Class picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7ec37610, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@760074a7, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ef6fce8], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@15f25694, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7064c1cc], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5b4262b]}) | 0.982s | passed |
| pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4cdf8cd1, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a736647], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5cf66adb], 1AAXX.3.1=[]}) | 0.888s | passed |
| testBulkFragmentsNoDuplicates | 32.149s | passed |
| testBulkFragmentsWithDuplicates | 5.424s | passed |
| testDifferentChromosomesInOppositeOrder | 0.789s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.805s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.827s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.961s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.852s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 1.179s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.889s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.990s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.793s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.969s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.907s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 1.153s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 1.012s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.970s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.977s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.893s | passed |
| testMappedPairWithSamePosition | 0.955s | passed |
| testMappedPairWithSamePositionSameCigar | 0.806s | passed |
| testMatePairFirstUnmapped | 1.055s | passed |
| testMatePairSecondUnmapped | 0.921s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 1.065s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates | 0.870s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.943s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.835s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.970s | passed |
| testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) | 1.015s | passed |
| testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) | 0.888s | passed |
| testOpticalDuplicateFinding | 0.874s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.918s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.857s | passed |
| testSingleMappedFragment | 0.808s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 1.009s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.892s | passed |
| testSingleMappedPair | 1.153s | passed |
| testSingleUnmappedFragment | 0.830s | passed |
| testSingleUnmappedPair | 0.877s | passed |
| testStackOverFlowPairSetSwap | 1.096s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.954s | passed |
| testThreeMappedPairs | 1.061s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.855s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.906s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.956s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.962s | passed |
| testTwoMappedFragments | 0.992s | passed |
| testTwoMappedPairWithSamePosition | 0.858s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 1.072s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.987s | passed |
| testTwoMappedPairs | 0.941s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.802s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.934s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 1.073s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.872s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.824s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.833s | passed |
| testTwoMappedPairsWithSoftClipping | 1.038s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.979s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 1.025s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.964s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 1.071s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.870s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.958s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.866s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.949s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.871s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.915s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.940s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 1.013s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.906s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.912s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.812s | passed |
| testTwoUnmappedFragments | 0.996s | passed |
| testWithBarcodeComplex | 0.892s | passed |
| testWithBarcodeDuplicate | 0.958s | passed |
| testWithBarcodeFragmentDuplicate | 0.915s | passed |
| testWithIndividualReadBarcodes | 0.856s | passed |
Standard error
[Tue Aug 16 04:05:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2838978416885514533.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2838978416885514533.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2838978416885514533.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 04:05:30 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 04:05:31 MarkDuplicates Start of doWork freeMemory: 1257642208; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:05:31 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:05:31 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:05:31 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 04:05:31 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2016-08-16 04:05:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 1207998072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:05:33 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:05:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:05:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:05:41 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 780828336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:00 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:01 MarkDuplicates Before output close freeMemory: 1257734032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:01 MarkDuplicates After output close freeMemory: 1256260536; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.51 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8858107064958598830.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8858107064958598830.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8858107064958598830.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 04:06:01 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 04:06:01 MarkDuplicates Start of doWork freeMemory: 1236146304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:01 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:01 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:01 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 04:06:02 MarkDuplicates Read 50000 records. 0 pairs never matched. INFO 2016-08-16 04:06:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 1182560768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:03 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:03 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 758688488; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:05 MarkDuplicates Marking 40000 records as duplicates. INFO 2016-08-16 04:06:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:05 MarkDuplicates Before output close freeMemory: 1235599392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:06 MarkDuplicates After output close freeMemory: 1235599224; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2598993600369351926.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2598993600369351926.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2598993600369351926.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 04:06:06 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 04:06:06 MarkDuplicates Start of doWork freeMemory: 1263149088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:06 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:06 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213567400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:06 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:06 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 785733584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:07 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:07 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:07 MarkDuplicates Before output close freeMemory: 1262647704; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:07 MarkDuplicates After output close freeMemory: 1262647536; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1207097265594091306.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1207097265594091306.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1207097265594091306.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 04:06:07 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 04:06:07 MarkDuplicates Start of doWork freeMemory: 1262968568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:07 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:07 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:07 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:06:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213378152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:07 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:07 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 785610944; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:08 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:06:08 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:06:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:08 MarkDuplicates Before output close freeMemory: 1262521592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:08 MarkDuplicates After output close freeMemory: 1262521424; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1922666610646933915.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1922666610646933915.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1922666610646933915.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 04:06:08 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 04:06:08 MarkDuplicates Start of doWork freeMemory: 1262849336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:08 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:08 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:08 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:06:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213258920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:08 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:08 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 785532384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:08 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:06:08 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:06:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:09 MarkDuplicates Before output close freeMemory: 1262442328; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:09 MarkDuplicates After output close freeMemory: 1262442160; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5915247050046128112.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5915247050046128112.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5915247050046128112.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 04:06:09 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 04:06:09 MarkDuplicates Start of doWork freeMemory: 1262769640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:09 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:09 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:09 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:06:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213179048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:09 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:09 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 785479216; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:09 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:06:09 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:06:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:09 MarkDuplicates Before output close freeMemory: 1262389864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:10 MarkDuplicates After output close freeMemory: 1262389696; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4650929939095075448.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4650929939095075448.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4650929939095075448.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 04:06:10 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 04:06:10 MarkDuplicates Start of doWork freeMemory: 1262717160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:10 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:10 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:10 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:06:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213127200; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:10 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:10 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 785444888; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:10 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:06:10 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:06:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:10 MarkDuplicates Before output close freeMemory: 1262355376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:10 MarkDuplicates After output close freeMemory: 1262355208; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8888514602942002998.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8888514602942002998.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8888514602942002998.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 04:06:10 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 04:06:11 MarkDuplicates Start of doWork freeMemory: 1262681472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:11 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:11 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:11 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:06:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213090944; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:11 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 785431136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:11 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:06:11 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:06:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:12 MarkDuplicates Before output close freeMemory: 1262341784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:12 MarkDuplicates After output close freeMemory: 1262341616; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8156541538169009390.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8156541538169009390.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8156541538169009390.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 04:06:12 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 04:06:12 MarkDuplicates Start of doWork freeMemory: 1262668536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:12 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:12 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:12 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2016-08-16 04:06:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213078120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:12 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:12 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 785410912; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:12 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:06:12 MarkDuplicates Found 2 optical duplicate clusters. INFO 2016-08-16 04:06:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:12 MarkDuplicates Before output close freeMemory: 1262321560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:12 MarkDuplicates After output close freeMemory: 1262321392; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4469618283694703402.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4469618283694703402.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4469618283694703402.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 04:06:12 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 04:06:13 MarkDuplicates Start of doWork freeMemory: 1262655168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:13 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:13 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:13 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 04:06:13 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:06:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213065656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:13 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:13 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 785404040; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:13 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:13 MarkDuplicates Before output close freeMemory: 1262314648; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:13 MarkDuplicates After output close freeMemory: 1262314480; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:13 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1391431143007310648.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1391431143007310648.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1391431143007310648.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 04:06:13 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 04:06:13 MarkDuplicates Start of doWork freeMemory: 1262641304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:13 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:13 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:14 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:06:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213052088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:14 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:14 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 785394720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:14 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:06:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:14 MarkDuplicates Before output close freeMemory: 1262305432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:14 MarkDuplicates After output close freeMemory: 1262305264; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.581222354317280828.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.581222354317280828.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.581222354317280828.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 04:06:14 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 04:06:14 MarkDuplicates Start of doWork freeMemory: 1262632728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:14 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:14 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:14 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:06:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213043808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:14 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:15 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 785388848; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:15 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:06:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:15 MarkDuplicates Before output close freeMemory: 1262299560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:15 MarkDuplicates After output close freeMemory: 1262299392; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2517560685004761526.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2517560685004761526.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2517560685004761526.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 04:06:15 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 04:06:15 MarkDuplicates Start of doWork freeMemory: 1262625408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:15 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:15 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:15 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:06:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213036088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:15 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:16 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 785383152; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:16 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:16 MarkDuplicates Before output close freeMemory: 1262293424; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:16 MarkDuplicates After output close freeMemory: 1262284808; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.210062054391477244.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.210062054391477244.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.210062054391477244.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 04:06:16 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 04:06:16 MarkDuplicates Start of doWork freeMemory: 1262620544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:16 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:16 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:16 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:06:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213022584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:17 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:17 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 785379512; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:17 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:17 MarkDuplicates Before output close freeMemory: 1262289888; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:17 MarkDuplicates After output close freeMemory: 1262289720; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6906391955284930271.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6906391955284930271.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6906391955284930271.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 04:06:17 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 04:06:17 MarkDuplicates Start of doWork freeMemory: 1262617944; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:17 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:17 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:17 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 04:06:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213028408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:18 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:18 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 785387960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:18 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:18 MarkDuplicates Before output close freeMemory: 1262299016; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:18 MarkDuplicates After output close freeMemory: 1262295304; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5601382411973210505.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5601382411973210505.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5601382411973210505.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 04:06:18 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 04:06:18 MarkDuplicates Start of doWork freeMemory: 1262625568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:18 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:18 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:18 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 04:06:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213036032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:19 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:19 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 785381752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:19 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:06:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:19 MarkDuplicates Before output close freeMemory: 1262292128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:19 MarkDuplicates After output close freeMemory: 1262289656; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:19 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:19 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2079972755169627841.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2079972755169627841.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2079972755169627841.