Class picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4573f402, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@19fbbabb, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2d3de774], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24690d02, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7ee03e69], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3a0a7d6c]}) | 1.085s | passed |
| pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1823fafa, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4317c792], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7a53bcb0], 1AAXX.3.1=[]}) | 0.885s | passed |
| testBulkFragmentsNoDuplicates | 1.487s | passed |
| testBulkFragmentsWithDuplicates | 3.317s | passed |
| testDifferentChromosomesInOppositeOrder | 1.000s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.877s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.766s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.716s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.765s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.742s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.804s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.736s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.968s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.965s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.839s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.705s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.711s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.709s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.736s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.890s | passed |
| testMappedPairWithSamePosition | 0.691s | passed |
| testMappedPairWithSamePositionSameCigar | 0.803s | passed |
| testMatePairFirstUnmapped | 0.949s | passed |
| testMatePairSecondUnmapped | 0.731s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.784s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates | 0.701s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.968s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.810s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.704s | passed |
| testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) | 0.929s | passed |
| testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) | 0.883s | passed |
| testOpticalDuplicateFinding | 0.703s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.727s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.673s | passed |
| testSingleMappedFragment | 0.727s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.686s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.806s | passed |
| testSingleMappedPair | 0.855s | passed |
| testSingleUnmappedFragment | 0.810s | passed |
| testSingleUnmappedPair | 0.839s | passed |
| testStackOverFlowPairSetSwap | 1.009s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.896s | passed |
| testThreeMappedPairs | 0.853s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 1.082s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.862s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.817s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.808s | passed |
| testTwoMappedFragments | 0.920s | passed |
| testTwoMappedPairWithSamePosition | 0.791s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.863s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.772s | passed |
| testTwoMappedPairs | 0.823s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.814s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.830s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.829s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.829s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.708s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.798s | passed |
| testTwoMappedPairsWithSoftClipping | 0.752s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.806s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 0.987s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.718s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.695s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.880s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.761s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.723s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.762s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.712s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.787s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.732s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.882s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.727s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.893s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.847s | passed |
| testTwoUnmappedFragments | 0.767s | passed |
| testWithBarcodeComplex | 0.908s | passed |
| testWithBarcodeDuplicate | 0.861s | passed |
| testWithBarcodeFragmentDuplicate | 0.830s | passed |
| testWithIndividualReadBarcodes | 0.880s | passed |
Standard error
[Tue Aug 16 04:08:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2700870096247928297.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2700870096247928297.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2700870096247928297.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 04:08:32 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 04:08:32 MarkDuplicates Start of doWork freeMemory: 1257090696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:32 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:32 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:32 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 04:08:32 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2016-08-16 04:08:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 1206701632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:33 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:33 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 779849544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:33 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:33 MarkDuplicates Before output close freeMemory: 1256812328; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:34 MarkDuplicates After output close freeMemory: 1257084936; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4304379181393231177.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4304379181393231177.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4304379181393231177.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 04:08:34 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 04:08:34 MarkDuplicates Start of doWork freeMemory: 1235191536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:34 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:34 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:34 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 04:08:35 MarkDuplicates Read 50000 records. 0 pairs never matched. INFO 2016-08-16 04:08:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 1181602152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:35 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:35 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 757952440; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:36 MarkDuplicates Marking 40000 records as duplicates. INFO 2016-08-16 04:08:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:36 MarkDuplicates Before output close freeMemory: 1234912840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:36 MarkDuplicates After output close freeMemory: 1235185056; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7710002498611548057.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7710002498611548057.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7710002498611548057.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 04:08:37 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 04:08:37 MarkDuplicates Start of doWork freeMemory: 1262424696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:37 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:37 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212834160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:37 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:37 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 785185224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:38 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:38 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:38 MarkDuplicates Before output close freeMemory: 1262145352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:38 MarkDuplicates After output close freeMemory: 1262418240; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2374773564997632219.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2374773564997632219.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2374773564997632219.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 04:08:38 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 04:08:38 MarkDuplicates Start of doWork freeMemory: 1262418272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:38 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:38 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:38 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:08:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212827536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:38 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:38 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 785178336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:39 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:08:39 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:08:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:39 MarkDuplicates Before output close freeMemory: 1262139088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:39 MarkDuplicates After output close freeMemory: 1262409512; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7152534851041819435.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7152534851041819435.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7152534851041819435.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 04:08:39 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 04:08:39 MarkDuplicates Start of doWork freeMemory: 1262417448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:39 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:39 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:39 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:08:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212824656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:39 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:39 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 785178144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:39 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:08:39 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:08:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:40 MarkDuplicates Before output close freeMemory: 1262138272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:40 MarkDuplicates After output close freeMemory: 1262410760; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4761641712834082.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4761641712834082.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4761641712834082.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 04:08:40 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 04:08:40 MarkDuplicates Start of doWork freeMemory: 1262416744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:40 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:40 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:40 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:08:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212826008; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:40 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:40 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 785177432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:40 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:08:40 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:08:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:40 MarkDuplicates Before output close freeMemory: 1262137560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:40 MarkDuplicates After output close freeMemory: 1262410024; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4706727432146439237.