:11 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:12 MarkDuplicates Before output close freeMemory: 852952720; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:11:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:12 MarkDuplicates After output close freeMemory: 853091600; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:12 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:12 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8590245572142525678/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8590245572142525678/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8590245572142525678/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:12 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 13:11:12 MarkDuplicates Start of doWork freeMemory: 986271448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:12 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:12 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 923348608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:12 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 715730864; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:11:12 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:12 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:12 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:12 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:12 MarkDuplicates Before output close freeMemory: 863437808; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:11:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:13 MarkDuplicates After output close freeMemory: 859385040; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:11:13 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:11:13 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp17863769050605221820/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17863769050605221820/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17863769050605221820/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:13 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 13:11:13 MarkDuplicates Start of doWork freeMemory: 986270760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:13 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:13 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 923347920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:13 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 715730176; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:11:13 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:13 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:13 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:13 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:13 MarkDuplicates Before output close freeMemory: 863437120; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:11:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:14 MarkDuplicates After output close freeMemory: 859384344; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:11:14 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:11:14 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8056207761385794297/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8056207761385794297/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8056207761385794297/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:14 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 13:11:14 MarkDuplicates Start of doWork freeMemory: 986270096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:14 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:14 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 923347256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:14 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 715729512; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:11:14 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:14 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:14 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:14 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:14 MarkDuplicates Before output close freeMemory: 863436456; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:11:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:15 MarkDuplicates After output close freeMemory: 859383760; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:11:15 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:11:15 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1359366937247852058/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1359366937247852058/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1359366937247852058/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:15 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 13:11:15 MarkDuplicates Start of doWork freeMemory: 986269448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:15 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:15 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 923346592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:15 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 716774352; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:15 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:15 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:15 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:15 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:15 MarkDuplicates Before output close freeMemory: 852950040; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:11:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:15 MarkDuplicates After output close freeMemory: 853088920; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:15 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:15 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp1896494273429150541/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1896494273429150541/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1896494273429150541/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:15 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 13:11:16 MarkDuplicates Start of doWork freeMemory: 986267816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:16 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:16 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 923344976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:16 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 790176128; totalMemory: 1416626176; maxMemory: 2147483648 INFO 2025-04-24 13:11:16 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:16 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:16 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:16 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:16 MarkDuplicates Before output close freeMemory: 863434336; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:11:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:16 MarkDuplicates After output close freeMemory: 859381400; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:11:16 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:11:16 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2315074487519238137/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2315074487519238137/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2315074487519238137/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:16 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 13:11:17 MarkDuplicates Start of doWork freeMemory: 986267136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:17 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:17 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 923344112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:17 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 716775128; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:17 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:17 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:17 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:17 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:17 MarkDuplicates Before output close freeMemory: 859239352; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:11:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:17 MarkDuplicates After output close freeMemory: 856234992; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:11:17 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:11:17 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8427721971016613883/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8427721971016613883/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8427721971016613883/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:17 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 13:11:18 MarkDuplicates Start of doWork freeMemory: 986266464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:18 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:18 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 923343608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:18 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 716774440; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:18 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:18 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:18 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:18 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:18 MarkDuplicates Before output close freeMemory: 859238672; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:11:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:18 MarkDuplicates After output close freeMemory: 856231768; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:11:18 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:11:18 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp11138243717054619695/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11138243717054619695/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11138243717054619695/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:18 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 13:11:18 MarkDuplicates Start of doWork freeMemory: 986265768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:18 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:19 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 923342912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:19 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 986257776; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2025-04-24 13:11:19 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:19 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:19 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:19 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:19 MarkDuplicates Before output close freeMemory: 