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 04:06:19 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 04:06:19 MarkDuplicates Start of doWork freeMemory: 1262618736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:19 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:19 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:19 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 04:06:19 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213029200; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:19 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:20 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 785376688; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:20 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:06:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:20 MarkDuplicates Before output close freeMemory: 1262287032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:20 MarkDuplicates After output close freeMemory: 1262286864; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:20 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3759045138271464170.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3759045138271464170.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3759045138271464170.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 04:06:20 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 04:06:20 MarkDuplicates Start of doWork freeMemory: 1262605072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:20 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:20 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:20 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 04:06:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213016128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:20 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:21 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 785364576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:21 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:21 MarkDuplicates Before output close freeMemory: 1262274992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:21 MarkDuplicates After output close freeMemory: 1262272760; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:21 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2998925178519344091.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2998925178519344091.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2998925178519344091.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 04:06:21 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 04:06:21 MarkDuplicates Start of doWork freeMemory: 1262603120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:21 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:21 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:21 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 04:06:21 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:06:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213013960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:21 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:22 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 785362888; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:22 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:22 MarkDuplicates Before output close freeMemory: 1262273344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:22 MarkDuplicates After output close freeMemory: 1262273176; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:22 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:22 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5140671777926115638.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5140671777926115638.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5140671777926115638.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 04:06:22 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 04:06:22 MarkDuplicates Start of doWork freeMemory: 1262600320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:22 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:22 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:22 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 04:06:22 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:06:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213009128; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:22 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:22 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 785360560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:23 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:23 MarkDuplicates Before output close freeMemory: 1262270960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:23 MarkDuplicates After output close freeMemory: 1262270792; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:23 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.509549128033993070.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.509549128033993070.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.509549128033993070.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 04:06:23 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 04:06:23 MarkDuplicates Start of doWork freeMemory: 1262598400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:23 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:23 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:23 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 04:06:23 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:06:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213009560; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:23 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:23 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 785359088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:24 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:24 MarkDuplicates Before output close freeMemory: 1262269744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:24 MarkDuplicates After output close freeMemory: 1262269576; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:24 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4331893943524658586.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4331893943524658586.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4331893943524658586.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 04:06:24 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 04:06:24 MarkDuplicates Start of doWork freeMemory: 1262596872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:24 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:24 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:24 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 04:06:24 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:06:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213008032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:24 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:24 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 785357760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:25 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:25 MarkDuplicates Before output close freeMemory: 1262268480; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:25 MarkDuplicates After output close freeMemory: 1262268312; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:25 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5201381763742750831.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5201381763742750831.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5201381763742750831.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 04:06:25 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 04:06:25 MarkDuplicates Start of doWork freeMemory: 1262594232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:25 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:25 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213004536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:25 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:25 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 785355024; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:26 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:26 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:26 MarkDuplicates Before output close freeMemory: 1262265000; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:26 MarkDuplicates After output close freeMemory: 1262264832; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:26 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6020013196306113963.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6020013196306113963.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6020013196306113963.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 04:06:26 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 04:06:26 MarkDuplicates Start of doWork freeMemory: 1262592408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:26 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:26 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:26 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213000624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:26 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:26 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 785353336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:27 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:27 MarkDuplicates Before output close freeMemory: 1262263696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:27 MarkDuplicates After output close freeMemory: 1262261464; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:27 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:27 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5644258292014685237.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5644258292014685237.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5644258292014685237.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 04:06:27 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 04:06:27 MarkDuplicates Start of doWork freeMemory: 1262590992; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:27 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:27 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 1213001600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:27 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:27 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 785351976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:28 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:28 MarkDuplicates Before output close freeMemory: 1262262336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:28 MarkDuplicates After output close freeMemory: 1262262168; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:28 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4217505740673672321.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4217505740673672321.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4217505740673672321.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 04:06:28 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 04:06:28 MarkDuplicates Start of doWork freeMemory: 1262589968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:28 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:28 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212998184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:28 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:28 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 785350920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:28 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:28 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:29 MarkDuplicates Before output close freeMemory: 1262261344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:29 MarkDuplicates After output close freeMemory: 1262261176; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:29 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1222738444345391653.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1222738444345391653.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1222738444345391653.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 04:06:29 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 04:06:29 MarkDuplicates Start of doWork freeMemory: 1262588168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:29 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:29 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:29 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212995896; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:29 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:29 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 785348624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:29 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:29 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:29 MarkDuplicates Before output close freeMemory: 1262258768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:30 MarkDuplicates After output close freeMemory: 1262258600; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5459870477624084997.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5459870477624084997.