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4706727432146439237.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4706727432146439237.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 04:08:40 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 04:08:40 MarkDuplicates Start of doWork freeMemory: 1262414632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:40 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:40 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:40 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:08:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212821824; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:41 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:41 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 785175312; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:41 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:08:41 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:08:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:41 MarkDuplicates Before output close freeMemory: 1262135440; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:41 MarkDuplicates After output close freeMemory: 1262407928; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:41 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:41 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2471588488032267064.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2471588488032267064.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2471588488032267064.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 04:08:41 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 04:08:41 MarkDuplicates Start of doWork freeMemory: 1262413856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:41 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:41 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:41 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:08:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212823128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:41 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:41 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 785174552; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:42 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:08:42 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:08:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:42 MarkDuplicates Before output close freeMemory: 1262134680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:42 MarkDuplicates After output close freeMemory: 1262405080; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2573710040580080123.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2573710040580080123.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2573710040580080123.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 04:08:42 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 04:08:42 MarkDuplicates Start of doWork freeMemory: 1262413088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:42 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:42 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:42 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:08:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212822352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:42 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:42 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 785173776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:42 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:08:42 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:08:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:43 MarkDuplicates Before output close freeMemory: 1262133904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:43 MarkDuplicates After output close freeMemory: 1262404304; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.665963539979634866.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.665963539979634866.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.665963539979634866.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 04:08:43 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 04:08:43 MarkDuplicates Start of doWork freeMemory: 1262418640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:43 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:43 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:43 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:08:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212826472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:43 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:43 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 785178592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:43 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:43 MarkDuplicates Before output close freeMemory: 1262139928; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:43 MarkDuplicates After output close freeMemory: 1262412568; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1208733581261218196.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1208733581261218196.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1208733581261218196.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 04:08:43 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 04:08:43 MarkDuplicates Start of doWork freeMemory: 1262417504; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:43 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:43 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:43 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:08:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212828264; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:44 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:44 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 785177456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:44 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:08:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:44 MarkDuplicates Before output close freeMemory: 1262138728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:44 MarkDuplicates After output close freeMemory: 1262411032; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:44 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:44 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5680237468994563306.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5680237468994563306.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5680237468994563306.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 04:08:44 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 04:08:44 MarkDuplicates Start of doWork freeMemory: 1262416768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:44 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:44 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:44 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:08:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212826608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:45 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:45 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 785176720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:45 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:08:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:45 MarkDuplicates Before output close freeMemory: 1262137992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:45 MarkDuplicates After output close freeMemory: 1262410296; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5070874036536281033.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5070874036536281033.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5070874036536281033.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 04:08:45 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 04:08:45 MarkDuplicates Start of doWork freeMemory: 1262414776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:45 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:45 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:45 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212822776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:46 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:46 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 785174568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:46 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:46 MarkDuplicates Before output close freeMemory: 1262135688; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:46 MarkDuplicates After output close freeMemory: 1262408144; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2110632654816269.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2110632654816269.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2110632654816269.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 04:08:46 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 04:08:46 MarkDuplicates Start of doWork freeMemory: 1262413944; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:46 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:46 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:46 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:08:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212824304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:46 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:46 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 785173736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:47 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:47 MarkDuplicates Before output close freeMemory: 1262134856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:47 MarkDuplicates After output close freeMemory: 1262407312; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:47 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:47 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8366943443911124271.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8366943443911124271.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8366943443911124271.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 04:08:47 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 04:08:47 MarkDuplicates Start of doWork freeMemory: 1262413560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:47 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:47 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:47 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212823992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:47 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:47 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 785173680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:47 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:47 MarkDuplicates Before output close freeMemory: 1262134464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:48 MarkDuplicates After output close freeMemory: 1262404856; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1683957181171229740.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1683957181171229740.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1683957181171229740.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 04:08:48 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 04:08:48 MarkDuplicates Start of doWork freeMemory: 1262412656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:48 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:48 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212823096; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:48 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:48 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 785172448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:48 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:08:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:48 MarkDuplicates Before output close freeMemory: 1262133568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:48 MarkDuplicates After output close freeMemory: 1262406024; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1491615306098811433.