Class picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBulkFragmentsNoDuplicates | 0.664s | passed |
| testBulkFragmentsWithDuplicates | 1.761s | passed |
| testDifferentChromosomesInOppositeOrder | 0.023s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.031s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.023s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.022s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.022s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.021s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.022s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.022s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.025s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.022s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.021s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.020s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.021s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.021s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.021s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.022s | passed |
| testMappedPairWithSamePosition | 0.023s | passed |
| testMappedPairWithSamePositionSameCigar | 0.021s | passed |
| testMatePairFirstUnmapped | 0.021s | passed |
| testMatePairSecondUnmapped | 0.022s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.022s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicates | 0.023s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.024s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.026s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.022s | passed |
| testOpticalDuplicateFinding | 0.023s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.023s | passed |
| testScoringStrategyForMateReferenceLengthComparison | 0.034s | passed |
| testScoringStrategyForReadNameComparison | 0.035s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.022s | passed |
| testSingleMappedFragment | 0.023s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.022s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.024s | passed |
| testSingleMappedPair | 0.022s | passed |
| testSingleUnmappedFragment | 0.022s | passed |
| testSingleUnmappedPair | 0.023s | passed |
| testStackOverFlowPairSetSwap | 0.026s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.023s | passed |
| testThreeMappedPairs | 0.024s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.027s | passed |
| testTwoFragmentsLargeSoftClip | 0.030s | passed |
| testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure | 0.032s | passed |
| testTwoFragmentsLargeSoftClipWithMinimumDistanceOK | 0.030s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.025s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.022s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.022s | passed |
| testTwoMappedFragments | 0.021s | passed |
| testTwoMappedPairWithSamePosition | 0.022s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.023s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.030s | passed |
| testTwoMappedPairs | 0.023s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.023s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.024s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.023s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.023s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.022s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.030s | passed |
| testTwoMappedPairsWithSoftClipping | 0.025s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.024s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 0.029s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.024s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.021s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.022s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.024s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.026s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.021s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.032s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.024s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.023s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.023s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.025s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.059s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.021s | passed |
| testTwoUnmappedFragments | 0.040s | passed |
Standard error
[Tue Aug 16 04:10:52 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5561408205059291511.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5561408205059291511.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5561408205059291511.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:52 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:52 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2016-08-16 04:10:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:52 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:52 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:53 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3913724418388868019.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3913724418388868019.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3913724418388868019.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:53 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 50000 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 40000 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1297612800 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1220239957384082296.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1220239957384082296.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1220239957384082296.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:6:101:17616:6888 2/2 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1659435124894003366.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1659435124894003366.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1659435124894003366.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1978835171048359928.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1978835171048359928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1978835171048359928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3902990479801967624.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3902990479801967624.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3902990479801967624.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9206449227527117244.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9206449227527117244.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9206449227527117244.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4838454141505644197.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4838454141505644197.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4838454141505644197.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5871646526299278842.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5871646526299278842.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5871646526299278842.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 11 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8100332063958112803.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8100332063958112803.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8100332063958112803.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3716315992953389942.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3716315992953389942.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3716315992953389942.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 3 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2970133592083564446.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2970133592083564446.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2970133592083564446.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 3 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7322249110414843202.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7322249110414843202.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7322249110414843202.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7017923397527549281.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7017923397527549281.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7017923397527549281.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3932031279693011638.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3932031279693011638.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3932031279693011638.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b unmapped read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2842811931658833319.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2842811931658833319.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2842811931658833319.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4589913814393902369.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4589913814393902369.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4589913814393902369.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:54 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:54 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:54 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4849073276625341067.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4849073276625341067.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4849073276625341067.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2586025937205991230.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2586025937205991230.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2586025937205991230.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6809983843040365708.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6809983843040365708.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6809983843040365708.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2676979104626917639.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2676979104626917639.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2676979104626917639.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4719564487698049554.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4719564487698049554.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4719564487698049554.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.861720283898490748.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.861720283898490748.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.861720283898490748.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9102045283782030957.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9102045283782030957.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9102045283782030957.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16834 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8870964648293895273.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8870964648293895273.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8870964648293895273.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8864007723328498858.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8864007723328498858.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8864007723328498858.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3045809749653032825.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3045809749653032825.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3045809749653032825.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2642072314488934125.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2642072314488934125.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2642072314488934125.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0:1:1:1:1 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 6 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6268780090046736839.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6268780090046736839.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6268780090046736839.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:3:1:15013:113051 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7172782079537398847.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7172782079537398847.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7172782079537398847.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.499012313998708467.