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5459870477624084997.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 04:06:30 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 04:06:30 MarkDuplicates Start of doWork freeMemory: 1262585456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:30 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:30 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:06:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212993456; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:30 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:30 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 785346440; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:30 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:06:30 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:30 MarkDuplicates Before output close freeMemory: 1262256928; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:30 MarkDuplicates After output close freeMemory: 1262256760; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:30 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6349701871569201521.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6349701871569201521.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6349701871569201521.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 04:06:30 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 04:06:30 MarkDuplicates Start of doWork freeMemory: 1262585504; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:30 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:31 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212993752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:31 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:31 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 785346504; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:31 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:31 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:31 MarkDuplicates Before output close freeMemory: 1262256904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:31 MarkDuplicates After output close freeMemory: 1262254672; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:31 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3064637919822231500.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3064637919822231500.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3064637919822231500.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 04:06:31 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 04:06:31 MarkDuplicates Start of doWork freeMemory: 1262579800; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:31 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:31 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:31 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 04:06:31 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:06:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212990344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:32 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:32 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 785340864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:32 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:32 MarkDuplicates Before output close freeMemory: 1262251272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:32 MarkDuplicates After output close freeMemory: 1262249040; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:32 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3495704992668800601.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3495704992668800601.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3495704992668800601.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 04:06:32 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 04:06:32 MarkDuplicates Start of doWork freeMemory: 1262579712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:32 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:32 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:32 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 04:06:32 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2016-08-16 04:06:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212990576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:32 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:33 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 785340936; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:33 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:33 MarkDuplicates Before output close freeMemory: 1262251872; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:33 MarkDuplicates After output close freeMemory: 1262251704; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:33 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6436077077290864134.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6436077077290864134.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6436077077290864134.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 04:06:33 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 04:06:33 MarkDuplicates Start of doWork freeMemory: 1262577320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:33 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:33 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:33 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2016-08-16 04:06:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212985720; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:33 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:33 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 785338392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:34 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:06:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:34 MarkDuplicates Before output close freeMemory: 1262248856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:34 MarkDuplicates After output close freeMemory: 1262248688; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:34 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3003638847096922180.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3003638847096922180.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3003638847096922180.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 04:06:34 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 04:06:34 MarkDuplicates Start of doWork freeMemory: 1262575072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:34 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:34 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:34 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:06:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212983232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:34 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:34 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 785336136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:35 MarkDuplicates Marking 3 records as duplicates. INFO 2016-08-16 04:06:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:35 MarkDuplicates Before output close freeMemory: 1262246656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:35 MarkDuplicates After output close freeMemory: 1262246488; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:35 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:35 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6032655045777423328.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6032655045777423328.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6032655045777423328.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 04:06:35 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 04:06:35 MarkDuplicates Start of doWork freeMemory: 1262575744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:35 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:35 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:35 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:06:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212986584; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:35 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:35 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 785336816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:36 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:36 MarkDuplicates Before output close freeMemory: 1262247336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:36 MarkDuplicates After output close freeMemory: 1262247168; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:36 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7096574412944720262.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7096574412944720262.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7096574412944720262.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 04:06:36 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 04:06:36 MarkDuplicates Start of doWork freeMemory: 1262575176; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:36 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:36 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:36 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:06:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212986240; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:36 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:36 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 785333480; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:37 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:37 MarkDuplicates Before output close freeMemory: 1262247728; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:37 MarkDuplicates After output close freeMemory: 1262247560; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:37 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7632276365121915616.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7632276365121915616.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7632276365121915616.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 04:06:37 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 04:06:37 MarkDuplicates Start of doWork freeMemory: 1262573592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:37 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:37 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:37 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:06:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212984656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:37 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:37 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 785332912; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:38 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:38 MarkDuplicates Before output close freeMemory: 1262246144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:38 MarkDuplicates After output close freeMemory: 1262245976; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:38 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1067305116195437466.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1067305116195437466.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1067305116195437466.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 04:06:38 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 04:06:38 MarkDuplicates Start of doWork freeMemory: 1262414824; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:38 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:38 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212788960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:38 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:38 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 785139696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:39 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:39 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:39 MarkDuplicates Before output close freeMemory: 1261960448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:39 MarkDuplicates After output close freeMemory: 1261960280; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:39 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6184500700243692024.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6184500700243692024.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6184500700243692024.