Class picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBulkFragmentsNoDuplicates[0](.sam) | 0.335s | passed |
| testBulkFragmentsNoDuplicates[1](.bam) | 0.333s | passed |
| testBulkFragmentsNoDuplicates[2](.cram) | 0.644s | passed |
| testBulkFragmentsWithDuplicates[0](.sam) | 0.593s | passed |
| testBulkFragmentsWithDuplicates[1](.bam) | 0.633s | passed |
| testBulkFragmentsWithDuplicates[2](.cram) | 1.217s | passed |
| testBulkPairsNoDuplicates[0](.sam) | 0.662s | passed |
| testBulkPairsNoDuplicates[1](.bam) | 0.654s | passed |
| testBulkPairsNoDuplicates[2](.cram) | 1.287s | passed |
| testBulkPairsWithDuplicates[0](.sam) | 0.213s | passed |
| testBulkPairsWithDuplicates[1](.bam) | 0.201s | passed |
| testBulkPairsWithDuplicates[2](.cram) | 0.477s | passed |
| testDifferentChromosomesInOppositeOrder | 0.010s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.009s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.008s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.008s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.008s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.007s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.007s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.007s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.007s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.006s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.006s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.006s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.007s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.007s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.007s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.007s | passed |
| testMappedPairWithSamePosition | 0.007s | passed |
| testMappedPairWithSamePositionSameCigar | 0.007s | passed |
| testMatePairFirstUnmapped | 0.007s | passed |
| testMatePairSecondUnmapped | 0.006s | passed |
| testOpticalDuplicateBehaviorNullRegex | 0.008s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.006s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.006s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.007s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.006s | passed |
| testOpticalDuplicateFinding | 0.007s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.006s | passed |
| testScoringStrategyForMateReferenceLengthComparison | 0.008s | passed |
| testScoringStrategyForReadNameComparison | 0.007s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.007s | passed |
| testSingleMappedFragment | 0.006s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.007s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.006s | passed |
| testSingleMappedPair | 0.006s | passed |
| testSingleUnmappedFragment | 0.007s | passed |
| testSingleUnmappedPair | 0.006s | passed |
| testStackOverFlowPairSetSwap | 0.008s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.008s | passed |
| testThreeMappedPairs | 0.007s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.007s | passed |
| testTwoFragmentsLargeSoftClip | 0.007s | passed |
| testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure | 0.006s | passed |
| testTwoFragmentsLargeSoftClipWithMinimumDistanceOK | 0.007s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.008s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.006s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.007s | passed |
| testTwoMappedFragments | 0.007s | passed |
| testTwoMappedPairWithSamePosition | 0.006s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.007s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.008s | passed |
| testTwoMappedPairs | 0.007s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.007s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.007s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.007s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.006s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.007s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.007s | passed |
| testTwoMappedPairsWithSoftClipping | 0.007s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.007s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnly | 0.007s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.009s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.007s | passed |
| testTwoUnmappedFragments | 0.006s | passed |
Standard error
[Thu Apr 24 13:17:05 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15671677088940304282/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15671677088940304282/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp15671677088940304282/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:05 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:05 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2025-04-24 13:17:05 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:05 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:05 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:05 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:17:06 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16390321168516540330/input.bam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16390321168516540330/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp16390321168516540330/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:06 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:06 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:17:06 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp2964268836768292976/input.cram --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp2964268836768292976/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp2964268836768292976/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --REFERENCE_SEQUENCE /tmp/SamFileTester17411058688820343200/input.fasta --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:06 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:06 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:06 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:06 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp11434724398523552090/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp11434724398523552090/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp11434724398523552090/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:06 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:07 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:07 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:07 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:07 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2025-04-24 13:17:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:07 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:07 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15059939540763506180/input.bam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15059939540763506180/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp15059939540763506180/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:07 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:08 