Class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBulkFragmentsNoDuplicates | 0.882s | passed |
| testBulkFragmentsWithDuplicates | 2.449s | passed |
| testDifferentChromosomesInOppositeOrder | 0.049s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.023s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.021s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.023s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.118s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.120s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.120s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.021s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.020s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.021s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.021s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.024s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.024s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.021s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.067s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.070s | passed |
| testMappedPairWithSamePosition | 0.122s | passed |
| testMappedPairWithSamePositionSameCigar | 0.077s | passed |
| testMatePairFirstUnmapped | 0.099s | passed |
| testMatePairSecondUnmapped | 0.026s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.026s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates | 0.027s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.025s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.024s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.022s | passed |
| testOpticalDuplicateFinding | 0.024s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.023s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.032s | passed |
| testSingleMappedFragment | 0.033s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.026s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.023s | passed |
| testSingleMappedPair | 0.024s | passed |
| testSingleUnmappedFragment | 0.027s | passed |
| testSingleUnmappedPair | 0.024s | passed |
| testStackOverFlowPairSetSwap | 0.028s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.024s | passed |
| testThreeMappedPairs | 0.023s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.024s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.023s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.023s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.023s | passed |
| testTwoMappedFragments | 0.024s | passed |
| testTwoMappedPairWithSamePosition | 0.025s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.030s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.035s | passed |
| testTwoMappedPairs | 0.051s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.053s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.058s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.063s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.068s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.051s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.032s | passed |
| testTwoMappedPairsWithSoftClipping | 0.032s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.031s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.033s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.028s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.032s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.031s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.030s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.030s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.048s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.030s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.029s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.030s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.030s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.030s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.029s | passed |
| testTwoUnmappedFragments | 0.034s | passed |
Standard error
[Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7206339255011511020.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7206339255011511020.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7206339255011511020.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:10:56 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 04:10:57 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:57 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2016-08-16 04:10:57 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:10:57 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:58 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4724839657616649489.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4724839657616649489.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4724839657616649489.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:10:58 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 04:10:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Processed 50000 records INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Marking 40000 records as duplicates. [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6142701165345349930.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6142701165345349930.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6142701165345349930.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:10:59 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 04:10:59 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2678390283635691603.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2678390283635691603.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2678390283635691603.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:10:59 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 04:10:59 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6535612586172881213.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6535612586172881213.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6535612586172881213.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:10:59 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 04:10:59 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5690731358051953404.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5690731358051953404.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5690731358051953404.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:10:59 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 04:10:59 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:59 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Tue Aug 16 04:10:59 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6721732907246906482.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6721732907246906482.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6721732907246906482.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3058658601909048172.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3058658601909048172.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3058658601909048172.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7794163414233317557.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7794163414233317557.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7794163414233317557.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4189970419587763932.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4189970419587763932.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4189970419587763932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7679193778467708040.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7679193778467708040.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7679193778467708040.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 3 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7401235181715688449.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7401235181715688449.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7401235181715688449.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 3 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9202300640226996071.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9202300640226996071.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9202300640226996071.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 WARNING 2016-08-16 04:11:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3263376662703295660.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3263376662703295660.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3263376662703295660.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 WARNING 2016-08-16 04:11:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3130685623081682229.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3130685623081682229.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3130685623081682229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 WARNING 2016-08-16 04:11:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4768818025888123708.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4768818025888123708.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4768818025888123708.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 WARNING 2016-08-16 04:11:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7384532583666098679.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7384532583666098679.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7384532583666098679.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 WARNING 2016-08-16 04:11:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1395286876918439515.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1395286876918439515.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1395286876918439515.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 WARNING 2016-08-16 04:11:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8769569922137146434.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8769569922137146434.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8769569922137146434.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 WARNING 2016-08-16 04:11:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5852607497434132040.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5852607497434132040.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5852607497434132040.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 WARNING 2016-08-16 04:11:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1790967808 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3097322588382325045.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3097322588382325045.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3097322588382325045.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6257441164661244790.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6257441164661244790.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6257441164661244790.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9012563560900870015.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9012563560900870015.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9012563560900870015.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1931377940167124232.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1931377940167124232.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1931377940167124232.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:00 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6919591415688113115.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6919591415688113115.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6919591415688113115.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:00 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 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5826657620005015749.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5826657620005015749.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5826657620005015749.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.485894697431309715.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.485894697431309715.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.485894697431309715.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1627164243916204583.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1627164243916204583.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1627164243916204583.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 6 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7262566863238648332.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7262566863238648332.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7262566863238648332.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7392860201207459795.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7392860201207459795.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7392860201207459795.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8713358072299962892.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8713358072299962892.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8713358072299962892.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 1 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3719449304798710792.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3719449304798710792.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3719449304798710792.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 3 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6878273826685039318.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6878273826685039318.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6878273826685039318.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6068151637383354257.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6068151637383354257.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6068151637383354257.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703273474074106334.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703273474074106334.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703273474074106334.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 1 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1528149970688820614.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1528149970688820614.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1528149970688820614.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1038537497569537582.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1038537497569537582.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1038537497569537582.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8542951731457401805.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8542951731457401805.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8542951731457401805.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 18 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6006776446987508012.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6006776446987508012.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6006776446987508012.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 6 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7072536902208634365.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7072536902208634365.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7072536902208634365.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 6 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7123085031331274007.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7123085031331274007.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7123085031331274007.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 12 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5123651352813473222.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5123651352813473222.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5123651352813473222.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7832922844798167205.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7832922844798167205.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7832922844798167205.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 8 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2349177766363537750.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2349177766363537750.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2349177766363537750.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3333023869974636534.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3333023869974636534.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3333023869974636534.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3339408793063806945.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3339408793063806945.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3339408793063806945.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1843360050062596815.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1843360050062596815.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1843360050062596815.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8426129101915248069.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8426129101915248069.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8426129101915248069.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851973917972557564.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851973917972557564.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851973917972557564.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3457667889151676213.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3457667889151676213.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3457667889151676213.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6874497252117941010.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6874497252117941010.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6874497252117941010.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 6 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.293835315116233982.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.293835315116233982.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.293835315116233982.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.835094087100511950.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.835094087100511950.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.835094087100511950.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3992386811298856862.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3992386811298856862.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3992386811298856862.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7908183332307974429.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7908183332307974429.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7908183332307974429.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:01 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 WARNING 2016-08-16 04:11:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:01 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4968672525806065732.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4968672525806065732.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4968672525806065732.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 WARNING 2016-08-16 04:11:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8694004775203237780.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8694004775203237780.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8694004775203237780.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5052968555343110527.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5052968555343110527.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5052968555343110527.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3040850173851068699.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3040850173851068699.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3040850173851068699.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4726423727613095421.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4726423727613095421.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4726423727613095421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7662692502997504523.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7662692502997504523.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7662692502997504523.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5136011274322155876.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5136011274322155876.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5136011274322155876.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2767634794803394485.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2767634794803394485.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2767634794803394485.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5832941876835910528.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5832941876835910528.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5832941876835910528.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5025141084361357499.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5025141084361357499.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5025141084361357499.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6312449675759175895.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6312449675759175895.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6312449675759175895.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3860267117005410429.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3860267117005410429.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3860267117005410429.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3565905952786584674.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3565905952786584674.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3565905952786584674.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3960221695445066675.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3960221695445066675.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3960221695445066675.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 04:11:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:11:02 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8798982531591708880.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8798982531591708880.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8798982531591708880.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Tue Aug 16 04:11:02 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 [Tue Aug 16 04:11:02 CDT 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1747451904 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp