Class picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6f8da92a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@747d5343, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@53fe97fe], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@bdc78b5, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@99a541d], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1763f926]}) | 1.292s | passed |
| pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d8de710, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5d85cc5c], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6e56618], 1AAXX.3.1=[]}) | 0.996s | passed |
| testBulkFragmentsNoDuplicates | 1.849s | passed |
| testBulkFragmentsWithDuplicates | 3.451s | passed |
| testDifferentChromosomesInOppositeOrder | 1.048s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 1.065s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.950s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.948s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.895s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.913s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 1.010s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.906s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 1.002s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.843s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 1.143s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.944s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 1.055s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.853s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.719s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.846s | passed |
| testMappedPairWithSamePosition | 0.745s | passed |
| testMappedPairWithSamePositionSameCigar | 1.141s | passed |
| testMatePairFirstUnmapped | 0.845s | passed |
| testMatePairSecondUnmapped | 0.976s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.959s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates | 1.044s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.828s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.837s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.917s | passed |
| testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) | 0.867s | passed |
| testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) | 0.994s | passed |
| testOpticalDuplicateFinding | 0.832s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.971s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.770s | passed |
| testSingleMappedFragment | 1.030s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.817s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 1.015s | passed |
| testSingleMappedPair | 0.889s | passed |
| testSingleUnmappedFragment | 0.765s | passed |
| testSingleUnmappedPair | 0.784s | passed |
| testStackOverFlowPairSetSwap | 0.871s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.695s | passed |
| testThreeMappedPairs | 0.742s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.718s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.737s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.726s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.985s | passed |
| testTwoMappedFragments | 0.726s | passed |
| testTwoMappedPairWithSamePosition | 0.718s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.847s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.684s | passed |
| testTwoMappedPairs | 0.885s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.894s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.860s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.859s | passed |
| testTwoMappedPairsMatesSoftClipped | 1.035s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.918s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.834s | passed |
| testTwoMappedPairsWithSoftClipping | 0.855s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 1.031s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 0.843s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.829s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.886s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.931s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 1.036s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.896s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.855s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.842s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.748s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.921s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.912s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.951s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.866s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.861s | passed |
| testTwoUnmappedFragments | 0.797s | passed |
| testWithBarcodeComplex | 0.852s | passed |
| testWithBarcodeDuplicate | 0.801s | passed |
| testWithBarcodeFragmentDuplicate | 0.775s | passed |
| testWithIndividualReadBarcodes | 0.852s | passed |
Standard error
[Tue Aug 16 04:07:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.959965060312786192.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.959965060312786192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.959965060312786192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:18 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:18 MarkDuplicates Start of doWork freeMemory: 1257174384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:18 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:18 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:19 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2016-08-16 04:07:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 1206785320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:19 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:19 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 779935312; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:20 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:20 MarkDuplicates Before output close freeMemory: 1256896008; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:20 MarkDuplicates After output close freeMemory: 1257168616; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8678928295724443818.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8678928295724443818.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8678928295724443818.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:20 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:21 MarkDuplicates Start of doWork freeMemory: 1235274368; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:21 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:21 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:21 MarkDuplicates Read 50000 records. 0 pairs never matched. INFO 2016-08-16 04:07:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 1181685216; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:22 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:22 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 758035160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:22 MarkDuplicates Marking 40000 records as duplicates. INFO 2016-08-16 04:07:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:23 MarkDuplicates Before output close freeMemory: 1234995376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:23 MarkDuplicates After output close freeMemory: 1235267592; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.131493088965606664.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.131493088965606664.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.131493088965606664.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:24 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:24 MarkDuplicates Start of doWork freeMemory: 1262506736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:24 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:24 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:24 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212914136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:24 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:24 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 785267256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:24 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:25 MarkDuplicates Before output close freeMemory: 1262177648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:25 MarkDuplicates After output close freeMemory: 1262177480; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4384542465814080421.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4384542465814080421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4384542465814080421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:25 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:25 MarkDuplicates Start of doWork freeMemory: 1262499968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:25 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:25 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:25 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:07:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212909552; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:25 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:25 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 785260976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:26 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:07:26 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:07:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:26 MarkDuplicates Before output close freeMemory: 1262171336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:26 MarkDuplicates After output close freeMemory: 1262169104; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8279566677136854395.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8279566677136854395.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8279566677136854395.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:26 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:26 MarkDuplicates Start of doWork freeMemory: 1262499144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:26 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:26 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:26 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:07:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212906664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:26 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:26 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 785260144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:26 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:07:26 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:07:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:27 MarkDuplicates Before output close freeMemory: 1262170504; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:27 MarkDuplicates After output close freeMemory: 1262168272; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:27 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:27 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2408078323118446691.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2408078323118446691.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2408078323118446691.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:27 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:27 MarkDuplicates Start of doWork freeMemory: 1262497048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:27 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:27 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:27 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:07:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212907616; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:27 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:27 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 785259040; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:27 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:07:27 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:07:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:28 MarkDuplicates Before output close freeMemory: 1262169400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:28 MarkDuplicates After output close freeMemory: 1262169632; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8730604702617398564.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8730604702617398564.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8730604702617398564.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:28 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:28 MarkDuplicates Start of doWork freeMemory: 1262497184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:28 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:28 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:28 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:07:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212906768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:28 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:28 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 785258192; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:28 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:07:28 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:07:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:28 MarkDuplicates Before output close freeMemory: 1262168552; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:28 MarkDuplicates After output close freeMemory: 1262168384; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4318528577435357361.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4318528577435357361.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4318528577435357361.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:28 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:29 MarkDuplicates Start of doWork freeMemory: 1262496416; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:29 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:29 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:29 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:07:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212906000; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:29 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:29 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 785257424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:29 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:07:29 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:07:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:29 MarkDuplicates Before output close freeMemory: 1262167784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:29 MarkDuplicates After output close freeMemory: 1262167616; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1606357368217986482.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1606357368217986482.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1606357368217986482.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:29 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:29 MarkDuplicates Start of doWork freeMemory: 1262495640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:29 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:29 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:29 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:07:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212905224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:30 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:30 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 785256648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:30 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:07:30 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:07:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:30 MarkDuplicates Before output close freeMemory: 1262167008; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:30 MarkDuplicates After output close freeMemory: 1262166840; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5056267718255538260.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5056267718255538260.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5056267718255538260.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:30 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:30 MarkDuplicates Start of doWork freeMemory: 1262501184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:30 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:30 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:07:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212912344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:31 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:31 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 785261768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:31 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:31 MarkDuplicates Before output close freeMemory: 1262173304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:31 MarkDuplicates After output close freeMemory: 1262173136; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7305368430871908727.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7305368430871908727.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7305368430871908727.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:31 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:31 MarkDuplicates Start of doWork freeMemory: 1262500056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:31 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:31 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:31 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:07:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212911136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:32 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:32 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 785258576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:32 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:07:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:32 MarkDuplicates Before output close freeMemory: 1262172000; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:32 MarkDuplicates After output close freeMemory: 1262171832; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7747210779000525645.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7747210779000525645.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7747210779000525645.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:32 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:32 MarkDuplicates Start of doWork freeMemory: 1262499224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:32 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:32 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:32 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:07:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212910304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:33 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:33 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 785260456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:33 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:07:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:33 MarkDuplicates Before output close freeMemory: 1262171168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:33 MarkDuplicates After output close freeMemory: 1262170976; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7072207389084573642.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7072207389084573642.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7072207389084573642.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:33 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:33 MarkDuplicates Start of doWork freeMemory: 1262497232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:33 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:33 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:33 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212907616; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:33 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:33 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 785258304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:34 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:34 MarkDuplicates Before output close freeMemory: 1262168680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:34 MarkDuplicates After output close freeMemory: 1262168512; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3800698137873547109.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3800698137873547109.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3800698137873547109.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:34 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:34 MarkDuplicates Start of doWork freeMemory: 1262496336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:34 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:34 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:34 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212904632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:35 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:35 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 785254720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:35 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:35 MarkDuplicates Before output close freeMemory: 1262167784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:35 MarkDuplicates After output close freeMemory: 1262167616; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:35 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:35 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7969227622659100887.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7969227622659100887.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7969227622659100887.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:35 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:35 MarkDuplicates Start of doWork freeMemory: 1262496008; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:35 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:35 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212904392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:35 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:36 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 785256128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:36 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:36 MarkDuplicates Before output close freeMemory: 1262167520; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:36 MarkDuplicates After output close freeMemory: 1262165288; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2240408982582165218.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2240408982582165218.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2240408982582165218.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:36 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:36 MarkDuplicates Start of doWork freeMemory: 1262495120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:36 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:36 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212905584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:37 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:37 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 785256192; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:37 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:07:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:37 MarkDuplicates Before output close freeMemory: 1262166568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:37 MarkDuplicates After output close freeMemory: 1262164336; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8731169287854476284.