Class picard.sam.markduplicates.MarkDuplicatesForFlowHelperTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testForFlowMDCall[0](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@53a77f38, [Ljava.lang.String;@78043c61, null) | 0.849s | passed |
| testForFlowMDCall[10](SUM_OF_BASE_QUALITIES, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@35c0c042, [Ljava.lang.String;@5314f84c, picard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$3@276a6a49) | 0.970s | passed |
| testForFlowMDCall[11](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@624a2090, [Ljava.lang.String;@564d8f4d, null) | 0.967s | passed |
| testForFlowMDCall[12](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@21343840, [Ljava.lang.String;@7bd061af, null) | 0.994s | passed |
| testForFlowMDCall[13](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@63940ac, [Ljava.lang.String;@465ff5d5, null) | 1.021s | passed |
| testForFlowMDCall[14](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@1f444dc2, [Ljava.lang.String;@9612f67, null) | 0.960s | passed |
| testForFlowMDCall[15](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@647d3edf, [Ljava.lang.String;@5563b467, picard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$4@7ea58453) | 0.966s | passed |
| testForFlowMDCall[16](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@42b5a0c2, [Ljava.lang.String;@45b51325, picard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$5@7fbab375) | 0.964s | passed |
| testForFlowMDCall[1](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@5c3be565, [Ljava.lang.String;@479d15f5, null) | 0.945s | passed |
| testForFlowMDCall[2](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@6a18759a, [Ljava.lang.String;@634c727e, null) | 0.985s | passed |
| testForFlowMDCall[3](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@63f153b0, [Ljava.lang.String;@25288f18, null) | 0.995s | passed |
| testForFlowMDCall[4](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@8ecd192, [Ljava.lang.String;@11a1be5c, null) | 0.966s | passed |
| testForFlowMDCall[5](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@2ef62b1b, [Ljava.lang.String;@61446c48, null) | 0.959s | passed |
| testForFlowMDCall[6](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@da542a2, [Ljava.lang.String;@8bdea9, null) | 0.984s | passed |
| testForFlowMDCall[7](null, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@62499cde, [Ljava.lang.String;@315389e3, null) | 0.968s | passed |
| testForFlowMDCall[8](SUM_OF_BASE_QUALITIES, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@60563400, [Ljava.lang.String;@3d19365d, picard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$1@583cb1aa) | 0.953s | passed |
| testForFlowMDCall[9](SUM_OF_BASE_QUALITIES, [Lpicard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$TestRecordInfo;@7cff4bc5, [Ljava.lang.String;@5e678370, picard.sam.markduplicates.MarkDuplicatesForFlowHelperTest$2@c571cdc) | 0.965s | passed |
| testGetFlowEndBaseQualities[0](AAAA, [B@2912015c, 2, 50) | 0s | passed |
| testGetFlowEndBaseQualities[1](AAAA, [B@6410c08a, 4, 10) | 0s | passed |
| testGetFlowEndBaseQualities[2](ACCA, [B@7c5ee3b1, 1, 20) | 0.001s | passed |
| testGetFlowEndBaseQualities[3](AABBCC, [B@5c08f094, 30, 10) | 0s | passed |
| testGetFlowSumOfBaseQualities[0](AAAA, [B@6a17af5d, 30, 200) | 0s | passed |
| testGetFlowSumOfBaseQualities[1](AAAA, [B@3c297516, 30, 200) | 0s | passed |
| testGetFlowSumOfBaseQualities[2](AAAA, [B@768c25e8, 30, 0) | 0s | passed |
| testGetFlowSumOfBaseQualities[3](AABBCC, [B@53ffa94b, 30, 180) | 0s | passed |
Standard error
[Thu Apr 24 13:17:44 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS false --INPUT /tmp/MarkDuplicatesTester.tmp17638134155865970903/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp17638134155865970903/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp17638134155865970903/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:44 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 13:17:44 MarkDuplicates Start of doWork freeMemory: 982933320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:44 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:44 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 920010704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:44 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:44 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 570835240; totalMemory: 1200619520; maxMemory: 2147483648 INFO 2025-04-24 13:17:44 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:44 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:44 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:44 MarkDuplicates Before output close freeMemory: 840127648; totalMemory: 1200619520; maxMemory: 2147483648 INFO 2025-04-24 13:17:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:44 MarkDuplicates After output close freeMemory: 840124576; totalMemory: 1200619520; maxMemory: 2147483648 [Thu Apr 24 13:17:44 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1200619520 [Thu Apr 24 13:17:45 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --INPUT /tmp/MarkDuplicatesTester.tmp11294697807632850676/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11294697807632850676/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11294697807632850676/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:45 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 13:17:45 MarkDuplicates Start of doWork freeMemory: 982932432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:45 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:45 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 920009896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:45 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:45 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 713440328; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:45 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:17:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:45 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:45 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:45 MarkDuplicates Before output close freeMemory: 855855480; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:17:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:45 MarkDuplicates After output close freeMemory: 855852408; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:17:45 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:17:45 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_UNPAIRED_CLIPPED_END false --INPUT /tmp/MarkDuplicatesTester.tmp18174623225345985149/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp18174623225345985149/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp18174623225345985149/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS 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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:45 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 13:17:46 MarkDuplicates Start of doWork freeMemory: 982931944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:46 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:46 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 920009424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:46 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:46 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 713437208; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:46 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:17:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:46 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:46 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:46 MarkDuplicates Before output close freeMemory: 860049304; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:17:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:46 MarkDuplicates After output close freeMemory: 855851960; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:17:46 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:17:46 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_UNPAIRED_CLIPPED_END true --INPUT /tmp/MarkDuplicatesTester.tmp13357470033481695628/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp13357470033481695628/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13357470033481695628/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS 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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:46 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 13:17:47 MarkDuplicates Start of doWork freeMemory: 982931384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:47 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 920008848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:47 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:47 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 713436632; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:47 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:47 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:47 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:47 MarkDuplicates Before output close freeMemory: 863194464; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:17:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:47 MarkDuplicates After output close freeMemory: 855854040; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:17:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160 [Thu Apr 24 13:17:47 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --FLOW_USE_UNPAIRED_CLIPPED_END false --INPUT /tmp/MarkDuplicatesTester.tmp4552340267754105886/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp4552340267754105886/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4552340267754105886/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:47 