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 04:06:39 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 04:06:39 MarkDuplicates Start of doWork freeMemory: 1262556112; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:39 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:39 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:39 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2016-08-16 04:06:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212964712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:39 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:39 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 785316864; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:40 MarkDuplicates Marking 12 records as duplicates. INFO 2016-08-16 04:06:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:40 MarkDuplicates Before output close freeMemory: 1262227384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:40 MarkDuplicates After output close freeMemory: 1262227216; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:40 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.942560216079477110.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.942560216079477110.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.942560216079477110.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 04:06:40 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 04:06:40 MarkDuplicates Start of doWork freeMemory: 1262562808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:40 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:40 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:40 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 04:06:40 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:06:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212971136; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:40 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:40 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 785323880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:41 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:06:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:41 MarkDuplicates Before output close freeMemory: 1262234400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:41 MarkDuplicates After output close freeMemory: 1262232168; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:41 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:41 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.976823140256744477.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.976823140256744477.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.976823140256744477.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 04:06:41 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:06:41 MarkDuplicates Start of doWork freeMemory: 1262561656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:41 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:41 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:41 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:06:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212969664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:41 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:41 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 785322736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:42 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:42 MarkDuplicates Before output close freeMemory: 1262233168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:42 MarkDuplicates After output close freeMemory: 1262233000; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:42 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8954907238329039515.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8954907238329039515.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8954907238329039515.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 04:06:42 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 04:06:42 MarkDuplicates Start of doWork freeMemory: 1262556472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:42 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:42 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:42 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 04:06:42 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2016-08-16 04:06:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212965984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:42 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:42 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 785317384; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:43 MarkDuplicates Marking 8 records as duplicates. INFO 2016-08-16 04:06:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:43 MarkDuplicates Before output close freeMemory: 1262227904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:43 MarkDuplicates After output close freeMemory: 1262227736; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:43 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3054493441168620431.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3054493441168620431.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3054493441168620431.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 04:06:43 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 04:06:43 MarkDuplicates Start of doWork freeMemory: 1262560952; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:43 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:43 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212969512; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:43 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:43 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 785322184; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:43 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:44 MarkDuplicates Before output close freeMemory: 1262233120; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:44 MarkDuplicates After output close freeMemory: 1262232952; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:44 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:44 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2804506655125777901.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2804506655125777901.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2804506655125777901.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 04:06:44 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 04:06:44 MarkDuplicates Start of doWork freeMemory: 1262557168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:44 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:44 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:44 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2016-08-16 04:06:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212966832; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:44 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:44 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 785318080; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:44 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:06:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:45 MarkDuplicates Before output close freeMemory: 1262228600; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:45 MarkDuplicates After output close freeMemory: 1262228432; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:45 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4237942061393696319.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4237942061393696319.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4237942061393696319.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 04:06:45 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 04:06:45 MarkDuplicates Start of doWork freeMemory: 1262557480; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:45 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:45 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:45 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:06:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212971200; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:45 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:45 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 785321352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:45 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:06:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:46 MarkDuplicates Before output close freeMemory: 1262232288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:46 MarkDuplicates After output close freeMemory: 1262232520; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.258533332532629658.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.258533332532629658.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.258533332532629658.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 04:06:46 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:06:46 MarkDuplicates Start of doWork freeMemory: 1262558256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:46 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:46 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212968856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:46 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:46 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 785319328; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:46 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:46 MarkDuplicates Before output close freeMemory: 1262229760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:46 MarkDuplicates After output close freeMemory: 1262229592; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:46 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.29855886372916059.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.29855886372916059.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.29855886372916059.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 04:06:46 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:06:46 MarkDuplicates Start of doWork freeMemory: 1262556824; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:46 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:46 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212964960; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:47 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:47 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 785317792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:47 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:47 MarkDuplicates Before output close freeMemory: 1262228280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:47 MarkDuplicates After output close freeMemory: 1262228112; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:47 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5170727185760061518.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5170727185760061518.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5170727185760061518.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 04:06:48 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 04:06:48 MarkDuplicates Start of doWork freeMemory: 1262555056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:48 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:48 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:48 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 04:06:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212965208; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:48 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:48 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 785315976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:48 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:48 MarkDuplicates Before output close freeMemory: 1262226464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:48 MarkDuplicates After output close freeMemory: 1262226296; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:48 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7267008130712691376.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7267008130712691376.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7267008130712691376.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 04:06:48 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 04:06:49 MarkDuplicates Start of doWork freeMemory: 1262553808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:49 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:49 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212964408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:49 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:49 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 785314880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:49 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:49 MarkDuplicates Before output close freeMemory: 1262225400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:49 MarkDuplicates After output close freeMemory: 1262225232; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:49 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4375527849421510998.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4375527849421510998.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4375527849421510998.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 04:06:49 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 04:06:49 MarkDuplicates Start of doWork freeMemory: 1262552304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:49 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:49 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:49 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:06:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212962608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:50 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:50 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 785312752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:50 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:50 MarkDuplicates Before output close freeMemory: 1262224040; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:50 MarkDuplicates After output close freeMemory: 1262223872; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:50 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.301458082183392585.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.301458082183392585.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.301458082183392585.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 04:06:50 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 04:06:50 MarkDuplicates Start of doWork freeMemory: 1262551432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:50 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:50 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:50 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 04:06:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212961736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:50 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:51 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 785312504; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:51 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:51 MarkDuplicates Before output close freeMemory: 1262223440; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:51 MarkDuplicates After output close freeMemory: 1262221184; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:51 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1321636569469715707.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1321636569469715707.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1321636569469715707.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 04:06:51 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 04:06:51 MarkDuplicates Start of doWork freeMemory: 1262549672; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:51 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:51 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:06:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212959976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:51 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:52 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 785310744; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:52 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:52 MarkDuplicates Before output close freeMemory: 1262221680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:52 MarkDuplicates After output close freeMemory: 1262221512; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:52 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7615115405011018718.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7615115405011018718.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7615115405011018718.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 04:06:52 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 04:06:52 MarkDuplicates Start of doWork freeMemory: 1262548968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:52 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:52 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:52 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 04:06:52 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212959592; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:52 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:53 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 785310064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:53 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:53 MarkDuplicates Before output close freeMemory: 1262220520; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:53 MarkDuplicates After output close freeMemory: 1262218288; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:53 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:53 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4628461770508121647.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4628461770508121647.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4628461770508121647.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 04:06:53 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 04:06:53 MarkDuplicates Start of doWork freeMemory: 1262545760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:53 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:53 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:53 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 04:06:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212954336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:53 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:54 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 785306840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:54 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:54 MarkDuplicates Before output close freeMemory: 1262217216; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:54 MarkDuplicates After output close freeMemory: 1262214984; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:54 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:54 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5928296785940685158.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5928296785940685158.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5928296785940685158.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 04:06:54 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 04:06:54 MarkDuplicates Start of doWork freeMemory: 1262544832; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:54 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:54 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:54 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 04:06:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212953400; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:54 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:54 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 785305904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:55 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:55 MarkDuplicates Before output close freeMemory: 1262216336; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:55 MarkDuplicates After output close freeMemory: 1262216568; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:55 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7522985523013310730.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7522985523013310730.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7522985523013310730.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 04:06:55 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 04:06:55 MarkDuplicates Start of doWork freeMemory: 1262543816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:55 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:55 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:55 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 04:06:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212954448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:55 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:55 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 785304888; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:56 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:56 MarkDuplicates Before output close freeMemory: 1262215344; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:56 MarkDuplicates After output close freeMemory: 1262215176; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:56 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8145570397375748240.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8145570397375748240.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8145570397375748240.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 04:06:56 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 04:06:56 MarkDuplicates Start of doWork freeMemory: 1262542792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:56 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:56 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:56 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 04:06:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:06:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212953096; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:56 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:56 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 785303576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:57 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:57 MarkDuplicates Before output close freeMemory: 1262214232; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:57 MarkDuplicates After output close freeMemory: 1262214064; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:57 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:57 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7440490776991383636.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7440490776991383636.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7440490776991383636.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 04:06:57 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 04:06:57 MarkDuplicates Start of doWork freeMemory: 1262542760; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:57 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:57 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:06:57 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 04:06:57 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2016-08-16 04:06:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212953680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:57 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:57 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 785301144; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:58 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:06:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:06:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:58 MarkDuplicates Before output close freeMemory: 1262214488; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:58 MarkDuplicates After output close freeMemory: 1262214320; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:58 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6995390217508767865.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6995390217508767865.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6995390217508767865.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 04:06:58 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 04:06:58 MarkDuplicates Start of doWork freeMemory: 1262538272; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:58 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:58 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:58 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:06:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212948576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:58 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:58 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 785299280; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:59 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:59 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:06:59 MarkDuplicates Before output close freeMemory: 1262209640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:59 MarkDuplicates After output close freeMemory: 1262209872; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:06:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:06:59 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4080454907870660261.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4080454907870660261.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4080454907870660261.