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8731169287854476284.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8731169287854476284.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:37 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:37 MarkDuplicates Start of doWork freeMemory: 1262493792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:37 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:37 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212904256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:37 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:37 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 785252152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:38 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:07:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:38 MarkDuplicates Before output close freeMemory: 1262165240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:38 MarkDuplicates After output close freeMemory: 1262165072; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.619580182672697229.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.619580182672697229.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.619580182672697229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:38 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:38 MarkDuplicates Start of doWork freeMemory: 1262492984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:38 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:38 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212901224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:38 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:38 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 785253096; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:39 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:39 MarkDuplicates Before output close freeMemory: 1262164472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:39 MarkDuplicates After output close freeMemory: 1262164304; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3938952098703941392.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3938952098703941392.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3938952098703941392.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:39 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:39 MarkDuplicates Start of doWork freeMemory: 1262493184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:39 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:39 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:39 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:07:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212904024; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:39 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:39 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 785253632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:39 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:39 MarkDuplicates Before output close freeMemory: 1262164712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:39 MarkDuplicates After output close freeMemory: 1262164544; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1826050127060587937.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1826050127060587937.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1826050127060587937.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:39 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:40 MarkDuplicates Start of doWork freeMemory: 1262492288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:40 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:40 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:40 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:07:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212903128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:40 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:40 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 785252736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:40 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:41 MarkDuplicates Before output close freeMemory: 1262163816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:41 MarkDuplicates After output close freeMemory: 1262164048; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:41 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:41 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3150955478133190566.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3150955478133190566.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3150955478133190566.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:41 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:41 MarkDuplicates Start of doWork freeMemory: 1262491344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:41 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:41 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:41 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:07:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212902208; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:41 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:41 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 785251616; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:41 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:41 MarkDuplicates Before output close freeMemory: 1262163232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:41 MarkDuplicates After output close freeMemory: 1262161432; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:41 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:41 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1522430687839920155.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1522430687839920155.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1522430687839920155.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:41 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:41 MarkDuplicates Start of doWork freeMemory: 1262490608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:41 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:41 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:42 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:07:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212899408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:42 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:42 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 785249128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:42 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:42 MarkDuplicates Before output close freeMemory: 1262162560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:42 MarkDuplicates After output close freeMemory: 1262162392; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3044048775819281353.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3044048775819281353.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3044048775819281353.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:42 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:42 MarkDuplicates Start of doWork freeMemory: 1262488296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:42 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:42 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212898600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:43 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:43 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 785249304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:43 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:43 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:43 MarkDuplicates Before output close freeMemory: 1262159664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:43 MarkDuplicates After output close freeMemory: 1262157432; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8892280575403271459.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8892280575403271459.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8892280575403271459.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:43 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:43 MarkDuplicates Start of doWork freeMemory: 1262487400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:43 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:43 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212895640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:44 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:44 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 785247848; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:44 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:44 MarkDuplicates Before output close freeMemory: 1262158832; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:44 MarkDuplicates After output close freeMemory: 1262158664; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:44 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:44 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6247457907784831707.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6247457907784831707.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6247457907784831707.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:44 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:44 MarkDuplicates Start of doWork freeMemory: 1262486504; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:44 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:44 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212896808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:45 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:45 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 785244864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:45 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:45 MarkDuplicates Before output close freeMemory: 1262157936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:45 MarkDuplicates After output close freeMemory: 1262157768; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1832757200419871927.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1832757200419871927.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1832757200419871927.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:45 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:45 MarkDuplicates Start of doWork freeMemory: 1262485656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:45 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:45 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212895960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:46 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:46 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 785246664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:46 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:46 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:46 MarkDuplicates Before output close freeMemory: 1262157088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:46 MarkDuplicates After output close freeMemory: 1262156920; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1138859149317955041.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1138859149317955041.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1138859149317955041.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:46 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:46 MarkDuplicates Start of doWork freeMemory: 1262484424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:46 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:46 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212894728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:46 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:46 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 785245432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:47 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:47 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:47 MarkDuplicates Before output close freeMemory: 1262155792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:47 MarkDuplicates After output close freeMemory: 1262153560; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:47 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:47 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4633285225373631193.