Class picard.sam.markduplicates.MarkDuplicatesTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@515168a3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@9b86133, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3f38e119], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2daade6, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5814c96e], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@126f9aa6]}) | 0.855s | passed |
| pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@65903a61, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@20f99cee], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@502883fc], 1AAXX.3.1=[]}) | 0.938s | passed |
| testBulkFragmentsNoDuplicates | 1.922s | passed |
| testBulkFragmentsWithDuplicates | 3.658s | passed |
| testDifferentChromosomesInOppositeOrder | 0.982s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 1.298s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.922s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.870s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.962s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.993s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.893s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.889s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.881s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.980s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.991s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.952s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.862s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.958s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.819s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.853s | passed |
| testMappedPairWithSamePosition | 0.834s | passed |
| testMappedPairWithSamePositionSameCigar | 0.890s | passed |
| testMatePairFirstUnmapped | 0.818s | passed |
| testMatePairSecondUnmapped | 0.983s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.905s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates | 0.858s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.889s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.751s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.817s | passed |
| testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) | 0.834s | passed |
| testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) | 0.731s | passed |
| testOpticalDuplicateFinding | 0.938s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.917s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.767s | passed |
| testSingleMappedFragment | 0.758s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.891s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.808s | passed |
| testSingleMappedPair | 0.824s | passed |
| testSingleUnmappedFragment | 0.780s | passed |
| testSingleUnmappedPair | 0.879s | passed |
| testStackOverFlowPairSetSwap | 0.745s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.889s | passed |
| testThreeMappedPairs | 0.766s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.744s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.836s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.867s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.737s | passed |
| testTwoMappedFragments | 0.808s | passed |
| testTwoMappedPairWithSamePosition | 0.810s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.865s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.787s | passed |
| testTwoMappedPairs | 0.835s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.781s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.823s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.760s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.840s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.787s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.835s | passed |
| testTwoMappedPairsWithSoftClipping | 0.803s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.772s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 0.745s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.743s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.917s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.874s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.982s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 1.072s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.877s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 1.072s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.771s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.777s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.814s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.748s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.853s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 1.021s | passed |
| testTwoUnmappedFragments | 0.957s | passed |
| testWithBarcodeComplex | 0.859s | passed |
| testWithBarcodeDuplicate | 0.701s | passed |
| testWithBarcodeFragmentDuplicate | 0.861s | passed |
| testWithIndividualReadBarcodes | 0.784s | passed |
Standard error
[Tue Aug 16 04:09:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8424345678716748600.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8424345678716748600.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8424345678716748600.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 04:09:40 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 04:09:40 MarkDuplicates Start of doWork freeMemory: 1257008488; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:40 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:40 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:40 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2016-08-16 04:09:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 1197545392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:41 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:41 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 779769400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:41 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:42 MarkDuplicates Before output close freeMemory: 1256729808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:42 MarkDuplicates After output close freeMemory: 1257002416; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2317785376935069823.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2317785376935069823.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2317785376935069823.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 04:09:42 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 04:09:42 MarkDuplicates Start of doWork freeMemory: 1235109152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:42 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:42 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:43 MarkDuplicates Read 50000 records. 0 pairs never matched. INFO 2016-08-16 04:09:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 1172763864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:43 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:44 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 757869960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:45 MarkDuplicates Marking 40000 records as duplicates. INFO 2016-08-16 04:09:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:45 MarkDuplicates Before output close freeMemory: 1234830360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:45 MarkDuplicates After output close freeMemory: 1235102976; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1008011353549516427.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1008011353549516427.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1008011353549516427.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 04:09:45 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 04:09:45 MarkDuplicates Start of doWork freeMemory: 1262342352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:45 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:45 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203598048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:46 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:46 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 785102776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:46 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:46 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:09:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:46 MarkDuplicates Before output close freeMemory: 1262062904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:46 MarkDuplicates After output close freeMemory: 1262333328; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:47 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3372453713309793797.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3372453713309793797.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3372453713309793797.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 04:09:47 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 04:09:47 MarkDuplicates Start of doWork freeMemory: 1262335960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:47 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:47 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:47 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:09:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203589464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:47 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:47 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 785096544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:48 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:09:48 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:09:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:48 MarkDuplicates Before output close freeMemory: 1262056672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:48 MarkDuplicates After output close freeMemory: 1262328960; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8834097509224221976.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8834097509224221976.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8834097509224221976.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 04:09:48 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 04:09:48 MarkDuplicates Start of doWork freeMemory: 1262334968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:48 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:48 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:48 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:09:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203588472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:48 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:48 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 785095552; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:49 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:09:49 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:09:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:49 MarkDuplicates Before output close freeMemory: 1262055680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:49 MarkDuplicates After output close freeMemory: 1262326080; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3397734299173229054.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3397734299173229054.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3397734299173229054.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 04:09:49 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 04:09:49 MarkDuplicates Start of doWork freeMemory: 1262333992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:49 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:49 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:49 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:09:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203589560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:49 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:49 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 785092544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:49 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:09:49 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:09:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:49 MarkDuplicates Before output close freeMemory: 1262054704; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:49 MarkDuplicates After output close freeMemory: 1262327192; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6243979131515353643.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6243979131515353643.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6243979131515353643.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 04:09:50 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 04:09:50 MarkDuplicates Start of doWork freeMemory: 1262333264; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:50 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:50 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:50 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:09:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203588832; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:50 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:50 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 785093848; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:50 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:09:50 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:09:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:50 MarkDuplicates Before output close freeMemory: 1262053976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:50 MarkDuplicates After output close freeMemory: 1262326464; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8522105639959893191.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8522105639959893191.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8522105639959893191.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 04:09:50 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 04:09:51 MarkDuplicates Start of doWork freeMemory: 1262332528; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:51 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:51 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:51 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:09:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203588096; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:51 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:51 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 785093112; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:51 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:09:51 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:09:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:51 MarkDuplicates Before output close freeMemory: 1262053240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:51 MarkDuplicates After output close freeMemory: 1262325728; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.966574212043267988.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.966574212043267988.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.966574212043267988.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 04:09:51 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 04:09:52 MarkDuplicates Start of doWork freeMemory: 1262331816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:52 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:52 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:09:52 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:09:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203585328; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:52 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:52 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 785091784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:52 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:09:52 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:09:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:52 MarkDuplicates Before output close freeMemory: 1262052536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:52 MarkDuplicates After output close freeMemory: 1262325024; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7077320461811828067.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7077320461811828067.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7077320461811828067.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 04:09:52 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 04:09:52 MarkDuplicates Start of doWork freeMemory: 1262337392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:52 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:52 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:52 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:09:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203593488; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:53 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:53 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 785097224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:53 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:53 MarkDuplicates Before output close freeMemory: 1262058560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:53 MarkDuplicates After output close freeMemory: 1262328712; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:53 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:53 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3209014968871465036.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3209014968871465036.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3209014968871465036.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 04:09:53 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 04:09:53 MarkDuplicates Start of doWork freeMemory: 1262336280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:53 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:53 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:53 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:09:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203590856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:54 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:54 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 785096464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:54 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:09:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:54 MarkDuplicates Before output close freeMemory: 1262057400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:54 MarkDuplicates After output close freeMemory: 1262327640; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:54 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:54 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8692725752070837092.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8692725752070837092.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8692725752070837092.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 04:09:54 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 04:09:54 MarkDuplicates Start of doWork freeMemory: 1262335576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:54 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:54 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:54 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:09:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203592536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:54 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:55 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 785093672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:55 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:09:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:55 MarkDuplicates Before output close freeMemory: 1262056696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:55 MarkDuplicates After output close freeMemory: 1262329000; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3669437237461061692.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3669437237461061692.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3669437237461061692.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 04:09:55 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 04:09:55 MarkDuplicates Start of doWork freeMemory: 1262333616; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:55 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:55 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:55 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203587816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:55 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:55 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 785091552; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:56 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:56 MarkDuplicates Before output close freeMemory: 1262054424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:56 MarkDuplicates After output close freeMemory: 1262326880; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5225831799537997809.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5225831799537997809.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5225831799537997809.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 04:09:56 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 04:09:56 MarkDuplicates Start of doWork freeMemory: 1262332752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:56 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:56 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:56 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:09:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203589336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:56 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:57 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 785090688; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:57 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:09:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:57 MarkDuplicates Before output close freeMemory: 1262053560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:57 MarkDuplicates After output close freeMemory: 1262326016; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:57 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:57 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2608591948109513826.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2608591948109513826.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2608591948109513826.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 04:09:57 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 04:09:57 MarkDuplicates Start of doWork freeMemory: 1262332456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:57 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:57 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:57 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203589120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:57 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:57 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 785090064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:58 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:09:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:58 MarkDuplicates Before output close freeMemory: 1262053272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:58 MarkDuplicates After output close freeMemory: 1262325728; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6572553821488802085.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6572553821488802085.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6572553821488802085.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 04:09:58 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 04:09:58 MarkDuplicates Start of doWork freeMemory: 1262331600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:58 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:58 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:09:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203588256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:58 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:58 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:09:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 785091288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:59 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:09:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:09:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:09:59 MarkDuplicates Before output close freeMemory: 1262052408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:59 MarkDuplicates After output close freeMemory: 1262322800; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:09:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:09:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3701220789376439518.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3701220789376439518.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3701220789376439518.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 04:09:59 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 04:09:59 MarkDuplicates Start of doWork freeMemory: 1262330736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:59 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:09:59 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:09:59 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 04:09:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:09:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203587392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:09:59 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:09:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:09:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:09:59 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 785090424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:00 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:10:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:00 MarkDuplicates Before output close freeMemory: 1262051544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:00 MarkDuplicates After output close freeMemory: 1262324400; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:00 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:00 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2584511608225357298.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2584511608225357298.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2584511608225357298.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 04:10:00 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 04:10:00 MarkDuplicates Start of doWork freeMemory: 1262329944; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:00 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:00 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203586456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:00 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:00 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 785089968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:00 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:00 MarkDuplicates Before output close freeMemory: 1262050752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:01 MarkDuplicates After output close freeMemory: 1262321032; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8600045899692903640.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8600045899692903640.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8600045899692903640.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 04:10:01 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 04:10:01 MarkDuplicates Start of doWork freeMemory: 1262325984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:01 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:01 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:01 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:10:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203582416; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:01 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:01 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 785086008; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:01 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:01 MarkDuplicates Before output close freeMemory: 1262046792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:01 MarkDuplicates After output close freeMemory: 1262317160; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6701397166577595277.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6701397166577595277.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6701397166577595277.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 04:10:01 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 04:10:01 MarkDuplicates Start of doWork freeMemory: 1262325008; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:01 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:01 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:01 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:10:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203581736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:02 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:02 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 785085032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:02 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:02 MarkDuplicates Before output close freeMemory: 1262045816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:02 MarkDuplicates After output close freeMemory: 1262318672; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.367880765880111153.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.367880765880111153.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.367880765880111153.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 04:10:02 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 04:10:02 MarkDuplicates Start of doWork freeMemory: 1262324248; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:02 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:02 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:02 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:10:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203578928; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:03 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:03 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 785084104; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:03 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:03 MarkDuplicates Before output close freeMemory: 1262045344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:03 MarkDuplicates After output close freeMemory: 1262317680; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5763428517335526782.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5763428517335526782.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5763428517335526782.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 04:10:03 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 04:10:03 MarkDuplicates Start of doWork freeMemory: 1262323544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:03 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:03 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:03 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:10:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203580560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:03 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:03 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 785083376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:04 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:04 MarkDuplicates Before output close freeMemory: 1262044776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:04 MarkDuplicates After output close freeMemory: 1262317384; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:04 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:04 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.176902718973357388.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.176902718973357388.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.176902718973357388.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 04:10:04 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 04:10:04 MarkDuplicates Start of doWork freeMemory: 1262321336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:04 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:04 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203577552; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:04 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:05 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 785081952; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:05 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:05 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:05 MarkDuplicates Before output close freeMemory: 1262042048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:05 MarkDuplicates After output close freeMemory: 1262314536; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:05 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:05 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5752905341884145753.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5752905341884145753.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5752905341884145753.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 04:10:05 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 04:10:05 MarkDuplicates Start of doWork freeMemory: 1262320464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:05 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:05 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203576664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:05 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:05 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 785080472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:06 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:06 MarkDuplicates Before output close freeMemory: 1262041224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:06 MarkDuplicates After output close freeMemory: 1262314112; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6385353481844654647.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6385353481844654647.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6385353481844654647.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 04:10:06 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 04:10:06 MarkDuplicates Start of doWork freeMemory: 1262319584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:06 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:06 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203573736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:06 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:06 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 785079608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:07 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:07 MarkDuplicates Before output close freeMemory: 1262040360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:07 MarkDuplicates After output close freeMemory: 1262310784; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8900276768936177488.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8900276768936177488.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8900276768936177488.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 04:10:07 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 04:10:07 MarkDuplicates Start of doWork freeMemory: 1262318768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:07 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:07 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203572920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:07 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:07 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 785079352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:07 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:07 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:07 MarkDuplicates Before output close freeMemory: 1262039520; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:07 MarkDuplicates After output close freeMemory: 1262312368; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6269033841898626267.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6269033841898626267.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6269033841898626267.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 04:10:07 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 04:10:08 MarkDuplicates Start of doWork freeMemory: 1262317568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:08 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:08 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:08 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203571720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:08 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:08 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 785078152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:08 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:08 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:08 MarkDuplicates Before output close freeMemory: 1262038280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:08 MarkDuplicates After output close freeMemory: 1262310768; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6787995281141939909.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6787995281141939909.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6787995281141939909.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 04:10:08 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 04:10:08 MarkDuplicates Start of doWork freeMemory: 1262315960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:08 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:08 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:08 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:10:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203569896; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:09 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:09 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 785076544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:09 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:10:09 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:09 MarkDuplicates Before output close freeMemory: 1262036728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:09 MarkDuplicates After output close freeMemory: 1262309560; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.270403069751323892.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.270403069751323892.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.270403069751323892.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 04:10:09 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 04:10:09 MarkDuplicates Start of doWork freeMemory: 1262316360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:09 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:09 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203570512; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:10 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:10 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 785076944; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:10 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:10 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:10 MarkDuplicates Before output close freeMemory: 1262037112; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:10 MarkDuplicates After output close freeMemory: 1262309560; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2879209487015680370.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2879209487015680370.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2879209487015680370.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 04:10:10 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 04:10:10 MarkDuplicates Start of doWork freeMemory: 1262316432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:10 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:10 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:10 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:10:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203573144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:10 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 785076104; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:11 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:11 MarkDuplicates Before output close freeMemory: 1262037224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:11 MarkDuplicates After output close freeMemory: 1262307616; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:11 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:11 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8096850138840419634.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8096850138840419634.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8096850138840419634.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 04:10:11 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 04:10:11 MarkDuplicates Start of doWork freeMemory: 1262316408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:11 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:11 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:11 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2016-08-16 04:10:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203572520; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:11 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 785076592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:12 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:12 MarkDuplicates Before output close freeMemory: 1262037624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:12 MarkDuplicates After output close freeMemory: 1262309832; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.354557257793106066.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.354557257793106066.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.354557257793106066.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 04:10:12 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 04:10:12 MarkDuplicates Start of doWork freeMemory: 1262314424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:12 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:12 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:12 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:10:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203568720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:12 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:12 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 785074448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:12 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:10:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:12 MarkDuplicates Before output close freeMemory: 1262035272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:13 MarkDuplicates After output close freeMemory: 1262308088; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7409763848030225700.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7409763848030225700.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7409763848030225700.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 04:10:13 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 04:10:13 MarkDuplicates Start of doWork freeMemory: 1262312240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:13 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:13 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:13 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203568664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:13 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:13 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 785070184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:13 MarkDuplicates Marking 3 records as duplicates. INFO 2016-08-16 04:10:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:13 MarkDuplicates Before output close freeMemory: 1262033072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:13 MarkDuplicates After output close freeMemory: 1262305488; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3250122304128977493.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3250122304128977493.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3250122304128977493.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 04:10:13 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 04:10:13 MarkDuplicates Start of doWork freeMemory: 1262313232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:13 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:13 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:13 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:10:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203569960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:14 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:14 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 785070832; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:14 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:14 MarkDuplicates Before output close freeMemory: 1262034080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:14 MarkDuplicates After output close freeMemory: 1262306928; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2274583016407228945.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2274583016407228945.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2274583016407228945.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 04:10:14 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 04:10:14 MarkDuplicates Start of doWork freeMemory: 1262313160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:14 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:14 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:14 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:10:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203568016; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:14 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:15 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 785074080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:15 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:15 MarkDuplicates Before output close freeMemory: 1262034736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:15 MarkDuplicates After output close freeMemory: 1262305064; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.9009825692850136678.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9009825692850136678.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9009825692850136678.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 04:10:15 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 04:10:15 MarkDuplicates Start of doWork freeMemory: 1262312008; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:15 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:15 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:15 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:10:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203569232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:15 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:15 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 785069888; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:16 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:16 MarkDuplicates Before output close freeMemory: 1262033592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:16 MarkDuplicates After output close freeMemory: 1262305552; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1870050611134830336.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1870050611134830336.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1870050611134830336.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 04:10:16 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 04:10:16 MarkDuplicates Start of doWork freeMemory: 1262166136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:16 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:16 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203378560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:16 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:16 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 784882600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:16 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:16 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:17 MarkDuplicates Before output close freeMemory: 1261798112; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:17 MarkDuplicates After output close freeMemory: 1262115616; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7315410777338743951.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7315410777338743951.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7315410777338743951.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 04:10:17 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 04:10:17 MarkDuplicates Start of doWork freeMemory: 1262299544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:17 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:17 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:17 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2016-08-16 04:10:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203554224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:17 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:17 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 785059872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:17 MarkDuplicates Marking 12 records as duplicates. INFO 2016-08-16 04:10:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:17 MarkDuplicates Before output close freeMemory: 1262020072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:17 MarkDuplicates After output close freeMemory: 1262292496; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5163756246068426357.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5163756246068426357.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5163756246068426357.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 04:10:17 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 04:10:18 MarkDuplicates Start of doWork freeMemory: 1262306296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:18 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:18 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:18 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:10:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203560240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:18 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:18 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 785063904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:18 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:10:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:18 MarkDuplicates Before output close freeMemory: 1262027152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:18 MarkDuplicates After output close freeMemory: 1262297504; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.712416616553439398.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.712416616553439398.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.712416616553439398.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 04:10:18 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 04:10:18 MarkDuplicates Start of doWork freeMemory: 1262305640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:18 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:18 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:18 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:10:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203559576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:19 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:19 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 785063600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:19 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:19 MarkDuplicates Before output close freeMemory: 1262026448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:19 MarkDuplicates After output close freeMemory: 1262298904; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:19 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:19 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8022953921316776185.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8022953921316776185.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8022953921316776185.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 04:10:19 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 04:10:19 MarkDuplicates Start of doWork freeMemory: 1262300664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:19 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:19 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:19 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2016-08-16 04:10:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203555840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:19 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:19 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 785061136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:20 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:10:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:20 MarkDuplicates Before output close freeMemory: 1262021336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:20 MarkDuplicates After output close freeMemory: 1262294184; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2844864682078356736.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2844864682078356736.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2844864682078356736.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 04:10:20 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 04:10:20 MarkDuplicates Start of doWork freeMemory: 1262305256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:20 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:20 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203562072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:20 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:20 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 785066064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:21 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:21 MarkDuplicates Before output close freeMemory: 1262026472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:21 MarkDuplicates After output close freeMemory: 1262297048; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2519896104536351151.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2519896104536351151.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2519896104536351151.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 04:10:21 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 04:10:21 MarkDuplicates Start of doWork freeMemory: 1262301544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:21 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:21 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:21 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2016-08-16 04:10:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203557464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:21 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:21 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 785062032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:21 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:10:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:21 MarkDuplicates Before output close freeMemory: 1262022232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:21 MarkDuplicates After output close freeMemory: 1262294648; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2512703602244515097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2512703602244515097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2512703602244515097.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 04:10:21 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 04:10:21 MarkDuplicates Start of doWork freeMemory: 1262304648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:21 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:21 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:22 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:10:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203560688; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:22 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:22 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 785064864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:22 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:10:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:22 MarkDuplicates Before output close freeMemory: 1262025864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:22 MarkDuplicates After output close freeMemory: 1262295976; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:22 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:22 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4596142983123891795.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4596142983123891795.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4596142983123891795.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 04:10:22 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 04:10:22 MarkDuplicates Start of doWork freeMemory: 1262302840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:22 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:22 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:22 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203559352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:23 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:23 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 785063488; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:23 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:23 MarkDuplicates Before output close freeMemory: 1262023648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:23 MarkDuplicates After output close freeMemory: 1262294008; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5861254722272503546.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5861254722272503546.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5861254722272503546.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 04:10:23 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 04:10:23 MarkDuplicates Start of doWork freeMemory: 1262301736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:23 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:23 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203558248; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:23 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:24 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 785062384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:24 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:24 MarkDuplicates Before output close freeMemory: 1262022584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:24 MarkDuplicates After output close freeMemory: 1262295000; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7339438976390089075.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7339438976390089075.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7339438976390089075.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 04:10:24 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 04:10:24 MarkDuplicates Start of doWork freeMemory: 1262300872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:24 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:24 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:24 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203557384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:24 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:24 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 785061520; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:25 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:25 MarkDuplicates Before output close freeMemory: 1262021720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:25 MarkDuplicates After output close freeMemory: 1262294136; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.638117490714183196.