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1491615306098811433.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1491615306098811433.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 04:08:48 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 04:08:48 MarkDuplicates Start of doWork freeMemory: 1262411760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:48 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:48 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212819840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:48 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:49 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 785171552; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:49 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:08:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:49 MarkDuplicates Before output close freeMemory: 1262132672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:49 MarkDuplicates After output close freeMemory: 1262403064; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1442431800609216946.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1442431800609216946.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1442431800609216946.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 04:08:49 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 04:08:49 MarkDuplicates Start of doWork freeMemory: 1262410936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:49 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:49 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:49 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 04:08:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212820920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:49 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:49 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 785170728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:50 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:50 MarkDuplicates Before output close freeMemory: 1262131848; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:50 MarkDuplicates After output close freeMemory: 1262404304; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8636487136042196361.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8636487136042196361.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8636487136042196361.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 04:08:50 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 04:08:50 MarkDuplicates Start of doWork freeMemory: 1262410880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:50 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:50 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:50 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 04:08:50 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:08:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212821400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:50 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:50 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 785170672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:50 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:50 MarkDuplicates Before output close freeMemory: 1262131792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:51 MarkDuplicates After output close freeMemory: 1262404648; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6206900668672081132.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6206900668672081132.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6206900668672081132.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 04:08:51 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 04:08:51 MarkDuplicates Start of doWork freeMemory: 1262408960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:51 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:51 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:51 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 04:08:51 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:08:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212819480; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:51 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:51 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 785166664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:51 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:51 MarkDuplicates Before output close freeMemory: 1262129872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:51 MarkDuplicates After output close freeMemory: 1262402728; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7307458187246789384.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7307458187246789384.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7307458187246789384.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 04:08:51 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 04:08:51 MarkDuplicates Start of doWork freeMemory: 1262408136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:51 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:51 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:51 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 04:08:51 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:08:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212818984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:52 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:52 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 785166296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:52 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:52 MarkDuplicates Before output close freeMemory: 1262129288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:52 MarkDuplicates After output close freeMemory: 1262401624; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1583979583364384816.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1583979583364384816.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1583979583364384816.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 04:08:52 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 04:08:52 MarkDuplicates Start of doWork freeMemory: 1262407360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:52 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:52 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:08:52 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:08:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212817904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:53 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:53 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 785167312; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:53 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:53 MarkDuplicates Before output close freeMemory: 1262128712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:53 MarkDuplicates After output close freeMemory: 1262400888; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:53 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:53 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4490729713295806263.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4490729713295806263.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4490729713295806263.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 04:08:53 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 04:08:53 MarkDuplicates Start of doWork freeMemory: 1262404936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:53 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:53 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212812856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:53 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:53 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 785165624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:54 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:54 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:54 MarkDuplicates Before output close freeMemory: 1262125752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:54 MarkDuplicates After output close freeMemory: 1262398240; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:54 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:54 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.965611797848074367.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.965611797848074367.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.965611797848074367.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 04:08:54 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 04:08:54 MarkDuplicates Start of doWork freeMemory: 1262404048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:54 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:54 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212814032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:54 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:54 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 785164176; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:54 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:54 MarkDuplicates Before output close freeMemory: 1262124928; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:55 MarkDuplicates After output close freeMemory: 1262397416; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7086856664024157518.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7086856664024157518.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7086856664024157518.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 04:08:55 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 04:08:55 MarkDuplicates Start of doWork freeMemory: 1262403144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:55 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:55 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212813128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:55 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:55 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 785161184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:55 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:55 MarkDuplicates Before output close freeMemory: 1262124024; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:55 MarkDuplicates After output close freeMemory: 1262396488; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5314472535247289345.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5314472535247289345.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5314472535247289345.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 04:08:55 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 04:08:56 MarkDuplicates Start of doWork freeMemory: 1262402296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:56 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:56 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212812256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:56 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:56 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 785160296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:56 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:56 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:56 MarkDuplicates Before output close freeMemory: 1262123152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:56 MarkDuplicates After output close freeMemory: 1262395600; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6206702921921082041.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6206702921921082041.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6206702921921082041.