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4633285225373631193.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4633285225373631193.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:47 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:47 MarkDuplicates Start of doWork freeMemory: 1262482784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:47 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:47 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:47 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:07:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212892848; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:47 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:47 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 785243792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:48 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:07:48 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:48 MarkDuplicates Before output close freeMemory: 1262154280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:48 MarkDuplicates After output close freeMemory: 1262154112; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.456059127111713036.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.456059127111713036.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.456059127111713036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:48 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:48 MarkDuplicates Start of doWork freeMemory: 1262482728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:48 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:48 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212893328; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:48 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:48 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 785243736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:49 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:49 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:49 MarkDuplicates Before output close freeMemory: 1262154136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:49 MarkDuplicates After output close freeMemory: 1262153968; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2603740957675359180.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2603740957675359180.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2603740957675359180.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:49 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:49 MarkDuplicates Start of doWork freeMemory: 1262482760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:49 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:49 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:49 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:07:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212893600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:49 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:49 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 785243832; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:49 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:50 MarkDuplicates Before output close freeMemory: 1262154240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:50 MarkDuplicates After output close freeMemory: 1262154072; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9102424470821582925.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9102424470821582925.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9102424470821582925.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:50 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:50 MarkDuplicates Start of doWork freeMemory: 1262482240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:50 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:50 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:50 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 2016-08-16 04:07:50 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2016-08-16 04:07:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212892936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:50 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:50 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 785242968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:50 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:51 MarkDuplicates Before output close freeMemory: 1262154864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:51 MarkDuplicates After output close freeMemory: 1262152632; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2935763218835057342.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2935763218835057342.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2935763218835057342.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:51 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:51 MarkDuplicates Start of doWork freeMemory: 1262480648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:51 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:51 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:51 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 2016-08-16 04:07:51 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:07:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212891408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:51 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:51 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 785240760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:51 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:07:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:51 MarkDuplicates Before output close freeMemory: 1262152184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:51 MarkDuplicates After output close freeMemory: 1262149952; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4209949904248261968.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4209949904248261968.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4209949904248261968.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:51 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:51 MarkDuplicates Start of doWork freeMemory: 1262478040; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:51 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:51 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:52 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 2016-08-16 04:07:52 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212888568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:52 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:52 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 785239120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:52 MarkDuplicates Marking 3 records as duplicates. INFO 2016-08-16 04:07:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:52 MarkDuplicates Before output close freeMemory: 1262149640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:52 MarkDuplicates After output close freeMemory: 1262149472; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7825304488439479686.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7825304488439479686.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7825304488439479686.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:52 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:53 MarkDuplicates Start of doWork freeMemory: 1262478872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:53 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:53 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:53 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 2016-08-16 04:07:53 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:07:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212889416; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:53 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:53 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 785238984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:53 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:53 MarkDuplicates Before output close freeMemory: 1262150464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:53 MarkDuplicates After output close freeMemory: 1262150296; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:53 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:53 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.756658226978546197.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.756658226978546197.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.756658226978546197.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:53 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:53 MarkDuplicates Start of doWork freeMemory: 1262478712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:53 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:53 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:53 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:07:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212889744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:54 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:54 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 785250064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:54 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:54 MarkDuplicates Before output close freeMemory: 1262162224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:54 MarkDuplicates After output close freeMemory: 1262159992; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:54 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:54 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9147065239750184920.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9147065239750184920.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9147065239750184920.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:54 MarkDuplicates Start of doWork freeMemory: 1262488480; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:54 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:54 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:54 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:07:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212899536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:54 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:54 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 785244904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:55 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:55 MarkDuplicates Before output close freeMemory: 1262157064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:55 MarkDuplicates After output close freeMemory: 1262156896; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.128040363837028121.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.128040363837028121.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.128040363837028121.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:55 MarkDuplicates Start of doWork freeMemory: 1262338624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:55 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:55 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212703072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:55 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:55 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 785052968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:56 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:56 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:56 MarkDuplicates Before output close freeMemory: 1261873752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:56 MarkDuplicates After output close freeMemory: 1261871520; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.759719668593165076.