Class picard.sam.markduplicates.AsIsMarkDuplicatesTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam) | 0.893s | passed |
| testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam) | 0.918s | passed |
| testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam) | 0.963s | passed |
| testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam) | 0.988s | passed |
| testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam) | 0.980s | passed |
| testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam) | 0.946s | passed |
| testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam) | 0.997s | passed |
| testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam) | 1.033s | passed |
Standard error
[Thu Apr 24 13:17:35 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp7532685983234282492/input.sam --OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp7532685983234282492/output.sam --METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp7532685983234282492/metrics.txt --ASSUME_SORT_ORDER queryname --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicates Start of doWork freeMemory: 982499600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:35 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:17:35 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2025-04-24 13:17:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 919590672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:17:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:35 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:17:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 981459976; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2025-04-24 13:17:35 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2025-04-24 13:17:35 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2025-04-24 13:17:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:35 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:35 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:36 MarkDuplicates Before output close freeMemory: 859665392; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:17:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:36 MarkDuplicates After output close freeMemory: 855630648; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:17:36 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:17:36 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp10213225537320861153/input.sam --OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp10213225537320861153/output.sam --METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp10213225537320861153/metrics.txt --ASSUME_SORT_ORDER queryname --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:36 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 13:17:36 MarkDuplicates Start of doWork freeMemory: 982530552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:36 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:17:36 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2025-04-24 13:17:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 919590088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:17:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:36 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:17:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 806347168; totalMemory: 1436549120; maxMemory: 2147483648 INFO 2025-04-24 13:17:36 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:36 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2025-04-24 13:17:36 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2025-04-24 13:17:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:36 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:36 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:37 MarkDuplicates Before output close freeMemory: 862813752; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:17:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:37 MarkDuplicates After output close freeMemory: 859821192; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:37 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:37 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp9161867345452654047/input.sam --OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp9161867345452654047/output.sam --METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp9161867345452654047/metrics.txt --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:37 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 13:17:37 MarkDuplicates Start of doWork freeMemory: 982939160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:37 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:17:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:17:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 920001528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:17:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:37 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:17:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 713432512; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:37 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:37 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2025-04-24 13:17:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:37 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:37 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:37 MarkDuplicates Before output close freeMemory: 860075584; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:17:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:38 MarkDuplicates After output close freeMemory: 856038072; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:17:38 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:17:38 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp548793860102132598/input.sam --OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp548793860102132598/output.sam --METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp548793860102132598/metrics.txt --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:38 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 13:17:38 MarkDuplicates Start of doWork freeMemory: 982938576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:38 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:17:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:17:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 920000944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:17:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:38 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:17:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 873864056; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:17:38 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:38 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2025-04-24 13:17:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:38 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:38 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:38 MarkDuplicates Before output close freeMemory: 866366360; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2025-04-24 13:17:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:39 MarkDuplicates After output close freeMemory: 860229184; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:39 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:39 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp3440385087279093167/input.sam --OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp3440385087279093167/output.sam --METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp3440385087279093167/metrics.txt --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:39 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 13:17:39 MarkDuplicates Start of doWork freeMemory: 982938304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:39 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:17:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:17:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 919997560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:17:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:39 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:17:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 713431376; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:39 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:17:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:39 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:39 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:39 MarkDuplicates Before output close freeMemory: 863220288; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:17:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:40 MarkDuplicates After output close freeMemory: 863374440; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:17:40 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:17:40 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp4826763876697436039/input.sam --OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp4826763876697436039/output.sam --METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp4826763876697436039/metrics.txt --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:40 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 13:17:40 MarkDuplicates Start of doWork freeMemory: 982937552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:40 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:17:40 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:17:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 919999624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:17:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:40 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:17:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 873862736; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:17:40 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:17:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:40 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:40 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:40 MarkDuplicates Before output close freeMemory: 863219528; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:17:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:41 MarkDuplicates After output close freeMemory: 863376304; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:17:41 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:17:41 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp4335860687564143406/input.sam --OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp4335860687564143406/output.sam --METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp4335860687564143406/metrics.txt --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:41 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 13:17:41 MarkDuplicates Start of doWork freeMemory: 982936880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:41 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:17:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:17:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 919996120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:17:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:41 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:17:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 712381360; totalMemory: 1342177280; maxMemory: 2147483648 INFO 2025-04-24 13:17:41 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:17:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:41 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:41 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:41 MarkDuplicates Before output close freeMemory: 866364560; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2025-04-24 13:17:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:42 MarkDuplicates After output close freeMemory: 860227248; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:42 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:42 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp15257478559107301533/input.sam --OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp15257478559107301533/output.sam --METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.tmp15257478559107301533/metrics.txt --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:42 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 13:17:42 MarkDuplicates Start of doWork freeMemory: 982936104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:42 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:17:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2025-04-24 13:17:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 919998192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:17:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:42 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:17:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 1035342008; totalMemory: 1665138688; maxMemory: 2147483648 INFO 2025-04-24 13:17:42 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:17:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:42 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:42 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:42 MarkDuplicates Before output close freeMemory: 855878032; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:17:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:43 MarkDuplicates After output close freeMemory: 856034856; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160