Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:35:24.537 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:35:24 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --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 --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --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 --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --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 --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:35:24 GMT 2026] Executing as ?@nf-e9f73e313d6bbb5d54fe61511e88c6a9-3399c-nl9d5 on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 08:35:24 MarkDuplicates Start of doWork freeMemory: 105828760; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:35:24 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:35:24 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:35:28 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:2,400,892
INFO 2026-06-08 08:35:28 MarkDuplicates Tracking 2692 as yet unmatched pairs. 129 records in RAM.
INFO 2026-06-08 08:35:30 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:10,692,813
INFO 2026-06-08 08:35:30 MarkDuplicates Tracking 5064 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-08 08:35:32 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:16,588,985
INFO 2026-06-08 08:35:32 MarkDuplicates Tracking 7365 as yet unmatched pairs. 44 records in RAM.
INFO 2026-06-08 08:35:34 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:21,838,898
INFO 2026-06-08 08:35:34 MarkDuplicates Tracking 10058 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 08:35:35 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr1:23,693,850
INFO 2026-06-08 08:35:35 MarkDuplicates Tracking 12679 as yet unmatched pairs. 100 records in RAM.
INFO 2026-06-08 08:35:37 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:27,935,210
INFO 2026-06-08 08:35:37 MarkDuplicates Tracking 14917 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 08:35:39 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr1:32,769,964
INFO 2026-06-08 08:35:39 MarkDuplicates Tracking 17422 as yet unmatched pairs. 121 records in RAM.
INFO 2026-06-08 08:35:41 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:38,019,291
INFO 2026-06-08 08:35:41 MarkDuplicates Tracking 19809 as yet unmatched pairs. 24 records in RAM.
INFO 2026-06-08 08:35:43 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:43,429,835
INFO 2026-06-08 08:35:43 MarkDuplicates Tracking 21985 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:35:44 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:46,689,659
INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 24598 as yet unmatched pairs. 103 records in RAM.
INFO 2026-06-08 08:35:47 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:61,864,575
INFO 2026-06-08 08:35:47 MarkDuplicates Tracking 26660 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-08 08:35:48 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:89,933,943
INFO 2026-06-08 08:35:48 MarkDuplicates Tracking 28959 as yet unmatched pairs. 36 records in RAM.
INFO 2026-06-08 08:35:51 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:103,078,859
INFO 2026-06-08 08:35:51 MarkDuplicates Tracking 31406 as yet unmatched pairs. 106 records in RAM.
INFO 2026-06-08 08:35:53 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:113,391,224
INFO 2026-06-08 08:35:53 MarkDuplicates Tracking 33539 as yet unmatched pairs. 73 records in RAM.
INFO 2026-06-08 08:35:55 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:119,915,562
INFO 2026-06-08 08:35:55 MarkDuplicates Tracking 36064 as yet unmatched pairs. 626 records in RAM.
INFO 2026-06-08 08:35:57 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:119,967,569
INFO 2026-06-08 08:35:57 MarkDuplicates Tracking 38067 as yet unmatched pairs. 224 records in RAM.
INFO 2026-06-08 08:35:58 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:145,359,821
INFO 2026-06-08 08:35:58 MarkDuplicates Tracking 39165 as yet unmatched pairs. 13 records in RAM.
INFO 2026-06-08 08:36:00 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:146,164,888
INFO 2026-06-08 08:36:00 MarkDuplicates Tracking 40290 as yet unmatched pairs. 67 records in RAM.
INFO 2026-06-08 08:36:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:148,607,410
INFO 2026-06-08 08:36:01 MarkDuplicates Tracking 41289 as yet unmatched pairs. 198 records in RAM.
INFO 2026-06-08 08:36:03 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:149,851,246
INFO 2026-06-08 08:36:03 MarkDuplicates Tracking 42305 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-08 08:36:05 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:150,627,526
INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 44734 as yet unmatched pairs. 530 records in RAM.
INFO 2026-06-08 08:36:06 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:151,518,894
INFO 2026-06-08 08:36:06 MarkDuplicates Tracking 46463 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 08:36:09 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr1:154,157,519
INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 49138 as yet unmatched pairs. 511 records in RAM.
INFO 2026-06-08 08:36:10 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:154,946,750
INFO 2026-06-08 08:36:10 MarkDuplicates Tracking 50731 as yet unmatched pairs. 38 records in RAM.
INFO 2026-06-08 08:36:12 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:155,189,997
INFO 2026-06-08 08:36:12 MarkDuplicates Tracking 52932 as yet unmatched pairs. 136 records in RAM.
INFO 2026-06-08 08:36:13 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:155,659,979
INFO 2026-06-08 08:36:13 MarkDuplicates Tracking 55003 as yet unmatched pairs. 240 records in RAM.
INFO 2026-06-08 08:36:15 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:156,260,576
INFO 2026-06-08 08:36:15 MarkDuplicates Tracking 57217 as yet unmatched pairs. 280 records in RAM.
INFO 2026-06-08 08:36:18 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: chr1:160,092,512
INFO 2026-06-08 08:36:18 MarkDuplicates Tracking 59292 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 08:36:19 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:161,526,238
INFO 2026-06-08 08:36:19 MarkDuplicates Tracking 61481 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 08:36:21 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:164,807,570
INFO 2026-06-08 08:36:21 MarkDuplicates Tracking 63528 as yet unmatched pairs. 238 records in RAM.
INFO 2026-06-08 08:36:23 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr1:171,517,760
INFO 2026-06-08 08:36:23 MarkDuplicates Tracking 65724 as yet unmatched pairs. 48 records in RAM.
INFO 2026-06-08 08:36:24 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:179,884,697
INFO 2026-06-08 08:36:24 MarkDuplicates Tracking 67987 as yet unmatched pairs. 103 records in RAM.
INFO 2026-06-08 08:36:26 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:183,630,577
INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 70292 as yet unmatched pairs. 149 records in RAM.
INFO 2026-06-08 08:36:27 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:193,181,080
INFO 2026-06-08 08:36:27 MarkDuplicates Tracking 72021 as yet unmatched pairs. 68 records in RAM.
INFO 2026-06-08 08:36:30 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: chr1:202,963,680
INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 74302 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 08:36:32 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:205,798,687
INFO 2026-06-08 08:36:32 MarkDuplicates Tracking 76490 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:36:33 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr1:213,241,535
INFO 2026-06-08 08:36:33 MarkDuplicates Tracking 78932 as yet unmatched pairs. 262 records in RAM.
INFO 2026-06-08 08:36:35 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:222,942,741
INFO 2026-06-08 08:36:35 MarkDuplicates Tracking 80812 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 08:36:36 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:225,987,995
INFO 2026-06-08 08:36:36 MarkDuplicates Tracking 83135 as yet unmatched pairs. 13 records in RAM.
INFO 2026-06-08 08:36:38 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:228,408,561
INFO 2026-06-08 08:36:38 MarkDuplicates Tracking 85678 as yet unmatched pairs. 6 records in RAM.
INFO 2026-06-08 08:36:39 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:235,435,814
INFO 2026-06-08 08:36:39 MarkDuplicates Tracking 88284 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-08 08:36:41 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:246,326,193
INFO 2026-06-08 08:36:41 MarkDuplicates Tracking 90629 as yet unmatched pairs. 65 records in RAM.
INFO 2026-06-08 08:36:43 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr2:15,276,981
INFO 2026-06-08 08:36:43 MarkDuplicates Tracking 92865 as yet unmatched pairs. 92709 records in RAM.
INFO 2026-06-08 08:36:46 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr2:27,083,654
INFO 2026-06-08 08:36:46 MarkDuplicates Tracking 95105 as yet unmatched pairs. 94945 records in RAM.
INFO 2026-06-08 08:36:48 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,254
INFO 2026-06-08 08:36:48 MarkDuplicates Tracking 125120 as yet unmatched pairs. 96736 records in RAM.
INFO 2026-06-08 08:36:50 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:36:50 MarkDuplicates Tracking 578331 as yet unmatched pairs. 87720 records in RAM.
INFO 2026-06-08 08:36:52 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:36:52 MarkDuplicates Tracking 830415 as yet unmatched pairs. 82913 records in RAM.
INFO 2026-06-08 08:36:53 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr2:39,022,943
INFO 2026-06-08 08:36:53 MarkDuplicates Tracking 875328 as yet unmatched pairs. 81404 records in RAM.
INFO 2026-06-08 08:36:55 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr2:53,932,639
INFO 2026-06-08 08:36:55 MarkDuplicates Tracking 872744 as yet unmatched pairs. 78818 records in RAM.
INFO 2026-06-08 08:36:56 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:62,707,167
INFO 2026-06-08 08:36:56 MarkDuplicates Tracking 870367 as yet unmatched pairs. 76437 records in RAM.
INFO 2026-06-08 08:36:58 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr2:73,958,764
INFO 2026-06-08 08:36:58 MarkDuplicates Tracking 868141 as yet unmatched pairs. 74208 records in RAM.
INFO 2026-06-08 08:36:59 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr2:86,773,383
INFO 2026-06-08 08:36:59 MarkDuplicates Tracking 865981 as yet unmatched pairs. 72048 records in RAM.
INFO 2026-06-08 08:37:01 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:97,181,613
INFO 2026-06-08 08:37:01 MarkDuplicates Tracking 863840 as yet unmatched pairs. 69907 records in RAM.
INFO 2026-06-08 08:37:02 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:106,423,527
INFO 2026-06-08 08:37:02 MarkDuplicates Tracking 861666 as yet unmatched pairs. 67728 records in RAM.
INFO 2026-06-08 08:37:03 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr2:110,568,007
INFO 2026-06-08 08:37:03 MarkDuplicates Tracking 861095 as yet unmatched pairs. 67156 records in RAM.
INFO 2026-06-08 08:37:05 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:127,048,586
INFO 2026-06-08 08:37:05 MarkDuplicates Tracking 858948 as yet unmatched pairs. 65005 records in RAM.
INFO 2026-06-08 08:37:06 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr2:132,731,937
INFO 2026-06-08 08:37:06 MarkDuplicates Tracking 856824 as yet unmatched pairs. 62879 records in RAM.
INFO 2026-06-08 08:37:08 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr2:151,593,054
INFO 2026-06-08 08:37:08 MarkDuplicates Tracking 855126 as yet unmatched pairs. 61180 records in RAM.
INFO 2026-06-08 08:37:10 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr2:159,349,086
INFO 2026-06-08 08:37:10 MarkDuplicates Tracking 853043 as yet unmatched pairs. 59097 records in RAM.
INFO 2026-06-08 08:37:12 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:173,955,388
INFO 2026-06-08 08:37:12 MarkDuplicates Tracking 850793 as yet unmatched pairs. 56845 records in RAM.
INFO 2026-06-08 08:37:14 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:178,539,580
INFO 2026-06-08 08:37:14 MarkDuplicates Tracking 848588 as yet unmatched pairs. 54635 records in RAM.
INFO 2026-06-08 08:37:16 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr2:178,566,624
INFO 2026-06-08 08:37:16 MarkDuplicates Tracking 846610 as yet unmatched pairs. 52656 records in RAM.
INFO 2026-06-08 08:37:17 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:178,591,285
INFO 2026-06-08 08:37:17 MarkDuplicates Tracking 844674 as yet unmatched pairs. 50720 records in RAM.
INFO 2026-06-08 08:37:19 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr2:178,632,153
INFO 2026-06-08 08:37:19 MarkDuplicates Tracking 842128 as yet unmatched pairs. 48174 records in RAM.
INFO 2026-06-08 08:37:21 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:178,715,531
INFO 2026-06-08 08:37:21 MarkDuplicates Tracking 840775 as yet unmatched pairs. 46821 records in RAM.
INFO 2026-06-08 08:37:22 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:178,776,107
INFO 2026-06-08 08:37:22 MarkDuplicates Tracking 838465 as yet unmatched pairs. 44511 records in RAM.
INFO 2026-06-08 08:37:24 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:188,984,848
INFO 2026-06-08 08:37:24 MarkDuplicates Tracking 836657 as yet unmatched pairs. 42698 records in RAM.
INFO 2026-06-08 08:37:25 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:188,999,540
INFO 2026-06-08 08:37:25 MarkDuplicates Tracking 834699 as yet unmatched pairs. 40738 records in RAM.
INFO 2026-06-08 08:37:27 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr2:189,034,087
INFO 2026-06-08 08:37:27 MarkDuplicates Tracking 830720 as yet unmatched pairs. 36759 records in RAM.
INFO 2026-06-08 08:37:29 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:197,416,742
INFO 2026-06-08 08:37:29 MarkDuplicates Tracking 828230 as yet unmatched pairs. 34268 records in RAM.
INFO 2026-06-08 08:37:30 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr2:207,561,116
INFO 2026-06-08 08:37:30 MarkDuplicates Tracking 825946 as yet unmatched pairs. 31984 records in RAM.
INFO 2026-06-08 08:37:32 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:215,365,509
INFO 2026-06-08 08:37:32 MarkDuplicates Tracking 827148 as yet unmatched pairs. 33185 records in RAM.
INFO 2026-06-08 08:37:33 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr2:215,372,228
INFO 2026-06-08 08:37:33 MarkDuplicates Tracking 824697 as yet unmatched pairs. 30733 records in RAM.
INFO 2026-06-08 08:37:35 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:215,376,614
INFO 2026-06-08 08:37:35 MarkDuplicates Tracking 823560 as yet unmatched pairs. 29596 records in RAM.
INFO 2026-06-08 08:37:36 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr2:215,384,035
INFO 2026-06-08 08:37:36 MarkDuplicates Tracking 818661 as yet unmatched pairs. 24696 records in RAM.
INFO 2026-06-08 08:37:38 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:215,393,121
INFO 2026-06-08 08:37:38 MarkDuplicates Tracking 818426 as yet unmatched pairs. 24461 records in RAM.
INFO 2026-06-08 08:37:41 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr2:215,406,277
INFO 2026-06-08 08:37:41 MarkDuplicates Tracking 815365 as yet unmatched pairs. 21400 records in RAM.
INFO 2026-06-08 08:37:43 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr2:215,409,963
INFO 2026-06-08 08:37:43 MarkDuplicates Tracking 812601 as yet unmatched pairs. 18635 records in RAM.
INFO 2026-06-08 08:37:44 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr2:215,423,483
INFO 2026-06-08 08:37:44 MarkDuplicates Tracking 812886 as yet unmatched pairs. 18920 records in RAM.
INFO 2026-06-08 08:37:46 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr2:215,433,406
INFO 2026-06-08 08:37:46 MarkDuplicates Tracking 808125 as yet unmatched pairs. 14158 records in RAM.
INFO 2026-06-08 08:37:47 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr2:219,164,179
INFO 2026-06-08 08:37:47 MarkDuplicates Tracking 803780 as yet unmatched pairs. 9813 records in RAM.
INFO 2026-06-08 08:37:49 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr2:229,859,213
INFO 2026-06-08 08:37:49 MarkDuplicates Tracking 801248 as yet unmatched pairs. 7272 records in RAM.
INFO 2026-06-08 08:37:50 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:237,336,471
INFO 2026-06-08 08:37:50 MarkDuplicates Tracking 799006 as yet unmatched pairs. 5025 records in RAM.
INFO 2026-06-08 08:37:52 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr2:237,762,986
INFO 2026-06-08 08:37:52 MarkDuplicates Tracking 796419 as yet unmatched pairs. 2437 records in RAM.
INFO 2026-06-08 08:37:53 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr3:4,800,424
INFO 2026-06-08 08:37:53 MarkDuplicates Tracking 793900 as yet unmatched pairs. 45275 records in RAM.
INFO 2026-06-08 08:37:55 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr3:12,901,152
INFO 2026-06-08 08:37:55 MarkDuplicates Tracking 791684 as yet unmatched pairs. 43058 records in RAM.
INFO 2026-06-08 08:37:56 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr3:32,238,887
INFO 2026-06-08 08:37:56 MarkDuplicates Tracking 789314 as yet unmatched pairs. 40687 records in RAM.
INFO 2026-06-08 08:37:58 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr3:40,515,904
INFO 2026-06-08 08:37:58 MarkDuplicates Tracking 787291 as yet unmatched pairs. 38662 records in RAM.
INFO 2026-06-08 08:37:59 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr3:47,120,432
INFO 2026-06-08 08:37:59 MarkDuplicates Tracking 784880 as yet unmatched pairs. 36250 records in RAM.
INFO 2026-06-08 08:38:01 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr3:48,970,686
INFO 2026-06-08 08:38:01 MarkDuplicates Tracking 782363 as yet unmatched pairs. 33732 records in RAM.
INFO 2026-06-08 08:38:02 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr3:49,676,201
INFO 2026-06-08 08:38:02 MarkDuplicates Tracking 779687 as yet unmatched pairs. 31055 records in RAM.
INFO 2026-06-08 08:38:04 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr3:52,378,687
INFO 2026-06-08 08:38:04 MarkDuplicates Tracking 777247 as yet unmatched pairs. 28615 records in RAM.
INFO 2026-06-08 08:38:05 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr3:57,575,612
INFO 2026-06-08 08:38:05 MarkDuplicates Tracking 775222 as yet unmatched pairs. 26590 records in RAM.
INFO 2026-06-08 08:38:06 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:71,015,572
INFO 2026-06-08 08:38:06 MarkDuplicates Tracking 772667 as yet unmatched pairs. 24033 records in RAM.