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 04:08:56 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 04:08:56 MarkDuplicates Start of doWork freeMemory: 1262401064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:56 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:56 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212811048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:57 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:57 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 785160792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:57 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:57 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:57 MarkDuplicates Before output close freeMemory: 1262121880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:57 MarkDuplicates After output close freeMemory: 1262394368; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:57 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:57 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3825483961391176594.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3825483961391176594.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3825483961391176594.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 04:08:57 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 04:08:57 MarkDuplicates Start of doWork freeMemory: 1262399424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:57 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:57 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:57 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:08:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212809168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:57 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:57 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 785160144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:58 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:08:58 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:58 MarkDuplicates Before output close freeMemory: 1262120296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:58 MarkDuplicates After output close freeMemory: 1262392728; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8128918969244865150.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8128918969244865150.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8128918969244865150.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 04:08:58 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 04:08:58 MarkDuplicates Start of doWork freeMemory: 1262399760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:58 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:58 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:08:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:08:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212809720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:58 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:58 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 785157736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:58 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:08:58 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:08:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:58 MarkDuplicates Before output close freeMemory: 1262120616; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:58 MarkDuplicates After output close freeMemory: 1262393064; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6160890511844743300.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6160890511844743300.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6160890511844743300.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 04:08:58 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 04:08:58 MarkDuplicates Start of doWork freeMemory: 1262399808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:58 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:58 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:58 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 04:08:58 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:08:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212810360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:59 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:59 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:08:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 785159600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:59 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:08:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:08:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:08:59 MarkDuplicates Before output close freeMemory: 1262120720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:59 MarkDuplicates After output close freeMemory: 1262391112; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:08:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:08:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3033143861316369655.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3033143861316369655.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3033143861316369655.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 04:08:59 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 04:08:59 MarkDuplicates Start of doWork freeMemory: 1262399768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:59 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:08:59 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:08:59 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 04:08:59 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2016-08-16 04:08:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212810288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:08:59 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:08:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:08:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:08:59 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 785159720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:00 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:00 MarkDuplicates Before output close freeMemory: 1262121088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:00 MarkDuplicates After output close freeMemory: 1262393296; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:00 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:00 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1446247120072589810.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1446247120072589810.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1446247120072589810.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 04:09:00 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 04:09:00 MarkDuplicates Start of doWork freeMemory: 1262397720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:00 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:00 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:00 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:09:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212808160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:00 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:00 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 785157512; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:00 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:09:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:00 MarkDuplicates Before output close freeMemory: 1262118672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:01 MarkDuplicates After output close freeMemory: 1262391088; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4521194516805949882.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4521194516805949882.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4521194516805949882.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 04:09:01 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 04:09:01 MarkDuplicates Start of doWork freeMemory: 1262395416; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:01 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:01 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:01 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212805320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:01 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:01 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 785156168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:01 MarkDuplicates Marking 3 records as duplicates. INFO 2016-08-16 04:09:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:01 MarkDuplicates Before output close freeMemory: 1262116368; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:01 MarkDuplicates After output close freeMemory: 1262388784; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7825360866778614200.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7825360866778614200.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7825360866778614200.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 04:09:01 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 04:09:01 MarkDuplicates Start of doWork freeMemory: 1262396392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:01 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:01 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:01 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:09:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212806912; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:02 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:02 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 785156184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:02 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:02 MarkDuplicates Before output close freeMemory: 1262117344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:02 MarkDuplicates After output close freeMemory: 1262389528; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4236145529676192488.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4236145529676192488.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4236145529676192488.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 04:09:02 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 04:09:02 MarkDuplicates Start of doWork freeMemory: 1262396288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:02 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:02 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:02 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:09:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212804960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:02 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:03 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 785156352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:03 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:03 MarkDuplicates Before output close freeMemory: 1262117968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:03 MarkDuplicates After output close freeMemory: 1262389928; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9001165866016260346.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9001165866016260346.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9001165866016260346.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 04:09:03 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 04:09:03 MarkDuplicates Start of doWork freeMemory: 1262395104; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:03 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:03 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:03 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:09:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212803776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:03 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:03 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 785153080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:04 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:04 MarkDuplicates Before output close freeMemory: 1262116784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:04 MarkDuplicates After output close freeMemory: 1262386680; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:04 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:04 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6947527641879219411.