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 13:17:48 MarkDuplicates Start of doWork freeMemory: 982927808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:48 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:48 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 920008264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:48 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:48 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 713438696; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:48 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:48 MarkDuplicates Before output close freeMemory: 860048096; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:17:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:48 MarkDuplicates After output close freeMemory: 860048168; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:48 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:48 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --FLOW_USE_UNPAIRED_CLIPPED_END true --INPUT /tmp/MarkDuplicatesTester.tmp13353169941928716363/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp13353169941928716363/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp13353169941928716363/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:48 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 13:17:49 MarkDuplicates Start of doWork freeMemory: 982930216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:49 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:49 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 920007680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:49 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:49 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 713435464; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:49 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:17:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:49 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:49 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:49 MarkDuplicates Before output close freeMemory: 860047512; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:17:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:49 MarkDuplicates After output close freeMemory: 860044472; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:49 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --FLOW_SKIP_FIRST_N_FLOWS 0 --INPUT /tmp/MarkDuplicatesTester.tmp9758867879592569380/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp9758867879592569380/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp9758867879592569380/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:49 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 13:17:50 MarkDuplicates Start of doWork freeMemory: 982929712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:50 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 920007192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:50 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:50 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 713434976; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:50 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:50 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:50 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:50 MarkDuplicates Before output close freeMemory: 866338528; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2025-04-24 13:17:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:50 MarkDuplicates After output close freeMemory: 860043960; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:50 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:50 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --FLOW_SKIP_FIRST_N_FLOWS 3 --INPUT /tmp/MarkDuplicatesTester.tmp4482966186696793536/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp4482966186696793536/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp4482966186696793536/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:50 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 13:17:50 MarkDuplicates Start of doWork freeMemory: 982929168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:51 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 920006648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:51 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:51 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 713434432; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:51 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:17:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:51 MarkDuplicates Before output close freeMemory: 866337984; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2025-04-24 13:17:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:51 MarkDuplicates After output close freeMemory: 860043384; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:51 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --INPUT /tmp/MarkDuplicatesTester.tmp8365586247377439208/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp8365586247377439208/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp8365586247377439208/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_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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:51 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 13:17:51 MarkDuplicates Start of doWork freeMemory: 982927680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:51 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:51 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 920005144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:52 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:52 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 713432928; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:52 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:52 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:52 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:52 MarkDuplicates Before output close freeMemory: 860044080; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:17:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:52 MarkDuplicates After output close freeMemory: 860041040; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:52 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:52 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --INPUT /tmp/MarkDuplicatesTester.tmp16971661976097866078/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp16971661976097866078/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp16971661976097866078/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_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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:52 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 13:17:52 MarkDuplicates Start of doWork freeMemory: 982926944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:52 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:52 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 920004408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:53 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:53 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 713432192; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:53 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:53 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:53 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:53 MarkDuplicates Before output close freeMemory: 863188744; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:17:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:53 MarkDuplicates After output close freeMemory: 863189192; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:17:53 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:17:53 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_DUP_STRATEGY FLOW_END_QUALITY_STRATEGY --INPUT /tmp/MarkDuplicatesTester.tmp369690936541573975/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp369690936541573975/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp369690936541573975/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_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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:53 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 13:17:53 MarkDuplicates Start of doWork freeMemory: 982926400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:53 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:53 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 920003880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:54 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:54 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 713434312; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:54 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:54 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:54 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:54 MarkDuplicates Before output close freeMemory: 863188536; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:17:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:54 MarkDuplicates After output close freeMemory: 860039736; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:54 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:54 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --FLOW_UNPAIRED_END_UNCERTAINTY 10 --INPUT /tmp/MarkDuplicatesTester.tmp11673495898299209047/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp11673495898299209047/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp11673495898299209047/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_UNPAIRED_CLIPPED_END false --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:54 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 13:17:54 