INFO 2026-06-08 08:38:09 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr3:101,853,262
INFO 2026-06-08 08:38:09 MarkDuplicates Tracking 770884 as yet unmatched pairs. 22246 records in RAM.
INFO 2026-06-08 08:38:12 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr3:120,410,971
INFO 2026-06-08 08:38:12 MarkDuplicates Tracking 768691 as yet unmatched pairs. 20052 records in RAM.
INFO 2026-06-08 08:38:14 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr3:125,233,835
INFO 2026-06-08 08:38:14 MarkDuplicates Tracking 766455 as yet unmatched pairs. 17815 records in RAM.
INFO 2026-06-08 08:38:16 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 2s. Last read position: chr3:129,570,835
INFO 2026-06-08 08:38:16 MarkDuplicates Tracking 763949 as yet unmatched pairs. 15307 records in RAM.
INFO 2026-06-08 08:38:17 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr3:138,714,673
INFO 2026-06-08 08:38:17 MarkDuplicates Tracking 761576 as yet unmatched pairs. 12933 records in RAM.
INFO 2026-06-08 08:38:19 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr3:150,742,623
INFO 2026-06-08 08:38:19 MarkDuplicates Tracking 759389 as yet unmatched pairs. 10735 records in RAM.
INFO 2026-06-08 08:38:21 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr3:170,384,634
INFO 2026-06-08 08:38:21 MarkDuplicates Tracking 757176 as yet unmatched pairs. 8521 records in RAM.
INFO 2026-06-08 08:38:22 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr3:184,166,955
INFO 2026-06-08 08:38:22 MarkDuplicates Tracking 754919 as yet unmatched pairs. 6263 records in RAM.
INFO 2026-06-08 08:38:24 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr3:185,418,005
INFO 2026-06-08 08:38:24 MarkDuplicates Tracking 752304 as yet unmatched pairs. 3648 records in RAM.
INFO 2026-06-08 08:38:25 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr3:195,908,939
INFO 2026-06-08 08:38:25 MarkDuplicates Tracking 750035 as yet unmatched pairs. 1377 records in RAM.
INFO 2026-06-08 08:38:27 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr4:1,213,019
INFO 2026-06-08 08:38:27 MarkDuplicates Tracking 747743 as yet unmatched pairs. 22295 records in RAM.
INFO 2026-06-08 08:38:28 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr4:3,463,518
INFO 2026-06-08 08:38:28 MarkDuplicates Tracking 745067 as yet unmatched pairs. 19618 records in RAM.
INFO 2026-06-08 08:38:30 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr4:22,387,813
INFO 2026-06-08 08:38:30 MarkDuplicates Tracking 742739 as yet unmatched pairs. 17290 records in RAM.
INFO 2026-06-08 08:38:31 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr4:48,609,756
INFO 2026-06-08 08:38:31 MarkDuplicates Tracking 740496 as yet unmatched pairs. 15045 records in RAM.
INFO 2026-06-08 08:38:32 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr4:73,418,241
INFO 2026-06-08 08:38:32 MarkDuplicates Tracking 738381 as yet unmatched pairs. 12917 records in RAM.
INFO 2026-06-08 08:38:34 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr4:87,614,493
INFO 2026-06-08 08:38:34 MarkDuplicates Tracking 736186 as yet unmatched pairs. 10720 records in RAM.
INFO 2026-06-08 08:38:36 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr4:109,524,830
INFO 2026-06-08 08:38:36 MarkDuplicates Tracking 733910 as yet unmatched pairs. 8443 records in RAM.
INFO 2026-06-08 08:38:37 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr4:139,890,842
INFO 2026-06-08 08:38:37 MarkDuplicates Tracking 731771 as yet unmatched pairs. 6302 records in RAM.
INFO 2026-06-08 08:38:39 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr4:151,102,986
INFO 2026-06-08 08:38:39 MarkDuplicates Tracking 729721 as yet unmatched pairs. 4246 records in RAM.
INFO 2026-06-08 08:38:40 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr4:168,225,549
INFO 2026-06-08 08:38:40 MarkDuplicates Tracking 727290 as yet unmatched pairs. 1815 records in RAM.
INFO 2026-06-08 08:38:42 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr5:1,079,393
INFO 2026-06-08 08:38:42 MarkDuplicates Tracking 725036 as yet unmatched pairs. 48543 records in RAM.
INFO 2026-06-08 08:38:43 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr5:14,388,667
INFO 2026-06-08 08:38:43 MarkDuplicates Tracking 722944 as yet unmatched pairs. 46450 records in RAM.
INFO 2026-06-08 08:38:45 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr5:35,065,226
INFO 2026-06-08 08:38:45 MarkDuplicates Tracking 720157 as yet unmatched pairs. 43661 records in RAM.
INFO 2026-06-08 08:38:46 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr5:44,809,334
INFO 2026-06-08 08:38:46 MarkDuplicates Tracking 718133 as yet unmatched pairs. 41636 records in RAM.
INFO 2026-06-08 08:38:48 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr5:66,078,456
INFO 2026-06-08 08:38:48 MarkDuplicates Tracking 715826 as yet unmatched pairs. 39325 records in RAM.
INFO 2026-06-08 08:38:49 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr5:70,440,762
INFO 2026-06-08 08:38:49 MarkDuplicates Tracking 715273 as yet unmatched pairs. 38772 records in RAM.
INFO 2026-06-08 08:38:50 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr5:73,892,101
INFO 2026-06-08 08:38:50 MarkDuplicates Tracking 713285 as yet unmatched pairs. 36784 records in RAM.
INFO 2026-06-08 08:38:52 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr5:83,512,336
INFO 2026-06-08 08:38:52 MarkDuplicates Tracking 711697 as yet unmatched pairs. 35193 records in RAM.
INFO 2026-06-08 08:38:53 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr5:98,876,399
INFO 2026-06-08 08:38:53 MarkDuplicates Tracking 709319 as yet unmatched pairs. 32813 records in RAM.
INFO 2026-06-08 08:38:56 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr5:123,636,408
INFO 2026-06-08 08:38:56 MarkDuplicates Tracking 707087 as yet unmatched pairs. 30580 records in RAM.
INFO 2026-06-08 08:38:58 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr5:134,703,826
INFO 2026-06-08 08:38:58 MarkDuplicates Tracking 704721 as yet unmatched pairs. 28212 records in RAM.
INFO 2026-06-08 08:39:01 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr5:135,571,229
INFO 2026-06-08 08:39:01 MarkDuplicates Tracking 710332 as yet unmatched pairs. 33822 records in RAM.
INFO 2026-06-08 08:39:03 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr5:135,883,094
INFO 2026-06-08 08:39:03 MarkDuplicates Tracking 700047 as yet unmatched pairs. 23537 records in RAM.
INFO 2026-06-08 08:39:04 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr5:140,445,742
INFO 2026-06-08 08:39:04 MarkDuplicates Tracking 697743 as yet unmatched pairs. 21191 records in RAM.
INFO 2026-06-08 08:39:06 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr5:141,863,522
INFO 2026-06-08 08:39:06 MarkDuplicates Tracking 695346 as yet unmatched pairs. 18794 records in RAM.
INFO 2026-06-08 08:39:07 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr5:150,121,882
INFO 2026-06-08 08:39:07 MarkDuplicates Tracking 692985 as yet unmatched pairs. 16431 records in RAM.
INFO 2026-06-08 08:39:09 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr5:150,403,282
INFO 2026-06-08 08:39:09 MarkDuplicates Tracking 693892 as yet unmatched pairs. 17338 records in RAM.
INFO 2026-06-08 08:39:10 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr5:150,412,657
INFO 2026-06-08 08:39:10 MarkDuplicates Tracking 687667 as yet unmatched pairs. 11113 records in RAM.
INFO 2026-06-08 08:39:12 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr5:154,863,229
INFO 2026-06-08 08:39:12 MarkDuplicates Tracking 685356 as yet unmatched pairs. 8800 records in RAM.
INFO 2026-06-08 08:39:13 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr5:172,422,430
INFO 2026-06-08 08:39:13 MarkDuplicates Tracking 683218 as yet unmatched pairs. 6661 records in RAM.
INFO 2026-06-08 08:39:14 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr5:177,516,310
INFO 2026-06-08 08:39:14 MarkDuplicates Tracking 680914 as yet unmatched pairs. 4354 records in RAM.
INFO 2026-06-08 08:39:16 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr5:179,824,243
INFO 2026-06-08 08:39:16 MarkDuplicates Tracking 679596 as yet unmatched pairs. 3036 records in RAM.
INFO 2026-06-08 08:39:18 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr6:3,154,478
INFO 2026-06-08 08:39:18 MarkDuplicates Tracking 676167 as yet unmatched pairs. 41168 records in RAM.