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.759719668593165076.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.759719668593165076.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:56 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:56 MarkDuplicates Start of doWork freeMemory: 1262469456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:56 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:56 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:56 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2016-08-16 04:07:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212878056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:56 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:56 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 785228568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:56 MarkDuplicates Marking 12 records as duplicates. INFO 2016-08-16 04:07:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:56 MarkDuplicates Before output close freeMemory: 1262139088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:56 MarkDuplicates After output close freeMemory: 1262138920; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3687899047081886699.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3687899047081886699.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3687899047081886699.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:56 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:57 MarkDuplicates Start of doWork freeMemory: 1262473224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:57 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:57 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:57 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 2016-08-16 04:07:57 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:07:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212883288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:57 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:57 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 785233248; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:57 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:07:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:57 MarkDuplicates Before output close freeMemory: 1262143768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:57 MarkDuplicates After output close freeMemory: 1262143600; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:57 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:57 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7789151526134909496.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7789151526134909496.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7789151526134909496.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:57 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:57 MarkDuplicates Start of doWork freeMemory: 1262471448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:57 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:57 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:57 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 2016-08-16 04:07:57 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:07:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212879448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:57 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:58 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 785230880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:58 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:58 MarkDuplicates Before output close freeMemory: 1262142272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:58 MarkDuplicates After output close freeMemory: 1262142104; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7310054269960193375.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7310054269960193375.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7310054269960193375.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:58 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:58 MarkDuplicates Start of doWork freeMemory: 1262465768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:58 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:58 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:58 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2016-08-16 04:07:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212875288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:58 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:58 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 785226256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:59 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:07:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:59 MarkDuplicates Before output close freeMemory: 1262136672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:59 MarkDuplicates After output close freeMemory: 1262136504; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3041435217894955224.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3041435217894955224.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3041435217894955224.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:59 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:59 MarkDuplicates Start of doWork freeMemory: 1262469816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:59 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:59 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212880736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:59 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:59 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 785230120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:59 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:59 MarkDuplicates Before output close freeMemory: 1262141704; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:59 MarkDuplicates After output close freeMemory: 1262141536; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3827149045155391933.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3827149045155391933.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3827149045155391933.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:59 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:07:59 MarkDuplicates Start of doWork freeMemory: 1262465336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:59 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:59 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:59 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2016-08-16 04:08:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212875696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:00 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:00 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 785237720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:00 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:08:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:00 MarkDuplicates Before output close freeMemory: 1262148240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:00 MarkDuplicates After output close freeMemory: 1262146008; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:00 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:00 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8040322158509960460.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8040322158509960460.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8040322158509960460.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:00 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:00 MarkDuplicates Start of doWork freeMemory: 1262479880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:00 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:00 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:00 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 2016-08-16 04:08:00 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:08:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212890960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:01 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:01 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 785234016; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:01 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:08:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:01 MarkDuplicates Before output close freeMemory: 1262147688; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:01 MarkDuplicates After output close freeMemory: 1262145888; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3288894106457653208.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3288894106457653208.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3288894106457653208.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:01 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:01 MarkDuplicates Start of doWork freeMemory: 1262473680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:01 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:01 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:01 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212883984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:01 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:01 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 785236296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:02 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:02 MarkDuplicates Before output close freeMemory: 1262146728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:02 MarkDuplicates After output close freeMemory: 1262146752; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.671644865304922052.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.671644865304922052.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.671644865304922052.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:02 MarkDuplicates Start of doWork freeMemory: 1262473136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:02 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:02 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:02 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 2016-08-16 04:08:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212881720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:02 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:02 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 785228680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:03 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:03 MarkDuplicates Before output close freeMemory: 1262139168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:03 MarkDuplicates After output close freeMemory: 1262139000; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4608795844281727386.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4608795844281727386.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4608795844281727386.