MarkDuplicates Start of doWork freeMemory: 982925640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:54 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:54 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:17:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 920003048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:55 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:55 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 713433552; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:55 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:17:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:55 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:55 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:55 MarkDuplicates Before output close freeMemory: 860042848; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2025-04-24 13:17:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:55 MarkDuplicates After output close freeMemory: 852699776; totalMemory: 1213202432; maxMemory: 2147483648 [Thu Apr 24 13:17:55 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1213202432 [Thu Apr 24 13:17:55 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --FLOW_UNPAIRED_START_UNCERTAINTY 10 --INPUT /tmp/MarkDuplicatesTester.tmp10153315200437541389/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp10153315200437541389/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp10153315200437541389/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:55 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 13:17:55 MarkDuplicates Start of doWork freeMemory: 982925336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:55 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:55 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:17:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 920002744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:56 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:56 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 713430600; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:56 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:17:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:56 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:56 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:56 MarkDuplicates Before output close freeMemory: 863188560; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:17:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:56 MarkDuplicates After output close freeMemory: 860039792; totalMemory: 1220542464; maxMemory: 2147483648 [Thu Apr 24 13:17:56 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1220542464 [Thu Apr 24 13:17:56 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --FLOW_UNPAIRED_END_UNCERTAINTY 10 --INPUT /tmp/MarkDuplicatesTester.tmp5162640784962657574/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp5162640784962657574/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp5162640784962657574/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_UNPAIRED_CLIPPED_END false --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:56 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 13:17:56 MarkDuplicates Start of doWork freeMemory: 982924144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:56 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:56 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:17:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 920001552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:57 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:57 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 713432056; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:57 MarkDuplicates Marking 2 records as duplicates. INFO 2025-04-24 13:17:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:57 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:57 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:57 MarkDuplicates Before output close freeMemory: 873672360; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2025-04-24 13:17:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:57 MarkDuplicates After output close freeMemory: 866329288; totalMemory: 1226833920; maxMemory: 2147483648 [Thu Apr 24 13:17:57 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1226833920 [Thu Apr 24 13:17:57 EDT 2025] MarkDuplicates --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS true --FLOW_UNPAIRED_END_UNCERTAINTY 10 --INPUT /tmp/MarkDuplicatesTester.tmp1523249933065784896/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp1523249933065784896/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp1523249933065784896/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_UNPAIRED_CLIPPED_END false --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:57 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 13:17:57 MarkDuplicates Start of doWork freeMemory: 982923144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:57 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:17:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:57 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2025-04-24 13:17:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 920000552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:58 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:58 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 713428408; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:58 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:58 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:58 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:58 MarkDuplicates Before output close freeMemory: 870575440; totalMemory: 1231028224; maxMemory: 2147483648 INFO 2025-04-24 13:17:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:58 MarkDuplicates After output close freeMemory: 863377688; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:17:58 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:17:58 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS false --INPUT /tmp/MarkDuplicatesTester.tmp2899807637809972766/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2899807637809972766/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2899807637809972766/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:58 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 13:17:58 MarkDuplicates Start of doWork freeMemory: 982922816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:58 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:17:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:58 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 928388872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:17:59 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:17:59 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:17:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 713430712; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:17:59 MarkDuplicates Marking 1 records as duplicates. INFO 2025-04-24 13:17:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:17:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:17:59 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:17:59 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:17:59 MarkDuplicates Before output close freeMemory: 863235208; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2025-04-24 13:17:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:17:59 MarkDuplicates After output close freeMemory: 863376856; totalMemory: 1223688192; maxMemory: 2147483648 [Thu Apr 24 13:17:59 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1223688192 [Thu Apr 24 13:17:59 EDT 2025] MarkDuplicates --BARCODE_TAG BC --TAGGING_POLICY OpticalOnly --FLOW_MODE true --FLOW_USE_END_IN_UNPAIRED_READS false --INPUT /tmp/MarkDuplicatesTester.tmp2117781283332148526/input.sam --OUTPUT /tmp/MarkDuplicatesTester.tmp2117781283332148526/output.sam --METRICS_FILE /tmp/MarkDuplicatesTester.tmp2117781283332148526/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --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 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:59 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 13:17:59 MarkDuplicates Start of doWork freeMemory: 982921280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:17:59 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:17:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. WARNING 2025-04-24 13:17:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:59 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2025-04-24 13:17:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 928387352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:18:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2025-04-24 13:18:00 MarkDuplicatesForFlowHelper Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:18:00 MarkDuplicatesForFlowHelper Sorting list of duplicate records. INFO 2025-04-24 13:18:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 713426544; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2025-04-24 13:18:00 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:18:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:18:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:18:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:18:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:18:00 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:18:00 MarkDuplicates Before output close freeMemory: 855893648; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2025-04-24 13:18:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:18:00 MarkDuplicates After output close freeMemory: 856035296; totalMemory: 1216348160; maxMemory: 2147483648 [Thu Apr 24 13:18:00 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1216348160