INFO 2026-06-08 08:39:19 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr6:15,507,220
INFO 2026-06-08 08:39:19 MarkDuplicates Tracking 673770 as yet unmatched pairs. 38766 records in RAM.
INFO 2026-06-08 08:39:21 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr6:26,468,290
INFO 2026-06-08 08:39:21 MarkDuplicates Tracking 671511 as yet unmatched pairs. 36507 records in RAM.
INFO 2026-06-08 08:39:22 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr6:30,705,512
INFO 2026-06-08 08:39:22 MarkDuplicates Tracking 669469 as yet unmatched pairs. 34464 records in RAM.
INFO 2026-06-08 08:39:23 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr6:31,629,187
INFO 2026-06-08 08:39:23 MarkDuplicates Tracking 667181 as yet unmatched pairs. 32176 records in RAM.
INFO 2026-06-08 08:39:25 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr6:31,817,098
INFO 2026-06-08 08:39:25 MarkDuplicates Tracking 665539 as yet unmatched pairs. 30533 records in RAM.
INFO 2026-06-08 08:39:26 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr6:31,983,276
INFO 2026-06-08 08:39:26 MarkDuplicates Tracking 663489 as yet unmatched pairs. 28483 records in RAM.
INFO 2026-06-08 08:39:27 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr6:32,157,675
INFO 2026-06-08 08:39:27 MarkDuplicates Tracking 661701 as yet unmatched pairs. 26693 records in RAM.
INFO 2026-06-08 08:39:29 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr6:33,087,685
INFO 2026-06-08 08:39:29 MarkDuplicates Tracking 659374 as yet unmatched pairs. 24366 records in RAM.
INFO 2026-06-08 08:39:30 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr6:34,539,337
INFO 2026-06-08 08:39:30 MarkDuplicates Tracking 656806 as yet unmatched pairs. 21791 records in RAM.
INFO 2026-06-08 08:39:32 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr6:42,663,365
INFO 2026-06-08 08:39:32 MarkDuplicates Tracking 654130 as yet unmatched pairs. 19115 records in RAM.
INFO 2026-06-08 08:39:34 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr6:47,478,166
INFO 2026-06-08 08:39:34 MarkDuplicates Tracking 651527 as yet unmatched pairs. 16511 records in RAM.
INFO 2026-06-08 08:39:37 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: chr6:73,373,167
INFO 2026-06-08 08:39:37 MarkDuplicates Tracking 649323 as yet unmatched pairs. 14303 records in RAM.
INFO 2026-06-08 08:39:38 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr6:82,957,312
INFO 2026-06-08 08:39:38 MarkDuplicates Tracking 647125 as yet unmatched pairs. 12104 records in RAM.
INFO 2026-06-08 08:39:40 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr6:110,228,838
INFO 2026-06-08 08:39:40 MarkDuplicates Tracking 645008 as yet unmatched pairs. 9986 records in RAM.
INFO 2026-06-08 08:39:41 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr6:132,475,601
INFO 2026-06-08 08:39:41 MarkDuplicates Tracking 642793 as yet unmatched pairs. 7767 records in RAM.
INFO 2026-06-08 08:39:43 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr6:151,351,812
INFO 2026-06-08 08:39:43 MarkDuplicates Tracking 640734 as yet unmatched pairs. 5707 records in RAM.
INFO 2026-06-08 08:39:44 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr6:157,207,184
INFO 2026-06-08 08:39:44 MarkDuplicates Tracking 638155 as yet unmatched pairs. 3128 records in RAM.
INFO 2026-06-08 08:39:46 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr6:167,951,673
INFO 2026-06-08 08:39:46 MarkDuplicates Tracking 635754 as yet unmatched pairs. 725 records in RAM.
INFO 2026-06-08 08:39:47 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr7:4,983,688
INFO 2026-06-08 08:39:47 MarkDuplicates Tracking 632987 as yet unmatched pairs. 41286 records in RAM.
INFO 2026-06-08 08:39:49 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,522
INFO 2026-06-08 08:39:49 MarkDuplicates Tracking 632095 as yet unmatched pairs. 40390 records in RAM.
INFO 2026-06-08 08:39:50 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr7:16,776,253
INFO 2026-06-08 08:39:50 MarkDuplicates Tracking 628404 as yet unmatched pairs. 36694 records in RAM.
INFO 2026-06-08 08:39:52 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr7:32,980,386
INFO 2026-06-08 08:39:52 MarkDuplicates Tracking 625971 as yet unmatched pairs. 34259 records in RAM.
INFO 2026-06-08 08:39:54 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr7:44,114,132
INFO 2026-06-08 08:39:54 MarkDuplicates Tracking 623837 as yet unmatched pairs. 32124 records in RAM.
INFO 2026-06-08 08:39:56 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr7:66,081,822
INFO 2026-06-08 08:39:56 MarkDuplicates Tracking 621426 as yet unmatched pairs. 29711 records in RAM.
INFO 2026-06-08 08:39:57 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr7:74,338,600
INFO 2026-06-08 08:39:57 MarkDuplicates Tracking 619700 as yet unmatched pairs. 27983 records in RAM.
INFO 2026-06-08 08:39:59 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr7:76,303,043
INFO 2026-06-08 08:39:59 MarkDuplicates Tracking 619560 as yet unmatched pairs. 27843 records in RAM.
INFO 2026-06-08 08:40:00 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr7:90,962,409
INFO 2026-06-08 08:40:00 MarkDuplicates Tracking 615932 as yet unmatched pairs. 24215 records in RAM.
INFO 2026-06-08 08:40:01 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr7:94,400,203
INFO 2026-06-08 08:40:01 MarkDuplicates Tracking 614718 as yet unmatched pairs. 23001 records in RAM.
INFO 2026-06-08 08:40:03 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr7:94,417,720
INFO 2026-06-08 08:40:03 MarkDuplicates Tracking 611523 as yet unmatched pairs. 19801 records in RAM.
INFO 2026-06-08 08:40:04 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr7:95,290,159
INFO 2026-06-08 08:40:04 MarkDuplicates Tracking 608428 as yet unmatched pairs. 16704 records in RAM.
INFO 2026-06-08 08:40:06 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr7:100,221,137
INFO 2026-06-08 08:40:06 MarkDuplicates Tracking 606182 as yet unmatched pairs. 14446 records in RAM.
INFO 2026-06-08 08:40:07 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr7:102,355,835
INFO 2026-06-08 08:40:07 MarkDuplicates Tracking 603931 as yet unmatched pairs. 12194 records in RAM.
INFO 2026-06-08 08:40:09 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr7:105,063,542
INFO 2026-06-08 08:40:09 MarkDuplicates Tracking 602940 as yet unmatched pairs. 11200 records in RAM.
INFO 2026-06-08 08:40:11 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr7:127,589,533
INFO 2026-06-08 08:40:11 MarkDuplicates Tracking 600751 as yet unmatched pairs. 9010 records in RAM.
INFO 2026-06-08 08:40:13 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr7:134,960,585
INFO 2026-06-08 08:40:13 MarkDuplicates Tracking 598555 as yet unmatched pairs. 6814 records in RAM.
INFO 2026-06-08 08:40:15 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr7:142,091,832
INFO 2026-06-08 08:40:15 MarkDuplicates Tracking 596038 as yet unmatched pairs. 4296 records in RAM.
INFO 2026-06-08 08:40:16 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr7:150,371,369
INFO 2026-06-08 08:40:16 MarkDuplicates Tracking 594847 as yet unmatched pairs. 3105 records in RAM.
INFO 2026-06-08 08:40:17 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr7:157,382,251
INFO 2026-06-08 08:40:17 MarkDuplicates Tracking 592223 as yet unmatched pairs. 481 records in RAM.
INFO 2026-06-08 08:40:19 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr8:18,064,459
INFO 2026-06-08 08:40:19 MarkDuplicates Tracking 589897 as yet unmatched pairs. 31108 records in RAM.
INFO 2026-06-08 08:40:21 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr8:30,352,215
INFO 2026-06-08 08:40:21 MarkDuplicates Tracking 587376 as yet unmatched pairs. 28585 records in RAM.
INFO 2026-06-08 08:40:23 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr8:39,017,220
INFO 2026-06-08 08:40:23 MarkDuplicates Tracking 585042 as yet unmatched pairs. 26248 records in RAM.
INFO 2026-06-08 08:40:24 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr8:48,060,699
INFO 2026-06-08 08:40:24 MarkDuplicates Tracking 582804 as yet unmatched pairs. 24009 records in RAM.
INFO 2026-06-08 08:40:27 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr8:69,627,212
INFO 2026-06-08 08:40:27 MarkDuplicates Tracking 580498 as yet unmatched pairs. 21702 records in RAM.