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:03 MarkDuplicates Start of doWork freeMemory: 1262466696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:03 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:03 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212877000; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:03 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:03 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 785225536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:03 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:03 MarkDuplicates Before output close freeMemory: 1262136024; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:03 MarkDuplicates After output close freeMemory: 1262133792; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.139635317647689979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.139635317647689979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.139635317647689979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:03 MarkDuplicates Start of doWork freeMemory: 1262463424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:03 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:03 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212874024; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:04 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:04 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 785223056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:04 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:04 MarkDuplicates Before output close freeMemory: 1262133576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:04 MarkDuplicates After output close freeMemory: 1262133288; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:04 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:04 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4925772411663128019.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4925772411663128019.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4925772411663128019.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:04 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:04 MarkDuplicates Start of doWork freeMemory: 1262460504; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:04 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:04 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:04 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212870232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:04 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:05 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 785219784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:05 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:05 MarkDuplicates Before output close freeMemory: 1262130376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:05 MarkDuplicates After output close freeMemory: 1262130208; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:05 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:05 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1701383979137779929.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1701383979137779929.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1701383979137779929.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:05 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:05 MarkDuplicates Start of doWork freeMemory: 1262457624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:05 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:05 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:05 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 2016-08-16 04:08:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212868224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:05 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:06 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 785218104; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:06 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:06 MarkDuplicates Before output close freeMemory: 1262129040; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:06 MarkDuplicates After output close freeMemory: 1262128872; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8267087000234686712.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8267087000234686712.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8267087000234686712.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:06 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:06 MarkDuplicates Start of doWork freeMemory: 1262455688; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:06 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:06 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212864256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:06 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:06 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 785216376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:07 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:07 MarkDuplicates Before output close freeMemory: 1262127312; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:07 MarkDuplicates After output close freeMemory: 1262127544; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3306916204182558551.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3306916204182558551.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3306916204182558551.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:07 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:07 MarkDuplicates Start of doWork freeMemory: 1262455488; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:07 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:07 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:07 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 2016-08-16 04:08:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212864056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:07 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:07 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 785213632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:08 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:08 MarkDuplicates Before output close freeMemory: 1262126776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:08 MarkDuplicates After output close freeMemory: 1262127008; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5083465783898177.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5083465783898177.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5083465783898177.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:08 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:08 MarkDuplicates Start of doWork freeMemory: 1262454424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:08 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:08 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:08 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212864736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:08 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:08 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 785215344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:09 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:09 MarkDuplicates Before output close freeMemory: 1262125720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:09 MarkDuplicates After output close freeMemory: 1262123488; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5811561720372736403.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5811561720372736403.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5811561720372736403.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:09 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:09 MarkDuplicates Start of doWork freeMemory: 1262453320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:09 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:09 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:09 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 2016-08-16 04:08:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212863904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:09 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:09 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 785214280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:09 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:10 MarkDuplicates Before output close freeMemory: 1262124712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:10 MarkDuplicates After output close freeMemory: 1262124544; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6147739154553797183.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6147739154553797183.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6147739154553797183.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:10 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:10 MarkDuplicates Start of doWork freeMemory: 1262452344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:10 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:10 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212862648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:10 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:10 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 785213344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:10 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:10 MarkDuplicates Before output close freeMemory: 1262123800; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:10 MarkDuplicates After output close freeMemory: 1262124032; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8638054151685188973.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8638054151685188973.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8638054151685188973.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:10 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:11 MarkDuplicates Start of doWork freeMemory: 1262450704; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:11 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:11 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212861008; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:11 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 785211736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:11 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:11 MarkDuplicates Before output close freeMemory: 1262121864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:11 MarkDuplicates After output close freeMemory: 1262122096; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:11 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7250816933652089876.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7250816933652089876.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7250816933652089876.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:12 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:12 MarkDuplicates Start of doWork freeMemory: 1262450648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:12 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:12 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:12 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2016-08-16 04:08:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212861568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:12 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:12 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 785208984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:12 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:12 MarkDuplicates Before output close freeMemory: 1262122352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:12 MarkDuplicates After output close freeMemory: 1262122184; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1764844514683069472.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1764844514683069472.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1764844514683069472.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:12 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:12 MarkDuplicates Start of doWork freeMemory: 1262447064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:12 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:12 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:12 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212857376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:13 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:13 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 785208064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:13 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:13 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:13 MarkDuplicates Before output close freeMemory: 1262118424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:13 MarkDuplicates After output close freeMemory: 1262118256; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.847423200236325742.