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6947527641879219411.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6947527641879219411.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 04:09:04 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 04:09:04 MarkDuplicates Start of doWork freeMemory: 1262249192; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:04 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:04 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212615056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:04 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:04 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 784965760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:05 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:05 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:05 MarkDuplicates Before output close freeMemory: 1261881272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:05 MarkDuplicates After output close freeMemory: 1262198376; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:05 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:05 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7926096282384393880.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7926096282384393880.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7926096282384393880.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 04:09:05 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 04:09:05 MarkDuplicates Start of doWork freeMemory: 1262382440; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:05 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:05 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:05 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2016-08-16 04:09:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212790424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:05 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:05 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 785142872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:06 MarkDuplicates Marking 12 records as duplicates. INFO 2016-08-16 04:09:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:06 MarkDuplicates Before output close freeMemory: 1262103072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:06 MarkDuplicates After output close freeMemory: 1262375488; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8600136905166653708.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8600136905166653708.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8600136905166653708.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 04:09:06 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 04:09:06 MarkDuplicates Start of doWork freeMemory: 1262389160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:06 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:06 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:06 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:09:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212799200; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:06 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:06 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 785149288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:06 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:09:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:07 MarkDuplicates Before output close freeMemory: 1262110112; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:07 MarkDuplicates After output close freeMemory: 1262380464; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1743700393308974052.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1743700393308974052.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1743700393308974052.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 04:09:07 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 04:09:07 MarkDuplicates Start of doWork freeMemory: 1262388432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:07 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:07 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:07 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:09:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212798176; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:07 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:07 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 785149184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:08 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:08 MarkDuplicates Before output close freeMemory: 1262109344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:08 MarkDuplicates After output close freeMemory: 1262381800; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7826485425340218384.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7826485425340218384.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7826485425340218384.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 04:09:08 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 04:09:08 MarkDuplicates Start of doWork freeMemory: 1262383432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:08 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:08 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:08 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2016-08-16 04:09:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212792600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:08 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:08 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 785144032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:08 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:09:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:08 MarkDuplicates Before output close freeMemory: 1262104232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:09 MarkDuplicates After output close freeMemory: 1262376648; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6078582584656677580.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6078582584656677580.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6078582584656677580.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 04:09:09 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 04:09:09 MarkDuplicates Start of doWork freeMemory: 1262387560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:09 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:09 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212798624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:09 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:09 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 785147976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:09 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:09 MarkDuplicates Before output close freeMemory: 1262109344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:09 MarkDuplicates After output close freeMemory: 1262381552; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3966985808269737173.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3966985808269737173.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3966985808269737173.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 04:09:09 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 04:09:09 MarkDuplicates Start of doWork freeMemory: 1262384280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:09 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:09 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:09 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2016-08-16 04:09:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212793920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:10 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:10 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 785142160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:10 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:09:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:10 MarkDuplicates Before output close freeMemory: 1262105072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:10 MarkDuplicates After output close freeMemory: 1262375424; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8848067165645271200.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8848067165645271200.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8848067165645271200.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 04:09:10 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 04:09:10 MarkDuplicates Start of doWork freeMemory: 1262387352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:10 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:10 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:10 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:09:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212798112; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:10 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 785147304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:11 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:09:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:11 MarkDuplicates Before output close freeMemory: 1262108672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:11 MarkDuplicates After output close freeMemory: 1262380880; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:11 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:11 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5618548107639867000.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5618548107639867000.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5618548107639867000.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 04:09:11 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 04:09:11 MarkDuplicates Start of doWork freeMemory: 1262385512; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:11 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:11 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212795792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:11 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 785145640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:12 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:12 MarkDuplicates Before output close freeMemory: 1262106424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:12 MarkDuplicates After output close freeMemory: 1262378880; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6321900219716081147.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6321900219716081147.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6321900219716081147.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 04:09:12 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 04:09:12 MarkDuplicates Start of doWork freeMemory: 1262384192; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:12 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:12 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212794472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:12 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:12 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 785144320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:13 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:13 MarkDuplicates Before output close freeMemory: 1262105144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:13 MarkDuplicates After output close freeMemory: 1262375496; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6867069111936611376.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6867069111936611376.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6867069111936611376.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 04:09:13 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 04:09:13 MarkDuplicates Start of doWork freeMemory: 1262383296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:13 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:13 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212793584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:13 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:13 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 785141344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:13 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:13 MarkDuplicates Before output close freeMemory: 1262104256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:13 MarkDuplicates After output close freeMemory: 1262374584; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2454675704581928692.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2454675704581928692.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2454675704581928692.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 04:09:14 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 04:09:14 MarkDuplicates Start of doWork freeMemory: 1262382248; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:14 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:14 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212790168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:14 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:14 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 785142376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:14 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:14 MarkDuplicates Before output close freeMemory: 1262103200; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:14 MarkDuplicates After output close freeMemory: 1262375616; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1759810137690338905.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1759810137690338905.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1759810137690338905.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 04:09:14 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 04:09:14 MarkDuplicates Start of doWork freeMemory: 1262380784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:14 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:14 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:14 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212791064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:15 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:15 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 785140912; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:15 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:15 MarkDuplicates Before output close freeMemory: 1262101848; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:15 MarkDuplicates After output close freeMemory: 1262374152; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1396728651733220665.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1396728651733220665.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1396728651733220665.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 04:09:15 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 04:09:15 MarkDuplicates Start of doWork freeMemory: 1262379936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:15 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:15 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212789920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:15 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:15 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 785140064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:16 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:16 MarkDuplicates Before output close freeMemory: 1262101248; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:16 MarkDuplicates After output close freeMemory: 1262373304; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4278263577434258493.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4278263577434258493.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4278263577434258493.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 04:09:16 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 04:09:16 MarkDuplicates Start of doWork freeMemory: 1262378592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:16 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:16 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212788872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:16 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:16 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 785138384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:17 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:17 MarkDuplicates Before output close freeMemory: 1262099904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:17 MarkDuplicates After output close freeMemory: 1262371960; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4424752431970363701.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4424752431970363701.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4424752431970363701.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 04:09:17 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 04:09:17 MarkDuplicates Start of doWork freeMemory: 1262378776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:17 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:17 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212789056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:17 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:17 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 785139528; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:18 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:18 MarkDuplicates Before output close freeMemory: 1262099696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:18 MarkDuplicates After output close freeMemory: 1262372144; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6191733450340517842.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6191733450340517842.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6191733450340517842.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 04:09:18 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 04:09:18 MarkDuplicates Start of doWork freeMemory: 1262377880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:18 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:18 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212785800; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:18 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:18 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 785138632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:18 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:18 MarkDuplicates Before output close freeMemory: 1262098792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:18 MarkDuplicates After output close freeMemory: 1262369160; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.152354525185570268.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.152354525185570268.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.152354525185570268.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 04:09:18 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 04:09:18 MarkDuplicates Start of doWork freeMemory: 1262376992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:18 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:18 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212787272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:19 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:19 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 785137744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:19 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:19 MarkDuplicates Before output close freeMemory: 1262097904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:19 MarkDuplicates After output close freeMemory: 1262370368; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:19 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:19 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3872008602656077100.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3872008602656077100.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3872008602656077100.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 04:09:19 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 04:09:19 MarkDuplicates Start of doWork freeMemory: 1262375456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:19 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:19 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:19 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212785448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:19 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:19 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 785135256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:20 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:20 MarkDuplicates Before output close freeMemory: 1262096376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:20 MarkDuplicates After output close freeMemory: 1262368832; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7150103748091699973.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7150103748091699973.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7150103748091699973.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 04:09:20 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 04:09:20 MarkDuplicates Start of doWork freeMemory: 1262371776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:20 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:20 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212782216; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:20 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:20 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 785132360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:21 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:21 MarkDuplicates Before output close freeMemory: 1262093144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:21 MarkDuplicates After output close freeMemory: 1262365600; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6306025385028289555.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6306025385028289555.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6306025385028289555.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 04:09:21 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 04:09:21 MarkDuplicates Start of doWork freeMemory: 1262371480; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:21 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:21 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:21 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 04:09:21 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2016-08-16 04:09:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212782080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:21 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:21 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 785131272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:21 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:21 MarkDuplicates Before output close freeMemory: 1262092496; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:21 MarkDuplicates After output close freeMemory: 1262362784; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7757190080263208632.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7757190080263208632.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7757190080263208632.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 04:09:21 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 04:09:22 MarkDuplicates Start of doWork freeMemory: 1262367920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:22 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:22 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:22 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212775816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:22 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:22 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 785125896; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:22 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:22 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:22 MarkDuplicates Before output close freeMemory: 1262088736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:22 MarkDuplicates After output close freeMemory: 1262359160; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:22 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:22 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5673656285438660897.