INFO 2026-06-08 08:40:28 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr8:86,472,357
INFO 2026-06-08 08:40:28 MarkDuplicates Tracking 578285 as yet unmatched pairs. 19489 records in RAM.
INFO 2026-06-08 08:40:30 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr8:100,527,873
INFO 2026-06-08 08:40:30 MarkDuplicates Tracking 576029 as yet unmatched pairs. 17232 records in RAM.
INFO 2026-06-08 08:40:31 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr8:109,296,400
INFO 2026-06-08 08:40:31 MarkDuplicates Tracking 573906 as yet unmatched pairs. 15108 records in RAM.
INFO 2026-06-08 08:40:32 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr8:122,951,572
INFO 2026-06-08 08:40:32 MarkDuplicates Tracking 571444 as yet unmatched pairs. 12646 records in RAM.
INFO 2026-06-08 08:40:34 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr8:140,702,609
INFO 2026-06-08 08:40:34 MarkDuplicates Tracking 569133 as yet unmatched pairs. 10333 records in RAM.
INFO 2026-06-08 08:40:35 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,132
INFO 2026-06-08 08:40:35 MarkDuplicates Tracking 566403 as yet unmatched pairs. 7601 records in RAM.
INFO 2026-06-08 08:40:36 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,043
INFO 2026-06-08 08:40:36 MarkDuplicates Tracking 565824 as yet unmatched pairs. 7022 records in RAM.
INFO 2026-06-08 08:40:37 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,300
INFO 2026-06-08 08:40:37 MarkDuplicates Tracking 564880 as yet unmatched pairs. 6078 records in RAM.
INFO 2026-06-08 08:40:39 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr8:143,936,988
INFO 2026-06-08 08:40:39 MarkDuplicates Tracking 562339 as yet unmatched pairs. 3536 records in RAM.
INFO 2026-06-08 08:40:40 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr8:144,516,271
INFO 2026-06-08 08:40:40 MarkDuplicates Tracking 559386 as yet unmatched pairs. 581 records in RAM.
INFO 2026-06-08 08:40:42 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr9:15,459,740
INFO 2026-06-08 08:40:42 MarkDuplicates Tracking 557208 as yet unmatched pairs. 27303 records in RAM.
INFO 2026-06-08 08:40:43 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr9:35,057,117
INFO 2026-06-08 08:40:43 MarkDuplicates Tracking 555098 as yet unmatched pairs. 25191 records in RAM.
INFO 2026-06-08 08:40:45 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr9:63,974,777
INFO 2026-06-08 08:40:45 MarkDuplicates Tracking 552885 as yet unmatched pairs. 22965 records in RAM.
INFO 2026-06-08 08:40:46 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr9:87,706,819
INFO 2026-06-08 08:40:46 MarkDuplicates Tracking 551022 as yet unmatched pairs. 21100 records in RAM.
INFO 2026-06-08 08:40:48 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr9:97,472,387
INFO 2026-06-08 08:40:48 MarkDuplicates Tracking 548871 as yet unmatched pairs. 18948 records in RAM.
INFO 2026-06-08 08:40:49 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr9:112,227,571
INFO 2026-06-08 08:40:49 MarkDuplicates Tracking 546683 as yet unmatched pairs. 16757 records in RAM.
INFO 2026-06-08 08:40:51 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr9:121,302,155
INFO 2026-06-08 08:40:51 MarkDuplicates Tracking 544448 as yet unmatched pairs. 14521 records in RAM.
INFO 2026-06-08 08:40:52 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr9:127,507,237
INFO 2026-06-08 08:40:52 MarkDuplicates Tracking 542142 as yet unmatched pairs. 12214 records in RAM.
INFO 2026-06-08 08:40:54 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr9:128,988,073
INFO 2026-06-08 08:40:54 MarkDuplicates Tracking 539281 as yet unmatched pairs. 9353 records in RAM.
INFO 2026-06-08 08:40:56 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: chr9:132,328,216
INFO 2026-06-08 08:40:56 MarkDuplicates Tracking 536972 as yet unmatched pairs. 7040 records in RAM.
INFO 2026-06-08 08:40:59 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 3s. Last read position: chr9:134,834,970
INFO 2026-06-08 08:40:59 MarkDuplicates Tracking 534418 as yet unmatched pairs. 4486 records in RAM.
INFO 2026-06-08 08:41:01 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr9:137,096,299
INFO 2026-06-08 08:41:01 MarkDuplicates Tracking 531780 as yet unmatched pairs. 1846 records in RAM.
INFO 2026-06-08 08:41:03 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr10:5,455,102
INFO 2026-06-08 08:41:03 MarkDuplicates Tracking 529320 as yet unmatched pairs. 26654 records in RAM.
INFO 2026-06-08 08:41:04 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr10:17,233,769
INFO 2026-06-08 08:41:04 MarkDuplicates Tracking 526956 as yet unmatched pairs. 24290 records in RAM.
INFO 2026-06-08 08:41:06 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr10:31,852,521
INFO 2026-06-08 08:41:06 MarkDuplicates Tracking 524793 as yet unmatched pairs. 22126 records in RAM.
INFO 2026-06-08 08:41:07 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr10:43,102,358
INFO 2026-06-08 08:41:07 MarkDuplicates Tracking 523407 as yet unmatched pairs. 20740 records in RAM.
INFO 2026-06-08 08:41:08 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr10:45,681,779
INFO 2026-06-08 08:41:08 MarkDuplicates Tracking 520044 as yet unmatched pairs. 17377 records in RAM.
INFO 2026-06-08 08:41:10 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr10:59,832,646
INFO 2026-06-08 08:41:10 MarkDuplicates Tracking 519015 as yet unmatched pairs. 16348 records in RAM.
INFO 2026-06-08 08:41:11 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr10:73,498,615
INFO 2026-06-08 08:41:11 MarkDuplicates Tracking 516309 as yet unmatched pairs. 13636 records in RAM.
INFO 2026-06-08 08:41:13 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr10:79,710,440
INFO 2026-06-08 08:41:13 MarkDuplicates Tracking 514090 as yet unmatched pairs. 11416 records in RAM.
INFO 2026-06-08 08:41:14 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr10:92,016,342
INFO 2026-06-08 08:41:14 MarkDuplicates Tracking 512313 as yet unmatched pairs. 9639 records in RAM.
INFO 2026-06-08 08:41:15 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr10:99,888,932
INFO 2026-06-08 08:41:15 MarkDuplicates Tracking 510033 as yet unmatched pairs. 7357 records in RAM.
INFO 2026-06-08 08:41:17 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr10:104,018,168
INFO 2026-06-08 08:41:17 MarkDuplicates Tracking 507649 as yet unmatched pairs. 4970 records in RAM.
INFO 2026-06-08 08:41:18 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr10:119,672,386
INFO 2026-06-08 08:41:18 MarkDuplicates Tracking 505423 as yet unmatched pairs. 2743 records in RAM.
INFO 2026-06-08 08:41:20 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr10:133,160,510
INFO 2026-06-08 08:41:20 MarkDuplicates Tracking 503077 as yet unmatched pairs. 392 records in RAM.
INFO 2026-06-08 08:41:22 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr11:319,937
INFO 2026-06-08 08:41:22 MarkDuplicates Tracking 502266 as yet unmatched pairs. 55728 records in RAM.
INFO 2026-06-08 08:41:23 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr11:1,277,032
INFO 2026-06-08 08:41:23 MarkDuplicates Tracking 498454 as yet unmatched pairs. 51910 records in RAM.
INFO 2026-06-08 08:41:25 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr11:6,458,228
INFO 2026-06-08 08:41:25 MarkDuplicates Tracking 495992 as yet unmatched pairs. 49445 records in RAM.
INFO 2026-06-08 08:41:26 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr11:10,803,029
INFO 2026-06-08 08:41:26 MarkDuplicates Tracking 494093 as yet unmatched pairs. 47544 records in RAM.
INFO 2026-06-08 08:41:28 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr11:28,113,562
INFO 2026-06-08 08:41:28 MarkDuplicates Tracking 491104 as yet unmatched pairs. 44553 records in RAM.
INFO 2026-06-08 08:41:30 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr11:45,935,227
INFO 2026-06-08 08:41:30 MarkDuplicates Tracking 488793 as yet unmatched pairs. 42242 records in RAM.
INFO 2026-06-08 08:41:31 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr11:57,309,730
INFO 2026-06-08 08:41:31 MarkDuplicates Tracking 486404 as yet unmatched pairs. 39852 records in RAM.
INFO 2026-06-08 08:41:34 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr11:61,314,315
INFO 2026-06-08 08:41:34 MarkDuplicates Tracking 484128 as yet unmatched pairs. 37575 records in RAM.
INFO 2026-06-08 08:41:36 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr11:62,273,010
INFO 2026-06-08 08:41:36 MarkDuplicates Tracking 482038 as yet unmatched pairs. 35473 records in RAM.
INFO 2026-06-08 08:41:38 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr11:62,525,033
INFO 2026-06-08 08:41:38 MarkDuplicates Tracking 480613 as yet unmatched pairs. 34048 records in RAM.
INFO 2026-06-08 08:41:39 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr11:62,532,430
INFO 2026-06-08 08:41:39 MarkDuplicates Tracking 478229 as yet unmatched pairs. 31664 records in RAM.
INFO 2026-06-08 08:41:40 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr11:63,904,951
INFO 2026-06-08 08:41:40 MarkDuplicates Tracking 475569 as yet unmatched pairs. 29004 records in RAM.
INFO 2026-06-08 08:41:42 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr11:65,187,235
INFO 2026-06-08 08:41:42 MarkDuplicates Tracking 472808 as yet unmatched pairs. 26242 records in RAM.
INFO 2026-06-08 08:41:43 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr11:66,063,007
INFO 2026-06-08 08:41:43 MarkDuplicates Tracking 470307 as yet unmatched pairs. 23740 records in RAM.
INFO 2026-06-08 08:41:45 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr11:68,047,443
INFO 2026-06-08 08:41:45 MarkDuplicates Tracking 467468 as yet unmatched pairs. 20901 records in RAM.
INFO 2026-06-08 08:41:46 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr11:72,004,662
INFO 2026-06-08 08:41:46 MarkDuplicates Tracking 465287 as yet unmatched pairs. 18719 records in RAM.
INFO 2026-06-08 08:41:48 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr11:73,365,818
INFO 2026-06-08 08:41:48 MarkDuplicates Tracking 462685 as yet unmatched pairs. 16117 records in RAM.
INFO 2026-06-08 08:41:49 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr11:75,571,786
INFO 2026-06-08 08:41:49 MarkDuplicates Tracking 460676 as yet unmatched pairs. 14108 records in RAM.
INFO 2026-06-08 08:41:51 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr11:77,676,921
INFO 2026-06-08 08:41:51 MarkDuplicates Tracking 458259 as yet unmatched pairs. 11691 records in RAM.
INFO 2026-06-08 08:41:52 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr11:78,568,739
INFO 2026-06-08 08:41:52 MarkDuplicates Tracking 456212 as yet unmatched pairs. 9644 records in RAM.
INFO 2026-06-08 08:41:54 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr11:102,377,656
INFO 2026-06-08 08:41:54 MarkDuplicates Tracking 453689 as yet unmatched pairs. 7116 records in RAM.
INFO 2026-06-08 08:41:55 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr11:118,504,632
INFO 2026-06-08 08:41:55 MarkDuplicates Tracking 451258 as yet unmatched pairs. 4684 records in RAM.
INFO 2026-06-08 08:41:57 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr11:123,059,558
INFO 2026-06-08 08:41:57 MarkDuplicates Tracking 449211 as yet unmatched pairs. 2637 records in RAM.
INFO 2026-06-08 08:41:58 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr12:295,607
INFO 2026-06-08 08:41:58 MarkDuplicates Tracking 446516 as yet unmatched pairs. 64019 records in RAM.
INFO 2026-06-08 08:42:00 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr12:6,200,430
INFO 2026-06-08 08:42:00 MarkDuplicates Tracking 444499 as yet unmatched pairs. 62002 records in RAM.
INFO 2026-06-08 08:42:02 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr12:6,872,721
INFO 2026-06-08 08:42:02 MarkDuplicates Tracking 441843 as yet unmatched pairs. 59345 records in RAM.
INFO 2026-06-08 08:42:04 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr12:10,702,034
INFO 2026-06-08 08:42:04 MarkDuplicates Tracking 439678 as yet unmatched pairs. 57178 records in RAM.
INFO 2026-06-08 08:42:05 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr12:22,062,291
INFO 2026-06-08 08:42:05 MarkDuplicates Tracking 437359 as yet unmatched pairs. 54858 records in RAM.
INFO 2026-06-08 08:42:07 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr12:40,414,821
INFO 2026-06-08 08:42:07 MarkDuplicates Tracking 436223 as yet unmatched pairs. 53722 records in RAM.
INFO 2026-06-08 08:42:08 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr12:40,480,984
INFO 2026-06-08 08:42:08 MarkDuplicates Tracking 433295 as yet unmatched pairs. 50793 records in RAM.
INFO 2026-06-08 08:42:10 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr12:40,486,548
INFO 2026-06-08 08:42:10 MarkDuplicates Tracking 432356 as yet unmatched pairs. 49854 records in RAM.
INFO 2026-06-08 08:42:12 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 2s. Last read position: chr12:40,488,168
INFO 2026-06-08 08:42:12 MarkDuplicates Tracking 432149 as yet unmatched pairs. 49646 records in RAM.
INFO 2026-06-08 08:42:14 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 1s. Last read position: chr12:40,490,626
INFO 2026-06-08 08:42:14 MarkDuplicates Tracking 426415 as yet unmatched pairs. 43912 records in RAM.
INFO 2026-06-08 08:42:16 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr12:40,535,012
INFO 2026-06-08 08:42:16 MarkDuplicates Tracking 425678 as yet unmatched pairs. 43175 records in RAM.
INFO 2026-06-08 08:42:17 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 1s. Last read position: chr12:45,891,840
INFO 2026-06-08 08:42:17 MarkDuplicates Tracking 422409 as yet unmatched pairs. 39906 records in RAM.
INFO 2026-06-08 08:42:19 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr12:49,040,243
INFO 2026-06-08 08:42:19 MarkDuplicates Tracking 420173 as yet unmatched pairs. 37670 records in RAM.
INFO 2026-06-08 08:42:20 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr12:49,755,660
INFO 2026-06-08 08:42:20 MarkDuplicates Tracking 418362 as yet unmatched pairs. 35858 records in RAM.
INFO 2026-06-08 08:43:23 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 63s. Last read position: chr12:52,951,550
INFO 2026-06-08 08:43:23 MarkDuplicates Tracking 415588 as yet unmatched pairs. 33082 records in RAM.
INFO 2026-06-08 08:43:25 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr12:54,282,412
INFO 2026-06-08 08:43:25 MarkDuplicates Tracking 413599 as yet unmatched pairs. 31092 records in RAM.
INFO 2026-06-08 08:43:26 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr12:56,143,270
INFO 2026-06-08 08:43:26 MarkDuplicates Tracking 410895 as yet unmatched pairs. 28388 records in RAM.
INFO 2026-06-08 08:43:28 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 1s. Last read position: chr12:56,645,901
INFO 2026-06-08 08:43:28 MarkDuplicates Tracking 408313 as yet unmatched pairs. 25806 records in RAM.
INFO 2026-06-08 08:43:29 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 1s. Last read position: chr12:57,178,202
INFO 2026-06-08 08:43:29 MarkDuplicates Tracking 406090 as yet unmatched pairs. 23583 records in RAM.
INFO 2026-06-08 08:43:31 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr12:62,321,580
INFO 2026-06-08 08:43:31 MarkDuplicates Tracking 403670 as yet unmatched pairs. 21160 records in RAM.
INFO 2026-06-08 08:43:32 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr12:71,663,056
INFO 2026-06-08 08:43:32 MarkDuplicates Tracking 401523 as yet unmatched pairs. 19013 records in RAM.
INFO 2026-06-08 08:43:34 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr12:95,022,272
INFO 2026-06-08 08:43:34 MarkDuplicates Tracking 399471 as yet unmatched pairs. 16960 records in RAM.
INFO 2026-06-08 08:43:35 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr12:102,958,894
INFO 2026-06-08 08:43:35 MarkDuplicates Tracking 397497 as yet unmatched pairs. 14985 records in RAM.
INFO 2026-06-08 08:43:37 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr12:110,013,123
INFO 2026-06-08 08:43:37 MarkDuplicates Tracking 394898 as yet unmatched pairs. 12386 records in RAM.
INFO 2026-06-08 08:43:38 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 1s. Last read position: chr12:112,911,092
INFO 2026-06-08 08:43:38 MarkDuplicates Tracking 392615 as yet unmatched pairs. 10101 records in RAM.
INFO 2026-06-08 08:43:40 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr12:119,721,380
INFO 2026-06-08 08:43:40 MarkDuplicates Tracking 390002 as yet unmatched pairs. 7488 records in RAM.
INFO 2026-06-08 08:43:41 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr12:122,133,530
INFO 2026-06-08 08:43:41 MarkDuplicates Tracking 387799 as yet unmatched pairs. 5284 records in RAM.
INFO 2026-06-08 08:43:43 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr12:124,372,291
INFO 2026-06-08 08:43:43 MarkDuplicates Tracking 385454 as yet unmatched pairs. 2936 records in RAM.
INFO 2026-06-08 08:43:44 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr12:132,807,226
INFO 2026-06-08 08:43:44 MarkDuplicates Tracking 382939 as yet unmatched pairs. 419 records in RAM.
INFO 2026-06-08 08:43:46 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr13:30,763,960
INFO 2026-06-08 08:43:46 MarkDuplicates Tracking 380770 as yet unmatched pairs. 8541 records in RAM.
INFO 2026-06-08 08:43:47 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr13:45,120,543
INFO 2026-06-08 08:43:47 MarkDuplicates Tracking 378757 as yet unmatched pairs. 6526 records in RAM.
INFO 2026-06-08 08:43:48 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr13:75,804,289
INFO 2026-06-08 08:43:48 MarkDuplicates Tracking 376688 as yet unmatched pairs. 4456 records in RAM.
INFO 2026-06-08 08:43:50 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr13:110,192,213
INFO 2026-06-08 08:43:50 MarkDuplicates Tracking 374234 as yet unmatched pairs. 1999 records in RAM.
INFO 2026-06-08 08:43:52 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 2s. Last read position: chr14:20,801,644
INFO 2026-06-08 08:43:52 MarkDuplicates Tracking 371787 as yet unmatched pairs. 27612 records in RAM.
INFO 2026-06-08 08:43:54 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 2s. Last read position: chr14:23,137,952
INFO 2026-06-08 08:43:54 MarkDuplicates Tracking 369361 as yet unmatched pairs. 25185 records in RAM.
INFO 2026-06-08 08:43:56 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr14:24,369,707
INFO 2026-06-08 08:43:56 MarkDuplicates Tracking 367176 as yet unmatched pairs. 23000 records in RAM.
INFO 2026-06-08 08:43:57 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr14:37,622,617
INFO 2026-06-08 08:43:57 MarkDuplicates Tracking 364980 as yet unmatched pairs. 20800 records in RAM.
INFO 2026-06-08 08:43:59 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 1s. Last read position: chr14:52,646,200
INFO 2026-06-08 08:43:59 MarkDuplicates Tracking 362866 as yet unmatched pairs. 18681 records in RAM.
INFO 2026-06-08 08:44:00 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr14:63,909,131
INFO 2026-06-08 08:44:00 MarkDuplicates Tracking 360915 as yet unmatched pairs. 16724 records in RAM.
INFO 2026-06-08 08:44:02 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr14:68,893,670
INFO 2026-06-08 08:44:02 MarkDuplicates Tracking 358891 as yet unmatched pairs. 14699 records in RAM.
INFO 2026-06-08 08:44:03 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr14:74,552,201
INFO 2026-06-08 08:44:03 MarkDuplicates Tracking 356534 as yet unmatched pairs. 12341 records in RAM.
INFO 2026-06-08 08:44:05 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr14:89,412,074
INFO 2026-06-08 08:44:05 MarkDuplicates Tracking 354252 as yet unmatched pairs. 10058 records in RAM.
INFO 2026-06-08 08:44:06 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr14:94,619,346
INFO 2026-06-08 08:44:06 MarkDuplicates Tracking 352445 as yet unmatched pairs. 8250 records in RAM.
INFO 2026-06-08 08:44:08 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr14:101,809,894
INFO 2026-06-08 08:44:08 MarkDuplicates Tracking 349741 as yet unmatched pairs. 5536 records in RAM.
INFO 2026-06-08 08:44:09 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr14:103,673,132
INFO 2026-06-08 08:44:09 MarkDuplicates Tracking 347208 as yet unmatched pairs. 3003 records in RAM.
INFO 2026-06-08 08:44:10 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr14:105,625,836
INFO 2026-06-08 08:44:10 MarkDuplicates Tracking 344917 as yet unmatched pairs. 712 records in RAM.
INFO 2026-06-08 08:44:12 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr15:28,191,217
INFO 2026-06-08 08:44:12 MarkDuplicates Tracking 343308 as yet unmatched pairs. 20967 records in RAM.
INFO 2026-06-08 08:44:13 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr15:39,584,039
INFO 2026-06-08 08:44:13 MarkDuplicates Tracking 341591 as yet unmatched pairs. 19249 records in RAM.
INFO 2026-06-08 08:44:15 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr15:41,813,749
INFO 2026-06-08 08:44:15 MarkDuplicates Tracking 339227 as yet unmatched pairs. 16883 records in RAM.
INFO 2026-06-08 08:44:17 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 2s. Last read position: chr15:44,332,067
INFO 2026-06-08 08:44:17 MarkDuplicates Tracking 337203 as yet unmatched pairs. 14859 records in RAM.
INFO 2026-06-08 08:44:18 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr15:52,064,537
INFO 2026-06-08 08:44:18 MarkDuplicates Tracking 334814 as yet unmatched pairs. 12470 records in RAM.
INFO 2026-06-08 08:44:20 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr15:63,057,022
INFO 2026-06-08 08:44:20 MarkDuplicates Tracking 332756 as yet unmatched pairs. 10412 records in RAM.
INFO 2026-06-08 08:44:21 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr15:69,444,880
INFO 2026-06-08 08:44:21 MarkDuplicates Tracking 330220 as yet unmatched pairs. 7872 records in RAM.
INFO 2026-06-08 08:44:23 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr15:75,206,561
INFO 2026-06-08 08:44:23 MarkDuplicates Tracking 327724 as yet unmatched pairs. 5373 records in RAM.
INFO 2026-06-08 08:44:24 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr15:84,784,313
INFO 2026-06-08 08:44:24 MarkDuplicates Tracking 325421 as yet unmatched pairs. 3060 records in RAM.
INFO 2026-06-08 08:44:26 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr15:99,633,139
INFO 2026-06-08 08:44:26 MarkDuplicates Tracking 322958 as yet unmatched pairs. 594 records in RAM.
INFO 2026-06-08 08:44:27 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr16:666,430
INFO 2026-06-08 08:44:27 MarkDuplicates Tracking 320262 as yet unmatched pairs. 47511 records in RAM.
INFO 2026-06-08 08:44:29 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr16:1,501,561
INFO 2026-06-08 08:44:29 MarkDuplicates Tracking 317421 as yet unmatched pairs. 44670 records in RAM.
INFO 2026-06-08 08:44:30 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr16:2,108,359
INFO 2026-06-08 08:44:30 MarkDuplicates Tracking 314696 as yet unmatched pairs. 41944 records in RAM.
INFO 2026-06-08 08:44:32 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr16:2,762,871
INFO 2026-06-08 08:44:32 MarkDuplicates Tracking 312240 as yet unmatched pairs. 39488 records in RAM.
INFO 2026-06-08 08:44:34 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr16:3,591,083
INFO 2026-06-08 08:44:34 MarkDuplicates Tracking 309742 as yet unmatched pairs. 36990 records in RAM.
INFO 2026-06-08 08:44:35 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr16:8,855,306
INFO 2026-06-08 08:44:35 MarkDuplicates Tracking 307203 as yet unmatched pairs. 34450 records in RAM.
INFO 2026-06-08 08:44:37 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 1s. Last read position: chr16:14,604,148
INFO 2026-06-08 08:44:37 MarkDuplicates Tracking 304936 as yet unmatched pairs. 32182 records in RAM.
INFO 2026-06-08 08:44:39 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: chr16:15,016,178
INFO 2026-06-08 08:44:39 MarkDuplicates Tracking 304290 as yet unmatched pairs. 31536 records in RAM.
INFO 2026-06-08 08:44:40 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr16:16,318,005
INFO 2026-06-08 08:44:40 MarkDuplicates Tracking 302996 as yet unmatched pairs. 30242 records in RAM.
INFO 2026-06-08 08:44:41 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr16:16,383,623
INFO 2026-06-08 08:44:41 MarkDuplicates Tracking 302300 as yet unmatched pairs. 29546 records in RAM.
INFO 2026-06-08 08:44:42 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr16:18,380,867
INFO 2026-06-08 08:44:42 MarkDuplicates Tracking 301332 as yet unmatched pairs. 28576 records in RAM.
INFO 2026-06-08 08:44:44 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr16:18,876,379
INFO 2026-06-08 08:44:44 MarkDuplicates Tracking 299718 as yet unmatched pairs. 26962 records in RAM.
INFO 2026-06-08 08:44:45 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr16:21,455,374
INFO 2026-06-08 08:44:45 MarkDuplicates Tracking 298246 as yet unmatched pairs. 25490 records in RAM.
INFO 2026-06-08 08:44:47 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr16:22,454,772
INFO 2026-06-08 08:44:47 MarkDuplicates Tracking 297291 as yet unmatched pairs. 24534 records in RAM.