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 04:06:59 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 04:06:59 MarkDuplicates Start of doWork freeMemory: 1262537448; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:59 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:06:59 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:06:59 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:06:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212947752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:59 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:06:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:06:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:06:59 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:06:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 785298168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:06:59 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:06:59 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:06:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:00 MarkDuplicates Before output close freeMemory: 1262208816; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:00 MarkDuplicates After output close freeMemory: 1262209048; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:00 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:00 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6765281131578214103.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6765281131578214103.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6765281131578214103.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:00 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 04:07:00 MarkDuplicates Start of doWork freeMemory: 1262535368; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:00 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:00 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:00 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212945968; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:00 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:00 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 785296376; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:00 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:00 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:01 MarkDuplicates Before output close freeMemory: 1262206736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:01 MarkDuplicates After output close freeMemory: 1262206568; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:01 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.659194663917816806.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.659194663917816806.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.659194663917816806.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:01 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 04:07:01 MarkDuplicates Start of doWork freeMemory: 1262534616; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:01 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:01 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:01 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212944920; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:01 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:01 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 785295624; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:01 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:01 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:01 MarkDuplicates Before output close freeMemory: 1262205984; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:02 MarkDuplicates After output close freeMemory: 1262205816; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7091074261915131667.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7091074261915131667.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7091074261915131667.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:02 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 04:07:02 MarkDuplicates Start of doWork freeMemory: 1262533832; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:02 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:02 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:02 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212942072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:02 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:02 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 785294840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:02 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:02 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:02 MarkDuplicates Before output close freeMemory: 1262205200; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:02 MarkDuplicates After output close freeMemory: 1262205032; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:02 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6568086147149217800.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6568086147149217800.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6568086147149217800.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:02 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 04:07:02 MarkDuplicates Start of doWork freeMemory: 1262533064; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:02 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:02 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:03 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212941304; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:03 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:03 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 785294072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:03 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:03 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:03 MarkDuplicates Before output close freeMemory: 1262204432; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:03 MarkDuplicates After output close freeMemory: 1262204264; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:03 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5887095475285126395.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5887095475285126395.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5887095475285126395.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:03 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 04:07:03 MarkDuplicates Start of doWork freeMemory: 1262532168; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:03 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:03 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:03 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212942768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:04 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:04 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 785293176; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:04 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:04 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:04 MarkDuplicates Before output close freeMemory: 1262203536; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:04 MarkDuplicates After output close freeMemory: 1262201304; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:04 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:04 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.825210708442385868.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.825210708442385868.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.825210708442385868.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:04 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 04:07:04 MarkDuplicates Start of doWork freeMemory: 1262531360; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:04 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:04 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:04 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212941664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:05 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:05 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 785315840; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:05 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:05 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:05 MarkDuplicates Before output close freeMemory: 1262226200; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:05 MarkDuplicates After output close freeMemory: 1262226032; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:05 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:05 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4939585979654062820.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4939585979654062820.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4939585979654062820.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:05 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 04:07:05 MarkDuplicates Start of doWork freeMemory: 1262554048; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:05 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:05 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:05 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212964288; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:05 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:06 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 785306352; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:06 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:06 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:06 MarkDuplicates Before output close freeMemory: 1262216712; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:06 MarkDuplicates After output close freeMemory: 1262216544; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9181599231957013466.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9181599231957013466.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9181599231957013466.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:06 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 04:07:06 MarkDuplicates Start of doWork freeMemory: 1262544576; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:06 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:06 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:06 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212954880; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:06 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:07 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 785300032; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:07 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:07 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:07 MarkDuplicates Before output close freeMemory: 1262210392; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:07 MarkDuplicates After output close freeMemory: 1262210224; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5991973725126747384.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5991973725126747384.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5991973725126747384.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:07 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 04:07:07 MarkDuplicates Start of doWork freeMemory: 1262538256; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:07 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:07 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:07 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212948856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:07 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:07 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 785295696; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:08 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:08 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:08 MarkDuplicates Before output close freeMemory: 1262206056; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:08 MarkDuplicates After output close freeMemory: 1262203824; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1824218012706513695.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1824218012706513695.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1824218012706513695.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:08 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 04:07:08 MarkDuplicates Start of doWork freeMemory: 1262533856; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:08 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:08 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:08 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2016-08-16 04:07:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212942096; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:08 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:08 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 785292568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:09 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:09 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:09 MarkDuplicates Before output close freeMemory: 1262202928; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:09 MarkDuplicates After output close freeMemory: 1262203160; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3284150865297057923.