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5673656285438660897.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5673656285438660897.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 04:09:22 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 04:09:22 MarkDuplicates Start of doWork freeMemory: 1262367096; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:22 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:22 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:22 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212777088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:22 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:23 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 785127168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:23 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:23 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:23 MarkDuplicates Before output close freeMemory: 1262087920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:23 MarkDuplicates After output close freeMemory: 1262360408; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8735963758078264988.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8735963758078264988.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8735963758078264988.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 04:09:23 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 04:09:23 MarkDuplicates Start of doWork freeMemory: 1262366336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:23 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:23 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:23 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212776320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:23 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:23 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 785126400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:24 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:24 MarkDuplicates Before output close freeMemory: 1262087152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:24 MarkDuplicates After output close freeMemory: 1262359640; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7821939461145822043.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7821939461145822043.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7821939461145822043.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 04:09:24 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 04:09:24 MarkDuplicates Start of doWork freeMemory: 1262364536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:24 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:24 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:24 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212772456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:24 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:24 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 785125224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:24 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:24 MarkDuplicates Before output close freeMemory: 1262085352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:25 MarkDuplicates After output close freeMemory: 1262358240; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5594519214532760820.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5594519214532760820.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5594519214532760820.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 04:09:25 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 04:09:25 MarkDuplicates Start of doWork freeMemory: 1262363768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:25 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:25 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:25 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212773760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:25 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:25 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 785122432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:25 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:25 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:25 MarkDuplicates Before output close freeMemory: 1262084592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:25 MarkDuplicates After output close freeMemory: 1262357080; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6691631116155611627.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6691631116155611627.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6691631116155611627.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 04:09:25 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 04:09:26 MarkDuplicates Start of doWork freeMemory: 1262360464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:26 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:26 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:26 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212772992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:26 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:26 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 785123696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:26 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:26 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:26 MarkDuplicates Before output close freeMemory: 1262083824; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:26 MarkDuplicates After output close freeMemory: 1262354248; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4446509574140335827.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4446509574140335827.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4446509574140335827.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 04:09:26 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 04:09:26 MarkDuplicates Start of doWork freeMemory: 1262362152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:26 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:26 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:26 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212772144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:27 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:27 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 785122224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:27 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:27 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:27 MarkDuplicates Before output close freeMemory: 1262082976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:27 MarkDuplicates After output close freeMemory: 1262355464; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:27 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:27 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.319308397079588251.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.319308397079588251.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.319308397079588251.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 04:09:27 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 04:09:27 MarkDuplicates Start of doWork freeMemory: 1262361344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:27 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:27 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:27 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212769240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:27 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:27 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 785122032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:28 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:28 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:28 MarkDuplicates Before output close freeMemory: 1262082160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:28 MarkDuplicates After output close freeMemory: 1262354648; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18813716442539400.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18813716442539400.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18813716442539400.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 04:09:28 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 04:09:28 MarkDuplicates Start of doWork freeMemory: 1262360608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:28 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:28 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:28 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212770888; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:28 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:28 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 785118584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:29 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:29 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:29 MarkDuplicates Before output close freeMemory: 1262081424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:29 MarkDuplicates After output close freeMemory: 1262351848; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3036575330172126441.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3036575330172126441.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3036575330172126441.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 04:09:29 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 04:09:29 MarkDuplicates Start of doWork freeMemory: 1262358768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:29 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:29 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:29 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212768752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:29 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:29 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 785116744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:29 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:29 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:29 MarkDuplicates Before output close freeMemory: 1262079584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:29 MarkDuplicates After output close freeMemory: 1262350008; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6552047541781919148.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6552047541781919148.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6552047541781919148.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 04:09:29 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 04:09:29 MarkDuplicates Start of doWork freeMemory: 1262358000; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:29 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:29 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:29 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212768280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:30 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:30 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 785118688; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:30 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:30 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:30 MarkDuplicates Before output close freeMemory: 1262078816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:30 MarkDuplicates After output close freeMemory: 1262351304; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6677629654448054941.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6677629654448054941.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6677629654448054941.