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:08 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:08 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2025-04-24 13:17:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:08 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:08 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp18363629685666217069/input.cram --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp18363629685666217069/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp18363629685666217069/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --REFERENCE_SEQUENCE /tmp/SamFileTester28668260893344708/input.fasta --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:08 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:08 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:09 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:09 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14079682035251205995/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14079682035251205995/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp14079682035251205995/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:09 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:09 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:10 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1692348347068266538/input.bam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1692348347068266538/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp1692348347068266538/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:10 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:10 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:10 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:10 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:10 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:10 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:10 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:11 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10531901734476021008/input.cram --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10531901734476021008/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp10531901734476021008/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --REFERENCE_SEQUENCE /tmp/SamFileTester12308285896377306185/input.fasta --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:11 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:11 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:11 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:11 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:11 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:11 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:11 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:11 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp2901256881877178036/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp2901256881877178036/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp2901256881877178036/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:11 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp11642748104665630028/input.bam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp11642748104665630028/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp11642748104665630028/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17282341784700474595/input.cram --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17282341784700474595/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp17282341784700474595/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --REFERENCE_SEQUENCE /tmp/SamFileTester14298421390130387349/input.fasta --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp7385229077368421357/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp7385229077368421357/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp7385229077368421357/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:6:101:17616:6888 2/2 101b aligned to chr1:123989-124052. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14277597453926703736/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14277597453926703736/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp14277597453926703736/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp691835373720893740/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp691835373720893740/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp691835373720893740/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp5351758530908004627/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp5351758530908004627/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp5351758530908004627/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp8562523681933070563/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp8562523681933070563/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp8562523681933070563/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp7227395644865696924/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp7227395644865696924/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp7227395644865696924/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp673798511278644052/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp673798511278644052/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp673798511278644052/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15299422052768592603/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15299422052768592603/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp15299422052768592603/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 76b aligned to chr2:1-76. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp7060048023591877935/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp7060048023591877935/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp7060048023591877935/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp13355992709614338648/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp13355992709614338648/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp13355992709614338648/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10049-10122. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10289339975549261414/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10289339975549261414/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp10289339975549261414/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16004850788312289221/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16004850788312289221/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp16004850788312289221/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10040-10115. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1727416795469089999/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1727416795469089999/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp1727416795469089999/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 101b unmapped read. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16390701875511581885/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16390701875511581885/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp16390701875511581885/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10346717805407930195/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10346717805407930195/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp10346717805407930195/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10040-10115. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14386330162094720869/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14386330162094720869/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp14386330162094720869/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:5604914-5604950. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14469111651187175965/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14469111651187175965/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp14469111651187175965/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:4914-4950. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16301312007086470911/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16301312007086470911/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp16301312007086470911/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:4914-4950. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15785276510687885912/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15785276510687885912/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp15785276510687885912/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1406704626336800634/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1406704626336800634/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp1406704626336800634/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10049-10122. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp822399756731570632/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp822399756731570632/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp822399756731570632/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicatesWithMateCigar --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15845685702863413464/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15845685702863413464/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp15845685702863413464/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 2/2 101b aligned to chr2:485312-485382. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp2521358882670575332/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp2521358882670575332/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp2521358882670575332/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 2/2 101b aligned to chr2:485253-485294. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:12 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17804643312891744679/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17804643312891744679/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp17804643312891744679/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:12 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 1/2 45b aligned to chr2:485253-485297. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:12 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:12 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4650724516739919437/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4650724516739919437/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp4650724516739919437/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp8742618618577957804/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp8742618618577957804/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp8742618618577957804/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 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 to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4678101451271651288/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4678101451271651288/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp4678101451271651288/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:3:1:15013:113051 1/2 68b aligned to chr1:129384554-129384621. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4804757320365528433/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4804757320365528433/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp4804757320365528433/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 68b aligned to chr1:108855323-108855373. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14723058406576427413/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14723058406576427413/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp14723058406576427413/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 1 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp18369547962326712372/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp18369547962326712372/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp18369547962326712372/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp8147050503362212097/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp8147050503362212097/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp8147050503362212097/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14237008825295519007/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14237008825295519007/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp14237008825295519007/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3835186125103020143/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3835186125103020143/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp3835186125103020143/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 1 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4259900059309936983/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4259900059309936983/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp4259900059309936983/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15982402886537233794/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp15982402886537233794/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp15982402886537233794/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17001529555742040253/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17001529555742040253/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp17001529555742040253/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 18 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp12329172532830310664/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp12329172532830310664/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp12329172532830310664/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16283909439093022420/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16283909439093022420/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp16283909439093022420/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10058-10104. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp6814312940363939617/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp6814312940363939617/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp6814312940363939617/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 12 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4003715560377550084/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4003715560377550084/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp4003715560377550084/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10376904028126681231/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10376904028126681231/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp10376904028126681231/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 8 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp7276392904650855487/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp7276392904650855487/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp7276392904650855487/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp99634700483428757/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp99634700483428757/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp99634700483428757/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:5604914-5604950. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp9649127909476752933/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp9649127909476752933/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp9649127909476752933/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned to chr1:5604914-5604963. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp13902032873192526321/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp13902032873192526321/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp13902032873192526321/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:5604914-5604963. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14477315194653683435/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14477315194653683435/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp14477315194653683435/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17758940862881005206/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17758940862881005206/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp17758940862881005206/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3700921662819631528/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3700921662819631528/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp3700921662819631528/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp5607588038755860790/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp5607588038755860790/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp5607588038755860790/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1761366999939979619/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1761366999939979619/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp1761366999939979619/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10022-10097. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1724072889445933106/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1724072889445933106/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp1724072889445933106/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10038-10103. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3236338548693068781/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3236338548693068781/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp3236338548693068781/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10038-10107. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp11529926335652221147/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp11529926335652221147/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp11529926335652221147/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:2-43. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp5285324201310297661/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp5285324201310297661/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp5285324201310297661/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10002-10043. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp5923450793547204052/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp5923450793547204052/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp5923450793547204052/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:12-53. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 2 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1761405046989953199/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp1761405046989953199/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp1761405046989953199/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16151123852475199724/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp16151123852475199724/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp16151123852475199724/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10024943072706938855/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10024943072706938855/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp10024943072706938855/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4049875775340532501/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4049875775340532501/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp4049875775340532501/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4294931810174192844/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp4294931810174192844/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp4294931810174192844/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17508940954480203131/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17508940954480203131/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp17508940954480203131/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3444329196721406647/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3444329196721406647/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp3444329196721406647/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10236330995887229436/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp10236330995887229436/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp10236330995887229436/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17664239746846503578/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17664239746846503578/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp17664239746846503578/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp18438258111243982886/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp18438258111243982886/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp18438258111243982886/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17791358112006004924/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp17791358112006004924/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp17791358112006004924/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14798078709024152562/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp14798078709024152562/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp14798078709024152562/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3850384044062271280/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3850384044062271280/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp3850384044062271280/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp12799570736508943337/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp12799570736508943337/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp12799570736508943337/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 