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3284150865297057923.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3284150865297057923.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:09 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 04:07:09 MarkDuplicates Start of doWork freeMemory: 1262533680; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:09 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:09 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:09 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2016-08-16 04:07:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212944736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:09 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:09 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 785292928; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:10 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:10 MarkDuplicates Before output close freeMemory: 1262204752; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:10 MarkDuplicates After output close freeMemory: 1262204584; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:10 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.5146687420290947515.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.5146687420290947515.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 04:07:10 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 04:07:10 MarkDuplicates Start of doWork freeMemory: 1262535640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:10 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:10 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:07:10 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 04:07:10 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:07:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203764320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:10 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:10 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 785291808; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:11 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:07:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:11 MarkDuplicates Before output close freeMemory: 1262102464; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:11 MarkDuplicates After output close freeMemory: 1262102760; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:11 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:11 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.8084521623573938267.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.8084521623573938267.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 04:07:11 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 04:07:11 MarkDuplicates Start of doWork freeMemory: 1262530944; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:11 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:11 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. WARNING 2016-08-16 04:07:11 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 04:07:11 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:07:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203785472; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:11 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 785289976; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:12 MarkDuplicates Marking 4 records as duplicates. INFO 2016-08-16 04:07:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:12 MarkDuplicates Before output close freeMemory: 1262101768; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:12 MarkDuplicates After output close freeMemory: 1262100432; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:12 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 INFO 2016-08-16 04:07:12 MarkDuplicates Start of doWork freeMemory: 1262543640; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:12 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:12 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:07:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203801408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:12 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:12 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 785304784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:13 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:13 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:13 MarkDuplicates Before output close freeMemory: 1262218736; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:13 MarkDuplicates After output close freeMemory: 1262218568; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:13 MarkDuplicates Start of doWork freeMemory: 1262542784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:13 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:13 MarkDuplicates Will retain up to 7342048 data points before spilling to disk. INFO 2016-08-16 04:07:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 1203799792; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:13 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:13 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 785303608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:13 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:13 MarkDuplicates Found 1 optical duplicate clusters. INFO 2016-08-16 04:07:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:14 MarkDuplicates Before output close freeMemory: 1262217200; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:14 MarkDuplicates After output close freeMemory: 1262214968; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:14 CDT 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3866454769297879196.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3866454769297879196.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3866454769297879196.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:14 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 04:07:14 MarkDuplicates Start of doWork freeMemory: 1262519408; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:14 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:14 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:07:14 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2016-08-16 04:07:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212929176; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:14 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:14 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 785278544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:14 MarkDuplicates Marking 0 records as duplicates. INFO 2016-08-16 04:07:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:15 MarkDuplicates Before output close freeMemory: 1262189608; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:15 MarkDuplicates After output close freeMemory: 1262187376; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:15 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.263051679407854139.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.263051679407854139.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.263051679407854139.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:15 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 04:07:15 MarkDuplicates Start of doWork freeMemory: 1262510784; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:15 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:15 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:15 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:07:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212920616; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:15 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:15 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 785273320; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:15 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:15 MarkDuplicates Before output close freeMemory: 1262183656; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:16 MarkDuplicates After output close freeMemory: 1262183488; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4559427444144295141.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4559427444144295141.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4559427444144295141.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:16 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 04:07:16 MarkDuplicates Start of doWork freeMemory: 1262510544; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:16 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:16 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2016-08-16 04:07:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212923664; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:16 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:16 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 785274072; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:16 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:16 MarkDuplicates Before output close freeMemory: 1262184208; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:16 MarkDuplicates After output close freeMemory: 1262184040; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:16 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2731641739131791229.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2731641739131791229.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2731641739131791229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:16 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 04:07:17 MarkDuplicates Start of doWork freeMemory: 1262513904; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:17 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:17 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. WARNING 2016-08-16 04:07:17 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 04:07:17 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2016-08-16 04:07:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212924688; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:17 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:17 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 785275088; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:17 MarkDuplicates Marking 1 records as duplicates. INFO 2016-08-16 04:07:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:17 MarkDuplicates Before output close freeMemory: 1262185776; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:17 MarkDuplicates After output close freeMemory: 1262185608; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:07:17 CDT 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1584639975246769811.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1584639975246769811.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1584639975246769811.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:07:17 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 04:07:17 MarkDuplicates Start of doWork freeMemory: 1262509112; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:17 MarkDuplicates Reading input file and constructing read end information. INFO 2016-08-16 04:07:17 MarkDuplicates Will retain up to 6197833 data points before spilling to disk. INFO 2016-08-16 04:07:17 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2016-08-16 04:07:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 1212919176; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:18 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2016-08-16 04:07:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-08-16 04:07:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-08-16 04:07:18 MarkDuplicates Sorting list of duplicate records. INFO 2016-08-16 04:07:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 785270160; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:18 MarkDuplicates Marking 2 records as duplicates. INFO 2016-08-16 04:07:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-08-16 04:07:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2016-08-16 04:07:18 MarkDuplicates Before output close freeMemory: 1262180024; totalMemory: 1297612800; maxMemory: 1908932608 INFO 2016-08-16 04:07:18 MarkDuplicates After output close freeMemory: 1262179856; totalMemory: 1297612800; maxMemory: 1908932608 [Tue Aug 16 04:07:18 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800