852943240; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:11:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:19 MarkDuplicates After output close freeMemory: 853088456; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:19 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:19 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp5254998484216377760/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5254998484216377760/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5254998484216377760/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:19 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 13:11:20 MarkDuplicates Start of doWork freeMemory: 986265096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:20 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 923342072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:20 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 580458208; totalMemory: 1206910976; maxMemory: 2147483648 INFO 2025-04-24 13:11:20 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:20 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:20 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:20 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:20 MarkDuplicates Before output close freeMemory: 849800128; totalMemory: 1206910976; maxMemory: 2147483648 INFO 2025-04-24 13:11:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:20 MarkDuplicates After output close freeMemory: 849938952; totalMemory: 1206910976; maxMemory: 2147483648 [Thu Apr 24 13:11:20 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1206910976 [Thu Apr 24 13:11:20 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp2455770461264977358/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2455770461264977358/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2455770461264977358/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:20 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 13:11:20 MarkDuplicates Start of doWork freeMemory: 986264400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:20 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:20 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2025-04-24 13:11:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 923341560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:21 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 715723816; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:11:21 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:21 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:21 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:21 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:21 MarkDuplicates Before output close freeMemory: 856090888; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:11:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:21 MarkDuplicates After output close freeMemory: 856232328; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:11:21 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:11:21 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp9839980965110957443/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9839980965110957443/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9839980965110957443/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:21 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 13:11:21 MarkDuplicates Start of doWork freeMemory: 986265960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:21 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:21 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2025-04-24 13:11:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 923340992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:22 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 716773896; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:22 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:11:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:22 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:22 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:22 MarkDuplicates Before output close freeMemory: 856093320; totalMemory: 1213202432; maxMemory: 2147483648 INFO 2025-04-24 13:11:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:22 MarkDuplicates After output close freeMemory: 856234504; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:11:22 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:11:22 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp7778427649725280435/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp7778427649725280435/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp7778427649725280435/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:22 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 13:11:22 MarkDuplicates Start of doWork freeMemory: 986263520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:22 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:22 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:11:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 923340680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:23 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 715722936; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:11:23 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:11:23 MarkDuplicates Found 1 optical duplicate clusters. INFO 2025-04-24 13:11:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:23 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:23 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:23 MarkDuplicates Before output close freeMemory: 866575704; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:11:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:23 MarkDuplicates After output close freeMemory: 863568832; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:11:23 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:11:23 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp8345166406415283502/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8345166406415283502/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8345166406415283502/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:23 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 13:11:23 MarkDuplicates Start of doWork freeMemory: 986256640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:23 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:23 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2025-04-24 13:11:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 923333088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:24 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 716764704; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:24 MarkDuplicates Marking 6 records as duplicates. INFO 2025-04-24 13:11:24 MarkDuplicates Found 3 optical duplicate clusters. INFO 2025-04-24 13:11:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:24 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:24 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:24 MarkDuplicates Before output close freeMemory: 852937360; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2025-04-24 13:11:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:24 MarkDuplicates After output close freeMemory: 853078944; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:24 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:24 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp13000491008890557135/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp13000491008890557135/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13000491008890557135/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:24 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 13:11:24 MarkDuplicates Start of doWork freeMemory: 986258736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:24 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:24 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2025-04-24 13:11:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 923335448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:25 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 716766712; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:25 MarkDuplicates Marking 6 records as duplicates. INFO 2025-04-24 13:11:25 MarkDuplicates Found 2 optical duplicate clusters. INFO 2025-04-24 13:11:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:25 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:25 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:25 MarkDuplicates Before output close freeMemory: 859230856; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:11:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:25 MarkDuplicates After output close freeMemory: 853078208; totalMemory: 1210056704; maxMemory: 2147483648 [Thu Apr 24 13:11:25 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1210056704 [Thu Apr 24 13:11:25 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/MarkDuplicatesTester.tmp16471181594629122720/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp16471181594629122720/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16471181594629122720/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:11:25 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 13:11:25 MarkDuplicates Start of doWork freeMemory: 986261688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:25 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:11:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:11:25 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:11:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 923339048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:11:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:11:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:11:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:11:25 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:11:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 716766504; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:11:26 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:11:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:11:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:11:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:11:26 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:11:26 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:11:26 MarkDuplicates Before output close freeMemory: 866573992; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:11:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:11:26 MarkDuplicates After output close freeMemory: 859372792; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:11:26 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160