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 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READX 1/2 50b aligned to chr2:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp2328749529455215867/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp2328749529455215867/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp2328749529455215867/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp13258248260568499768/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp13258248260568499768/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp13258248260568499768/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. record #1: READ1 0 chr1 2000 255 10S100M * 0 0 CAGTGGCAGCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAGACCCGCCCTACTGTTGTCGCTGACTCCTTACTCCCTCTCAACGTATTCATACAGGCCCTTTTCGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 record #2: READ2 0 chr1 3000 255 2000S100M * 0 0 TAGCTGGCGTGCACGATTGGCGTGTACATGCTGCCTTTGAGGCACAGTTTCGTAGGGTTTCGTAGCAATGGCTTTGTCTGAAGAGAAGGGGTCTGTCGACAGACACTACGTCCCCAAAGTACCAGCGGGTGATCTCCGCAGACCTCGGAGCCGAGTGCGCTATTCTGGTGACTAGGGGATTAGGTCGGAGCAAGCGGCGTCCGTTAGAAAGCGTCGCTACTAGCCCGCGAGAGGCGACGTCTCACTCCCCGTAACAGCAGGACTGGTCTGGGTACGGCTGGCGCAGGCATGAATGGGATACCCGTGTTCTGCCTTCTGTGTCTACATCCGGTTATGGGAGCTAGCGAAAGTCACGCGAACCAGTAAGGTTAGAGTAGAAACGGAGTACTACTTAGCTATTGAAAAAAGGTGCTGCATCTGAGCCACGCCTAATTGCTGAGCTCTAAGGCTGTGAGTGCGTGAGTAAATGTGATCGGTTAACCTGGCCGAATTGCCCACCTGAGTGCAAGAGTACAAAGCGAAGTATAGTGCAGGCCTCAGCCCCTCCCCGCCAGAATACTACAGGCCGAGGAGGATGAGCTCTTATGGGCGTGTCGTTGGACGATTTATACTGGTGAAGTTGTCTGAAGAACGGTCTTGTTACGACTCACGTCGGGTACCTCTTCCCAGCATCTCGACGCCCCCTTCAGCCTTCGGACCGGTAACCACCGGCCTTGATCTCTGCCCAATAGTAAATGTCGCGGAACTCGTCAGAAATGACGACTCTAGGTGGAGTGTCGCAGTCGAGGTCGGGAGTAGTTCACTACGAACCGTTCGCCTAGGGTGCGAGTGTTCTAGATTCCGCTTGCTCATCGGGCGGAGGGGTCCCTTCGCGGGTGAAAAGCAGTCTCGATTGGGCGATGTTAAGCAATCGGCTGCACCTTGCAGCATCGACTAGAATAAATTGACTGCTCGTATTATTTTGCTCATCGTTGTTCAGTTTTGCGCGCCCAATGTTATTTAAGCTCAAGTGTCTGAAAGACTTCAATATGACGGCTCGATACTGAAGGGACGTCGCGTGCAGCAACACATACTTTTCGTAACGACCAAGTTGCCTCCTCCCTTTAGCACGACCCGGAGTATGCCAGGCCGGCATACTGAGTACACATCCATCATGTGCGTATTCCGGGTTCCTTCGACTCCATAGAGGACTACTGTCAAACGCGAGTCTGAATGGGTCGTTGAATCTACTTACCGTAGGGTGACAGAATGCTGGGCTTTTCTGATTTAGTAAAAGTCAACGCGTGCAAAGTTGCGATCGGGACTCGGCTTGTTCGCAAGGTATTATACTGTAGGATTTCTTTGCACGGTGTGCGACGTTGTCCAATCTGATCTTTCACCGTGTAAGTTCCCTATAGCCTGCACACCGTCAAGACCCGGGTGTCCGCAGACGTTCGCACGTTATCTACGGGTCGATTGTTACACTACCTGTAATACATCTTCATCTGATAGATAGTTTAAGCAATAATCCATGACGCTGCCCGTTGCCAGTAGCCAGCGTTCCGTCCTGCTAGAGCGCCCAAGTCCCACACGGGTAGCGGTTTTCTGGTCCAGGAGGGAAAGTCCTAAATGCAACTGTACACAAGACGGATACCTCTAGCTCCTAAATTCCCGTTGCAGGATGCCAAAAGCTTGACCATCGGGTGAGTGTATCAATGTTGGCGGACATAGGAGGTAGCAGAGACGTCACCGTTTTCGCATGGCCTGTCAAGATCGACTAGAAACAGACTTTATATTATCGGTCAACTATCGCCGATGATGGTCGGAAAGCATTCCTGGGGACCGAGCCGGCGTCCAGGGCGTCAGGGCCAATCCTCCGCATTACCTATAGTTAGGTTACATAGCTCTTGTGGCGTGGGGGTCCTTCCCACCCATCAATCCACTGCCTTGACATGCGCACTGGGGTCTTAGCCCTTTTTATAAACTTTAAACGCATCAGCGCACAAGGTAGAAAGCTGGAACGTAGTTTGTACAAAAAGTCCAGGAGTCCAAGCCGCCATTTCGTTTCCGTTATCGCGACGCTGGACAGAGTGGTGCGAGCTGCACAATCAAGCTGCGGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --MINIMUM_DISTANCE 989 --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3845107741366467742/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3845107741366467742/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp3845107741366467742/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. record #1: READ1 0 chr1 2000 255 10S100M * 0 0 CAGTGGCAGCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAGACCCGCCCTACTGTTGTCGCTGACTCCTTACTCCCTCTCAACGTATTCATACAGGCCCTTTTCGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 record #2: READ2 0 chr1 3000 255 2000S100M * 0 0 TAGCTGGCGTGCACGATTGGCGTGTACATGCTGCCTTTGAGGCACAGTTTCGTAGGGTTTCGTAGCAATGGCTTTGTCTGAAGAGAAGGGGTCTGTCGACAGACACTACGTCCCCAAAGTACCAGCGGGTGATCTCCGCAGACCTCGGAGCCGAGTGCGCTATTCTGGTGACTAGGGGATTAGGTCGGAGCAAGCGGCGTCCGTTAGAAAGCGTCGCTACTAGCCCGCGAGAGGCGACGTCTCACTCCCCGTAACAGCAGGACTGGTCTGGGTACGGCTGGCGCAGGCATGAATGGGATACCCGTGTTCTGCCTTCTGTGTCTACATCCGGTTATGGGAGCTAGCGAAAGTCACGCGAACCAGTAAGGTTAGAGTAGAAACGGAGTACTACTTAGCTATTGAAAAAAGGTGCTGCATCTGAGCCACGCCTAATTGCTGAGCTCTAAGGCTGTGAGTGCGTGAGTAAATGTGATCGGTTAACCTGGCCGAATTGCCCACCTGAGTGCAAGAGTACAAAGCGAAGTATAGTGCAGGCCTCAGCCCCTCCCCGCCAGAATACTACAGGCCGAGGAGGATGAGCTCTTATGGGCGTGTCGTTGGACGATTTATACTGGTGAAGTTGTCTGAAGAACGGTCTTGTTACGACTCACGTCGGGTACCTCTTCCCAGCATCTCGACGCCCCCTTCAGCCTTCGGACCGGTAACCACCGGCCTTGATCTCTGCCCAATAGTAAATGTCGCGGAACTCGTCAGAAATGACGACTCTAGGTGGAGTGTCGCAGTCGAGGTCGGGAGTAGTTCACTACGAACCGTTCGCCTAGGGTGCGAGTGTTCTAGATTCCGCTTGCTCATCGGGCGGAGGGGTCCCTTCGCGGGTGAAAAGCAGTCTCGATTGGGCGATGTTAAGCAATCGGCTGCACCTTGCAGCATCGACTAGAATAAATTGACTGCTCGTATTATTTTGCTCATCGTTGTTCAGTTTTGCGCGCCCAATGTTATTTAAGCTCAAGTGTCTGAAAGACTTCAATATGACGGCTCGATACTGAAGGGACGTCGCGTGCAGCAACACATACTTTTCGTAACGACCAAGTTGCCTCCTCCCTTTAGCACGACCCGGAGTATGCCAGGCCGGCATACTGAGTACACATCCATCATGTGCGTATTCCGGGTTCCTTCGACTCCATAGAGGACTACTGTCAAACGCGAGTCTGAATGGGTCGTTGAATCTACTTACCGTAGGGTGACAGAATGCTGGGCTTTTCTGATTTAGTAAAAGTCAACGCGTGCAAAGTTGCGATCGGGACTCGGCTTGTTCGCAAGGTATTATACTGTAGGATTTCTTTGCACGGTGTGCGACGTTGTCCAATCTGATCTTTCACCGTGTAAGTTCCCTATAGCCTGCACACCGTCAAGACCCGGGTGTCCGCAGACGTTCGCACGTTATCTACGGGTCGATTGTTACACTACCTGTAATACATCTTCATCTGATAGATAGTTTAAGCAATAATCCATGACGCTGCCCGTTGCCAGTAGCCAGCGTTCCGTCCTGCTAGAGCGCCCAAGTCCCACACGGGTAGCGGTTTTCTGGTCCAGGAGGGAAAGTCCTAAATGCAACTGTACACAAGACGGATACCTCTAGCTCCTAAATTCCCGTTGCAGGATGCCAAAAGCTTGACCATCGGGTGAGTGTATCAATGTTGGCGGACATAGGAGGTAGCAGAGACGTCACCGTTTTCGCATGGCCTGTCAAGATCGACTAGAAACAGACTTTATATTATCGGTCAACTATCGCCGATGATGGTCGGAAAGCATTCCTGGGGACCGAGCCGGCGTCCAGGGCGTCAGGGCCAATCCTCCGCATTACCTATAGTTAGGTTACATAGCTCTTGTGGCGTGGGGGTCCTTCCCACCCATCAATCCACTGCCTTGACATGCGCACTGGGGTCTTAGCCCTTTTTATAAACTTTAAACGCATCAGCGCACAAGGTAGAAAGCTGGAACGTAGTTTGTACAAAAAGTCCAGGAGTCCAAGCCGCCATTTCGTTTCCGTTATCGCGACGCTGGACAGAGTGGTGCGAGCTGCACAATCAAGCTGCGGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --MINIMUM_DISTANCE 990 --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp9003278279922643040/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp9003278279922643040/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp9003278279922643040/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1000-1099. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] MarkDuplicatesWithMateCigar --BLOCK_SIZE 250 --INPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3736312512097290607/input.sam --OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.tmp3736312512097290607/output.sam --METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.tmp3736312512097290607/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --ADD_PG_TAG_TO_READS 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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:12-53. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824