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 04:09:30 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 04:09:30 MarkDuplicates Start of doWork freeMemory: 1262357232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:30 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:30 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212767216; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:30 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:30 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 785115208; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:31 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:31 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:31 MarkDuplicates Before output close freeMemory: 1262078048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:31 MarkDuplicates After output close freeMemory: 1262350536; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5519591995098596230.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5519591995098596230.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5519591995098596230.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 04:09:31 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 04:09:31 MarkDuplicates Start of doWork freeMemory: 1262359392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:31 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:31 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:31 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:09:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212770432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:31 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:31 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 785119464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:31 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:32 MarkDuplicates Before output close freeMemory: 1262081080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:32 MarkDuplicates After output close freeMemory: 1262353040; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:32 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.5618029525914584532.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.5618029525914584532.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 04:09:32 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 04:09:32 MarkDuplicates Start of doWork freeMemory: 1262363824; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:32 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:32 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:32 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. INFO 2016-08-16 04:09:32 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:09:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203617872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:32 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:32 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 785121728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:33 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:09:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:33 MarkDuplicates Before output close freeMemory: 1262080016; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:33 MarkDuplicates After output close freeMemory: 1262354608; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:33 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.2327878733668170458.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.2327878733668170458.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 04:09:33 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 04:09:33 MarkDuplicates Start of doWork freeMemory: 1262362360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:33 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:33 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:33 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. INFO 2016-08-16 04:09:33 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:09:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203616992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:33 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:33 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 785119056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:33 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:09:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:34 MarkDuplicates Before output close freeMemory: 1262080632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:34 MarkDuplicates After output close freeMemory: 1262352672; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 INFO 2016-08-16 04:09:34 MarkDuplicates Start of doWork freeMemory: 1262375416; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:34 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:34 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:34 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203630536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:34 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:34 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 785136344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:34 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:34 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:34 MarkDuplicates Before output close freeMemory: 1262099064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:34 MarkDuplicates After output close freeMemory: 1262369600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:35 MarkDuplicates Start of doWork freeMemory: 1262374776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:35 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:35 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203631368; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:35 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:35 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 785135736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:35 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:35 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:35 MarkDuplicates Before output close freeMemory: 1262097808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:35 MarkDuplicates After output close freeMemory: 1262366072; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:35 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7905388161945055431.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7905388161945055431.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7905388161945055431.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 04:09:35 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 04:09:35 MarkDuplicates Start of doWork freeMemory: 1262351824; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:35 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:35 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:35 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 04:09:35 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2016-08-16 04:09:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212761472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:36 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:36 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 785110664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:36 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:36 MarkDuplicates Before output close freeMemory: 1262071760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:36 MarkDuplicates After output close freeMemory: 1262344240; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6644419765058808220.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6644419765058808220.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6644419765058808220.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 04:09:36 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 04:09:36 MarkDuplicates Start of doWork freeMemory: 1262347016; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:36 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:36 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:36 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:09:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212756760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:37 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:37 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 785107768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:37 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:37 MarkDuplicates Before output close freeMemory: 1262067768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:37 MarkDuplicates After output close freeMemory: 1262338320; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7976848611776993250.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7976848611776993250.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7976848611776993250.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 04:09:37 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 04:09:37 MarkDuplicates Start of doWork freeMemory: 1262347592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:37 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:37 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212757584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:38 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:38 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 785107728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:38 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:38 MarkDuplicates Before output close freeMemory: 1262068352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:38 MarkDuplicates After output close freeMemory: 1262340968; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6705610141355043831.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6705610141355043831.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6705610141355043831.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 04:09:38 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 04:09:38 MarkDuplicates Start of doWork freeMemory: 1262348544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:38 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:38 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:09:38 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 04:09:38 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:09:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212759312; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:38 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:39 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 785106752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:39 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:09:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:39 MarkDuplicates Before output close freeMemory: 1262069744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:39 MarkDuplicates After output close freeMemory: 1262342480; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8238376305715558953.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8238376305715558953.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8238376305715558953.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 04:09:39 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 04:09:39 MarkDuplicates Start of doWork freeMemory: 1262344152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:39 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:39 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:09:39 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:09:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212753896; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:39 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:39 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 785104904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:40 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:40 MarkDuplicates Before output close freeMemory: 1262064776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:40 MarkDuplicates After output close freeMemory: 1262337520; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800