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.499012313998708467.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.499012313998708467.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 1 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3262338335504229015.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3262338335504229015.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3262338335504229015.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 3 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3229897311349749041.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3229897311349749041.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3229897311349749041.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3999487706430439380.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3999487706430439380.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3999487706430439380.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6509133883981030089.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6509133883981030089.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6509133883981030089.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 1 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8265772196632847896.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8265772196632847896.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8265772196632847896.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3377619852554804738.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3377619852554804738.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3377619852554804738.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4142570084030860541.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4142570084030860541.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4142570084030860541.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 18 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.500014933472901369.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.500014933472901369.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.500014933472901369.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 6 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9089242202854754769.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9089242202854754769.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9089242202854754769.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 6 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2227917614446729966.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2227917614446729966.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2227917614446729966.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 12 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.269069985346813466.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.269069985346813466.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.269069985346813466.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4981475225236804861.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4981475225236804861.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4981475225236804861.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 8 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8723602260947291823.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8723602260947291823.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8723602260947291823.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9047584591743759181.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9047584591743759181.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9047584591743759181.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1407647803289296188.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1407647803289296188.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1407647803289296188.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5991285965971276454.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5991285965971276454.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5991285965971276454.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.786869322732022916.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.786869322732022916.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.786869322732022916.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1471365454167111512.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1471365454167111512.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1471365454167111512.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5006562546698830432.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5006562546698830432.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5006562546698830432.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6637311431478319029.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6637311431478319029.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6637311431478319029.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 6 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8108276933795460367.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8108276933795460367.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8108276933795460367.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2864833370045996621.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2864833370045996621.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2864833370045996621.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6840567302807218599.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6840567302807218599.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6840567302807218599.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6594579681372339596.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6594579681372339596.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6594579681372339596.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3440367860265224382.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3440367860265224382.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3440367860265224382.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2264248217921963744.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2264248217921963744.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2264248217921963744.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 2 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2475738795536160378.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2475738795536160378.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2475738795536160378.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6311026083893875611.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6311026083893875611.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6311026083893875611.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 04:10:55 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null WARNING 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 50b aligned read. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:55 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:55 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4331324273809169274.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4331324273809169274.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4331324273809169274.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4673683854423399237.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4673683854423399237.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4673683854423399237.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5243200805161808525.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5243200805161808525.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5243200805161808525.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1318772488485232718.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1318772488485232718.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1318772488485232718.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1543710224970951241.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1543710224970951241.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1543710224970951241.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2276138086819787919.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2276138086819787919.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2276138086819787919.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6147062119375165089.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6147062119375165089.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6147062119375165089.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4658111086282967405.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4658111086282967405.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4658111086282967405.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8261642619421899469.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8261642619421899469.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8261642619421899469.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.490427684638949001.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.490427684638949001.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.490427684638949001.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 5 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3980244968891892183.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3980244968891892183.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3980244968891892183.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.300281509644595540.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.300281509644595540.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.300281509644595540.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READX. Cause: String 'READX' did not start with a parsable number. WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READX 1/2 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 4 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5951384561404673138.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5951384561404673138.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5951384561404673138.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1163321082621102870.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1163321082621102870.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1163321082621102870.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. record #1: READ1 0 chr1 2000 255 10S100M * 0 0 CAGACACATACCCCCCGTAAATCTACTAATTCTCGAGCCGGCTGTGTTGC ++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 record #2: READ2 0 chr1 3000 255 2000S100M * 0 0 GGAGCTACAAAATCCCAGGCATGATAGCGTGCACGGTCTTGAGCGAAAAT ++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=989 BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5167950422822697710.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5167950422822697710.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5167950422822697710.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. record #1: READ1 0 chr1 2000 255 10S100M * 0 0 ATACTAGTCTGACACTTACGGGATGCGTATCGAGTCTCTGATCAGTCTTT ++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 record #2: READ2 0 chr1 3000 255 2000S100M * 0 0 CGACAACTGTCGAGTTCGTTTCTTCCAGTTAAGCACAAGGTGCGTCAAGG ++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=990 BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1791391701338782066.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1791391701338782066.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1791391701338782066.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 3 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560 [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1725010558973864923.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1725010558973864923.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1725010558973864923.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized 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 WARNING 2016-08-16 04:10:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Processed 2 records INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2016-08-16 04:10:56 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Tue Aug 16 04:10:56 CDT 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1701314560