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.638117490714183196.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.638117490714183196.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 04:10:25 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 04:10:25 MarkDuplicates Start of doWork freeMemory: 1262299880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:25 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:25 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203556392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:25 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:25 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 785059568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:25 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:25 MarkDuplicates Before output close freeMemory: 1262020728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:26 MarkDuplicates After output close freeMemory: 1262293544; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1385220150025359842.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1385220150025359842.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1385220150025359842.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 04:10:26 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 04:10:26 MarkDuplicates Start of doWork freeMemory: 1262298440; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:26 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:26 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:26 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203554936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:26 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:26 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 785058448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:26 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:26 MarkDuplicates Before output close freeMemory: 1262019384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:26 MarkDuplicates After output close freeMemory: 1262289360; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6206397214928211228.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6206397214928211228.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6206397214928211228.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 04:10:26 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 04:10:26 MarkDuplicates Start of doWork freeMemory: 1262297608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:26 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:26 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:26 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203554120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:27 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:27 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 785058256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:27 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:27 MarkDuplicates Before output close freeMemory: 1262018184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:27 MarkDuplicates After output close freeMemory: 1262290640; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:27 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:27 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8437759220206008091.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8437759220206008091.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8437759220206008091.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 04:10:27 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 04:10:27 MarkDuplicates Start of doWork freeMemory: 1262295664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:27 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:27 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203552176; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:27 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:28 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 785056312; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:28 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:28 MarkDuplicates Before output close freeMemory: 1262016872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:28 MarkDuplicates After output close freeMemory: 1262289328; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.9012570132906625623.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9012570132906625623.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9012570132906625623.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 04:10:28 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 04:10:28 MarkDuplicates Start of doWork freeMemory: 1262295880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:28 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:28 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203552392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:28 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:28 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 785055904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:29 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:29 MarkDuplicates Before output close freeMemory: 1262016696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:29 MarkDuplicates After output close freeMemory: 1262289544; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3251077231885088751.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3251077231885088751.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3251077231885088751.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 04:10:29 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 04:10:29 MarkDuplicates Start of doWork freeMemory: 1262295016; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:29 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:29 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:29 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203551536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:29 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:29 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 785055672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:29 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:29 MarkDuplicates Before output close freeMemory: 1262015832; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:30 MarkDuplicates After output close freeMemory: 1262288288; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5591390316096747604.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5591390316096747604.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5591390316096747604.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 04:10:30 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 04:10:30 MarkDuplicates Start of doWork freeMemory: 1262294056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:30 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203550568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:30 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:30 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 785054704; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:30 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:30 MarkDuplicates Before output close freeMemory: 1262014864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:30 MarkDuplicates After output close freeMemory: 1262287720; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4640938535966657678.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4640938535966657678.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4640938535966657678.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 04:10:30 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 04:10:30 MarkDuplicates Start of doWork freeMemory: 1262293224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:30 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203549736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:31 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:31 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 785053872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:31 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:31 MarkDuplicates Before output close freeMemory: 1262014032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:31 MarkDuplicates After output close freeMemory: 1262286888; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1421525962699752649.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1421525962699752649.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1421525962699752649.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 04:10:31 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 04:10:31 MarkDuplicates Start of doWork freeMemory: 1262292328; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:31 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:31 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:10:31 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203546448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:31 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:32 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 785052352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:32 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:32 MarkDuplicates Before output close freeMemory: 1262012728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:32 MarkDuplicates After output close freeMemory: 1262285184; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4224149440751153102.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4224149440751153102.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4224149440751153102.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 04:10:32 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 04:10:32 MarkDuplicates Start of doWork freeMemory: 1262292000; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:32 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:32 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:32 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 04:10:32 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2016-08-16 04:10:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203546416; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:32 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:32 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 785049600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:33 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:33 MarkDuplicates Before output close freeMemory: 1262012912; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:33 MarkDuplicates After output close freeMemory: 1262285264; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1418108083067246767.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1418108083067246767.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1418108083067246767.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 04:10:33 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 04:10:33 MarkDuplicates Start of doWork freeMemory: 1262288472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:33 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:33 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:33 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203542592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:33 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:33 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 785049056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:33 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:33 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:33 MarkDuplicates Before output close freeMemory: 1262009184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:33 MarkDuplicates After output close freeMemory: 1262281672; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1086905830195907007.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1086905830195907007.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1086905830195907007.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 04:10:33 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 04:10:34 MarkDuplicates Start of doWork freeMemory: 1262287680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:34 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:34 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:34 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203543896; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:34 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:34 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 785048264; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:34 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:34 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:34 MarkDuplicates Before output close freeMemory: 1262008392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:34 MarkDuplicates After output close freeMemory: 1262281280; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2865088103726532693.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2865088103726532693.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2865088103726532693.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 04:10:34 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 04:10:34 MarkDuplicates Start of doWork freeMemory: 1262286944; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:34 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:34 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:34 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203543456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:35 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:35 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 785047528; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:35 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:35 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:35 MarkDuplicates Before output close freeMemory: 1262007328; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:35 MarkDuplicates After output close freeMemory: 1262277720; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:35 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:35 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8061981301329238181.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8061981301329238181.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8061981301329238181.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 04:10:35 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 04:10:35 MarkDuplicates Start of doWork freeMemory: 1262285880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:35 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:35 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:35 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203542096; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:35 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:35 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 785045840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:36 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:36 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:36 MarkDuplicates Before output close freeMemory: 1262006592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:36 MarkDuplicates After output close freeMemory: 1262279480; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.932465952576652706.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.932465952576652706.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.932465952576652706.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 04:10:36 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 04:10:36 MarkDuplicates Start of doWork freeMemory: 1262285176; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:36 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:36 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:36 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203541392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:36 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:36 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 785055632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:37 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:37 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:37 MarkDuplicates Before output close freeMemory: 1262015760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:37 MarkDuplicates After output close freeMemory: 1262288416; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7648269607826762385.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7648269607826762385.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7648269607826762385.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 04:10:37 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 04:10:37 MarkDuplicates Start of doWork freeMemory: 1262294304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:37 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:37 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:37 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203550504; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:37 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:37 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 785048160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:38 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:38 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:38 MarkDuplicates Before output close freeMemory: 1262011336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:38 MarkDuplicates After output close freeMemory: 1262284224; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7326814252007427266.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7326814252007427266.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7326814252007427266.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 04:10:38 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 04:10:38 MarkDuplicates Start of doWork freeMemory: 1262289800; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:38 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:38 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:38 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203546016; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:38 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:38 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 785045312; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:38 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:38 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:39 MarkDuplicates Before output close freeMemory: 1262008160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:39 MarkDuplicates After output close freeMemory: 1262280648; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5197399499528587627.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5197399499528587627.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5197399499528587627.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 04:10:39 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 04:10:39 MarkDuplicates Start of doWork freeMemory: 1262286656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:39 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:39 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:39 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203542872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:39 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:39 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 785045728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:39 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:39 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:39 MarkDuplicates Before output close freeMemory: 1262005856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:39 MarkDuplicates After output close freeMemory: 1262278112; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2866216485790510570.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2866216485790510570.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2866216485790510570.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 04:10:39 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 04:10:40 MarkDuplicates Start of doWork freeMemory: 1262284408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:40 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:40 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:40 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203540624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:40 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:40 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 785043392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:40 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:40 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:40 MarkDuplicates Before output close freeMemory: 1262004144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:40 MarkDuplicates After output close freeMemory: 1262277032; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4161688064259245200.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4161688064259245200.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4161688064259245200.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 04:10:40 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 04:10:41 MarkDuplicates Start of doWork freeMemory: 1262282696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:41 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:41 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:41 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203539208; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:41 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:41 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 785042656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:41 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:41 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:41 MarkDuplicates Before output close freeMemory: 1262002784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:42 MarkDuplicates After output close freeMemory: 1262275672; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6279637400614416342.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6279637400614416342.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6279637400614416342.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 04:10:42 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 04:10:42 MarkDuplicates Start of doWork freeMemory: 1262281336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:42 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:42 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:42 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203535456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:42 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:42 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 785041520; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:42 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:42 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:42 MarkDuplicates Before output close freeMemory: 1262001648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:42 MarkDuplicates After output close freeMemory: 1262272040; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.973316720353695589.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.973316720353695589.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.973316720353695589.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 04:10:42 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 04:10:42 MarkDuplicates Start of doWork freeMemory: 1262280160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:42 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:42 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:42 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:10:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203534288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:43 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:43 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 785040496; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:43 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:43 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:43 MarkDuplicates Before output close freeMemory: 1262000624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:43 MarkDuplicates After output close freeMemory: 1262273512; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8656530300853409476.