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.847423200236325742.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.847423200236325742.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:13 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:13 MarkDuplicates Start of doWork freeMemory: 1262446248; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:13 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:13 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:13 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212856560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:13 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:13 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 785207248; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:14 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:14 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:14 MarkDuplicates Before output close freeMemory: 1262117608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:14 MarkDuplicates After output close freeMemory: 1262117440; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.517506186045944579.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.517506186045944579.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.517506186045944579.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:14 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:14 MarkDuplicates Start of doWork freeMemory: 1262445224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:14 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:14 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:14 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212855528; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:14 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:14 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 785206224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:15 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:15 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:15 MarkDuplicates Before output close freeMemory: 1262116584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:15 MarkDuplicates After output close freeMemory: 1262114352; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.793143626742397679.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.793143626742397679.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.793143626742397679.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:15 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:15 MarkDuplicates Start of doWork freeMemory: 1262444448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:15 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:15 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:15 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212854728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:15 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:15 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 785205456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:16 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:16 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:16 MarkDuplicates Before output close freeMemory: 1262115816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:16 MarkDuplicates After output close freeMemory: 1262115648; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4773126170756787708.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4773126170756787708.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4773126170756787708.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:16 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:16 MarkDuplicates Start of doWork freeMemory: 1262443664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:16 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:16 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:16 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212853968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:16 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:16 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 785204664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:17 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:17 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:17 MarkDuplicates Before output close freeMemory: 1262115024; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:17 MarkDuplicates After output close freeMemory: 1262115256; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1687012551438108428.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1687012551438108428.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1687012551438108428.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:17 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:17 MarkDuplicates Start of doWork freeMemory: 1262442888; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:17 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:17 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:17 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212853488; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:17 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:17 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 785203896; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:17 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:17 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:18 MarkDuplicates Before output close freeMemory: 1262114256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:18 MarkDuplicates After output close freeMemory: 1262112024; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5469166932420879333.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5469166932420879333.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5469166932420879333.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:18 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:18 MarkDuplicates Start of doWork freeMemory: 1262442032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:18 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:18 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:18 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212852336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:18 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:18 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 785213968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:18 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:18 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:18 MarkDuplicates Before output close freeMemory: 1262124328; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:18 MarkDuplicates After output close freeMemory: 1262124456; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2256361687783756229.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2256361687783756229.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2256361687783756229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:18 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:19 MarkDuplicates Start of doWork freeMemory: 1262452032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:19 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:19 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:19 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212862336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:19 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:19 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 785209080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:19 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:19 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:19 MarkDuplicates Before output close freeMemory: 1262119440; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:19 MarkDuplicates After output close freeMemory: 1262119672; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:19 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:19 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4829105250637326126.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4829105250637326126.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4829105250637326126.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:19 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:19 MarkDuplicates Start of doWork freeMemory: 1262447304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:19 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:19 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:19 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212857608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:20 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:20 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 785205768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:20 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:20 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:20 MarkDuplicates Before output close freeMemory: 1262116128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:20 MarkDuplicates After output close freeMemory: 1262113896; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5452377060938850622.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5452377060938850622.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5452377060938850622.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:20 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:21 MarkDuplicates Start of doWork freeMemory: 1262443992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:21 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:21 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:21 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212852232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:21 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:21 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 785203360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:21 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:21 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:21 MarkDuplicates Before output close freeMemory: 1262113720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:21 MarkDuplicates After output close freeMemory: 1262113984; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7328753616076840893.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7328753616076840893.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7328753616076840893.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:21 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:21 MarkDuplicates Start of doWork freeMemory: 1262441584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:21 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:21 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:21 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212851888; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:22 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:22 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 785200584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:22 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:22 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:22 MarkDuplicates Before output close freeMemory: 1262111904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:22 MarkDuplicates After output close freeMemory: 1262111736; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:22 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:22 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3226881973650204730.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3226881973650204730.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3226881973650204730.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:22 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:22 MarkDuplicates Start of doWork freeMemory: 1262439648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:22 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:22 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:22 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212849952; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:22 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:23 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 785199976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:23 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:23 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:23 MarkDuplicates Before output close freeMemory: 1262110336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:23 MarkDuplicates After output close freeMemory: 1262110168; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8256198255998241328.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8256198255998241328.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8256198255998241328.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:23 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:23 MarkDuplicates Start of doWork freeMemory: 1262441128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:23 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:23 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:23 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:08:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212850120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:23 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:23 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 785201080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:24 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:24 MarkDuplicates Before output close freeMemory: 1262113240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:24 MarkDuplicates After output close freeMemory: 1262113472; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MarkDuplicates/merge1.sam, /bar/jli/Chip-seq/script/picard/testdata/picard/sam/MarkDuplicates/merge2.sam, /bar/jli/Chip-seq/script/picard/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.4651589627401435979.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.4651589627401435979.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:24 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:24 MarkDuplicates Start of doWork freeMemory: 1262444520; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:24 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:24 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:08:24 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. INFO 2016-08-16 04:08:24 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:08:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203699664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:24 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:24 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 785204496; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:25 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:08:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:25 MarkDuplicates Before output close freeMemory: 1262014864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:25 MarkDuplicates After output close freeMemory: 1262015160; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MarkDuplicates/merge1.sam, /bar/jli/Chip-seq/script/picard/testdata/picard/sam/MarkDuplicates/merge2.sam, /bar/jli/Chip-seq/script/picard/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.18833662021156118.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.18833662021156118.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:25 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:25 MarkDuplicates Start of doWork freeMemory: 1262443920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:25 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:25 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:08:25 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. INFO 2016-08-16 04:08:25 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:08:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203699136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:25 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:26 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 785203776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:26 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:08:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:26 MarkDuplicates Before output close freeMemory: 1262015568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:26 MarkDuplicates After output close freeMemory: 1262015864; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 INFO 2016-08-16 04:08:26 MarkDuplicates Start of doWork freeMemory: 1262457752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:26 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:26 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:08:26 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203713144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:26 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:27 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 785219464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:27 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:27 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:27 MarkDuplicates Before output close freeMemory: 1262133104; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:27 MarkDuplicates After output close freeMemory: 1262132936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:27 MarkDuplicates Start of doWork freeMemory: 1262457152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:27 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:27 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:08:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203713864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:27 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:27 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 785218152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:28 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:28 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:28 MarkDuplicates Before output close freeMemory: 1262131744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:28 MarkDuplicates After output close freeMemory: 1262129512; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8931937193764195116.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8931937193764195116.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8931937193764195116.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:28 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:28 MarkDuplicates Start of doWork freeMemory: 1262434080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:28 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:28 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:28 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2016-08-16 04:08:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212841464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:28 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:28 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 785192992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:29 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:29 MarkDuplicates Before output close freeMemory: 1262104392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:29 MarkDuplicates After output close freeMemory: 1262104624; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3995776647795442908.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3995776647795442908.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3995776647795442908.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:29 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:29 MarkDuplicates Start of doWork freeMemory: 1262428872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:29 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:29 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:29 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:08:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212838936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:29 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:29 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 785189920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:30 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:30 MarkDuplicates Before output close freeMemory: 1262099968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:30 MarkDuplicates After output close freeMemory: 1262099800; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6340243915487532446.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6340243915487532446.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6340243915487532446.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:30 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:30 MarkDuplicates Start of doWork freeMemory: 1262429424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:30 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212837664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:30 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:30 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 785189512; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:30 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:30 MarkDuplicates Before output close freeMemory: 1262100608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:30 MarkDuplicates After output close freeMemory: 1262098376; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8555484997170048116.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8555484997170048116.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8555484997170048116.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:31 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:31 MarkDuplicates Start of doWork freeMemory: 1262430344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:31 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:31 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:31 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:08:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212841424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:31 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:31 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 785188520; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:31 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:08:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:31 MarkDuplicates Before output close freeMemory: 1262102256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:31 MarkDuplicates After output close freeMemory: 1262102064; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8294168910733377927.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8294168910733377927.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8294168910733377927.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:08:31 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:08:31 MarkDuplicates Start of doWork freeMemory: 1262425056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:31 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:31 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:31 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:08:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212833056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:32 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:32 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 785185496; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:32 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:32 MarkDuplicates Before output close freeMemory: 1262095984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:32 MarkDuplicates After output close freeMemory: 1262095816; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800