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8656530300853409476.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8656530300853409476.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 04:10:43 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 04:10:44 MarkDuplicates Start of doWork freeMemory: 1262282096; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:44 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:44 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:44 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:10:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203539296; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:44 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:44 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 785041872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:44 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:44 MarkDuplicates Before output close freeMemory: 1262003488; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:44 MarkDuplicates After output close freeMemory: 1262275848; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:44 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:44 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.1065652274467242382.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.1065652274467242382.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 04:10:44 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 04:10:44 MarkDuplicates Start of doWork freeMemory: 1262285672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:44 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:44 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:44 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 04:10:44 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:10:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203540384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:45 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:45 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 785045392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:45 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:10:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:45 MarkDuplicates Before output close freeMemory: 1262002720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:45 MarkDuplicates After output close freeMemory: 1262275912; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:45 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.970957126829442986.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.970957126829442986.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 04:10:45 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 04:10:45 MarkDuplicates Start of doWork freeMemory: 1262285080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:45 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:45 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:45 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 04:10:45 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:10:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203539712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:46 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:46 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 785044752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:46 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:10:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:46 MarkDuplicates Before output close freeMemory: 1262003280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:46 MarkDuplicates After output close freeMemory: 1262277784; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 INFO 2016-08-16 04:10:46 MarkDuplicates Start of doWork freeMemory: 1262299024; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:46 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:46 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203556208; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:46 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:47 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 785060536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:47 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:47 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:47 MarkDuplicates Before output close freeMemory: 1262022632; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:47 MarkDuplicates After output close freeMemory: 1262293568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:47 MarkDuplicates Start of doWork freeMemory: 1262298344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:47 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:47 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:10:47 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203552840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:47 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:47 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 785059272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:48 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:48 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:48 MarkDuplicates Before output close freeMemory: 1262021344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:48 MarkDuplicates After output close freeMemory: 1262292304; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1156629689053205347.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1156629689053205347.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1156629689053205347.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 04:10:48 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 04:10:48 MarkDuplicates Start of doWork freeMemory: 1262276056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:48 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:48 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:10:48 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 04:10:48 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2016-08-16 04:10:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203531712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:48 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:48 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 785032792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:48 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:10:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:48 MarkDuplicates Before output close freeMemory: 1261995976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:49 MarkDuplicates After output close freeMemory: 1262268856; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesTester.8443248563736843956.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8443248563736843956.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8443248563736843956.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 04:10:49 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 04:10:49 MarkDuplicates Start of doWork freeMemory: 1262271208; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:49 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:49 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:10:49 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:10:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212678752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:49 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:49 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 785031224; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:49 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:49 MarkDuplicates Before output close freeMemory: 1261991848; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:49 MarkDuplicates After output close freeMemory: 1262262376; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesTester.8772334463504610073.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8772334463504610073.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8772334463504610073.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 04:10:49 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 04:10:49 MarkDuplicates Start of doWork freeMemory: 1262271808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:49 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:49 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:10:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:10:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212679592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:50 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:50 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 785032448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:50 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:50 MarkDuplicates Before output close freeMemory: 1261992448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:50 MarkDuplicates After output close freeMemory: 1262262968; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesTester.6947414064101430108.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6947414064101430108.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6947414064101430108.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 04:10:50 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 04:10:50 MarkDuplicates Start of doWork freeMemory: 1262272776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:50 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:50 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:10:50 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 04:10:50 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:10:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212683432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:50 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:50 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 785030528; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:51 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:10:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:51 MarkDuplicates Before output close freeMemory: 1261993856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:51 MarkDuplicates After output close freeMemory: 1262264096; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX INPUT=[/tmp/MarkDuplicatesTester.4354514227240377748.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4354514227240377748.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4354514227240377748.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 04:10:51 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 04:10:51 MarkDuplicates Start of doWork freeMemory: 1262268400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:51 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:10:51 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:10:51 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:10:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212675952; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:51 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:10:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:10:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:10:51 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:10:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 785029048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:52 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:10:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:10:52 MarkDuplicates Before output close freeMemory: 1261988920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:10:52 MarkDuplicates After output close freeMemory: 1262261664; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:10:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800