INFO 2026-06-08 08:44:48 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr16:24,569,681
INFO 2026-06-08 08:44:48 MarkDuplicates Tracking 296178 as yet unmatched pairs. 23421 records in RAM.
INFO 2026-06-08 08:44:49 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr16:28,830,968
INFO 2026-06-08 08:44:49 MarkDuplicates Tracking 294624 as yet unmatched pairs. 21867 records in RAM.
INFO 2026-06-08 08:44:51 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr16:29,487,028
INFO 2026-06-08 08:44:51 MarkDuplicates Tracking 293411 as yet unmatched pairs. 20654 records in RAM.
INFO 2026-06-08 08:44:52 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr16:30,070,048
INFO 2026-06-08 08:44:52 MarkDuplicates Tracking 291020 as yet unmatched pairs. 18263 records in RAM.
INFO 2026-06-08 08:44:53 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr16:30,532,723
INFO 2026-06-08 08:44:53 MarkDuplicates Tracking 289235 as yet unmatched pairs. 16478 records in RAM.
INFO 2026-06-08 08:44:54 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr16:31,182,397
INFO 2026-06-08 08:44:54 MarkDuplicates Tracking 286892 as yet unmatched pairs. 14134 records in RAM.
INFO 2026-06-08 08:44:56 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr16:51,646,308
INFO 2026-06-08 08:44:56 MarkDuplicates Tracking 284533 as yet unmatched pairs. 11772 records in RAM.
INFO 2026-06-08 08:44:57 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr16:58,581,345
INFO 2026-06-08 08:44:57 MarkDuplicates Tracking 282224 as yet unmatched pairs. 9463 records in RAM.
INFO 2026-06-08 08:44:59 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr16:68,829,713
INFO 2026-06-08 08:44:59 MarkDuplicates Tracking 279891 as yet unmatched pairs. 7130 records in RAM.
INFO 2026-06-08 08:45:00 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr16:74,391,657
INFO 2026-06-08 08:45:00 MarkDuplicates Tracking 277887 as yet unmatched pairs. 5124 records in RAM.
INFO 2026-06-08 08:45:01 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr16:88,428,304
INFO 2026-06-08 08:45:01 MarkDuplicates Tracking 275287 as yet unmatched pairs. 2524 records in RAM.
INFO 2026-06-08 08:45:04 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: chr17:156,317
INFO 2026-06-08 08:45:04 MarkDuplicates Tracking 272758 as yet unmatched pairs. 115462 records in RAM.
INFO 2026-06-08 08:45:05 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr17:3,941,485
INFO 2026-06-08 08:45:05 MarkDuplicates Tracking 270206 as yet unmatched pairs. 112910 records in RAM.
INFO 2026-06-08 08:45:07 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr17:7,235,982
INFO 2026-06-08 08:45:07 MarkDuplicates Tracking 267583 as yet unmatched pairs. 110287 records in RAM.
INFO 2026-06-08 08:45:09 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr17:7,904,523
INFO 2026-06-08 08:45:09 MarkDuplicates Tracking 265408 as yet unmatched pairs. 108111 records in RAM.
INFO 2026-06-08 08:45:10 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,044
INFO 2026-06-08 08:45:10 MarkDuplicates Tracking 263674 as yet unmatched pairs. 106376 records in RAM.
INFO 2026-06-08 08:45:11 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr17:27,597,389
INFO 2026-06-08 08:45:11 MarkDuplicates Tracking 260862 as yet unmatched pairs. 103564 records in RAM.
INFO 2026-06-08 08:45:13 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr17:29,615,729
INFO 2026-06-08 08:45:13 MarkDuplicates Tracking 258280 as yet unmatched pairs. 100982 records in RAM.
INFO 2026-06-08 08:45:14 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr17:35,353,587
INFO 2026-06-08 08:45:14 MarkDuplicates Tracking 255928 as yet unmatched pairs. 98630 records in RAM.
INFO 2026-06-08 08:45:16 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr17:37,981,561
INFO 2026-06-08 08:45:16 MarkDuplicates Tracking 254075 as yet unmatched pairs. 96777 records in RAM.
INFO 2026-06-08 08:45:17 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr17:39,201,260
INFO 2026-06-08 08:45:17 MarkDuplicates Tracking 252595 as yet unmatched pairs. 95297 records in RAM.
INFO 2026-06-08 08:45:19 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr17:39,712,359
INFO 2026-06-08 08:45:19 MarkDuplicates Tracking 250541 as yet unmatched pairs. 93243 records in RAM.
INFO 2026-06-08 08:45:20 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr17:39,725,352
INFO 2026-06-08 08:45:20 MarkDuplicates Tracking 248053 as yet unmatched pairs. 90755 records in RAM.
INFO 2026-06-08 08:45:22 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr17:40,352,352
INFO 2026-06-08 08:45:22 MarkDuplicates Tracking 244526 as yet unmatched pairs. 87228 records in RAM.
INFO 2026-06-08 08:45:23 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr17:41,767,428
INFO 2026-06-08 08:45:23 MarkDuplicates Tracking 241749 as yet unmatched pairs. 84451 records in RAM.
INFO 2026-06-08 08:45:25 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr17:42,565,269
INFO 2026-06-08 08:45:25 MarkDuplicates Tracking 239385 as yet unmatched pairs. 82087 records in RAM.
INFO 2026-06-08 08:45:26 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr17:44,211,079
INFO 2026-06-08 08:45:26 MarkDuplicates Tracking 237028 as yet unmatched pairs. 79730 records in RAM.
INFO 2026-06-08 08:45:28 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr17:46,330,703
INFO 2026-06-08 08:45:28 MarkDuplicates Tracking 234798 as yet unmatched pairs. 77500 records in RAM.
INFO 2026-06-08 08:45:29 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr17:48,892,826
INFO 2026-06-08 08:45:29 MarkDuplicates Tracking 232784 as yet unmatched pairs. 75486 records in RAM.
INFO 2026-06-08 08:45:30 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr17:50,185,820
INFO 2026-06-08 08:45:30 MarkDuplicates Tracking 232197 as yet unmatched pairs. 74897 records in RAM.
INFO 2026-06-08 08:45:32 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,784
INFO 2026-06-08 08:45:32 MarkDuplicates Tracking 231718 as yet unmatched pairs. 74418 records in RAM.
INFO 2026-06-08 08:45:34 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,483
INFO 2026-06-08 08:45:34 MarkDuplicates Tracking 234522 as yet unmatched pairs. 77221 records in RAM.
INFO 2026-06-08 08:45:35 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,135
INFO 2026-06-08 08:45:35 MarkDuplicates Tracking 231781 as yet unmatched pairs. 74480 records in RAM.
INFO 2026-06-08 08:45:37 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,922
INFO 2026-06-08 08:45:37 MarkDuplicates Tracking 229479 as yet unmatched pairs. 72177 records in RAM.
INFO 2026-06-08 08:45:38 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,464
INFO 2026-06-08 08:45:38 MarkDuplicates Tracking 224527 as yet unmatched pairs. 67225 records in RAM.
INFO 2026-06-08 08:45:40 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,030
INFO 2026-06-08 08:45:40 MarkDuplicates Tracking 222620 as yet unmatched pairs. 65317 records in RAM.
INFO 2026-06-08 08:45:42 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,883
INFO 2026-06-08 08:45:42 MarkDuplicates Tracking 218142 as yet unmatched pairs. 60839 records in RAM.
INFO 2026-06-08 08:45:43 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr17:50,191,987
INFO 2026-06-08 08:45:43 MarkDuplicates Tracking 218469 as yet unmatched pairs. 61165 records in RAM.
INFO 2026-06-08 08:45:45 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,001
INFO 2026-06-08 08:45:45 MarkDuplicates Tracking 216545 as yet unmatched pairs. 59241 records in RAM.
INFO 2026-06-08 08:45:46 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,145
INFO 2026-06-08 08:45:46 MarkDuplicates Tracking 222301 as yet unmatched pairs. 64997 records in RAM.
INFO 2026-06-08 08:45:48 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,724
INFO 2026-06-08 08:45:48 MarkDuplicates Tracking 210674 as yet unmatched pairs. 53370 records in RAM.
INFO 2026-06-08 08:45:49 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,313
INFO 2026-06-08 08:45:49 MarkDuplicates Tracking 207663 as yet unmatched pairs. 50359 records in RAM.
INFO 2026-06-08 08:45:51 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,965
INFO 2026-06-08 08:45:51 MarkDuplicates Tracking 210452 as yet unmatched pairs. 53147 records in RAM.
INFO 2026-06-08 08:45:53 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,491
INFO 2026-06-08 08:45:53 MarkDuplicates Tracking 202906 as yet unmatched pairs. 45600 records in RAM.
INFO 2026-06-08 08:45:54 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,179
INFO 2026-06-08 08:45:54 MarkDuplicates Tracking 206048 as yet unmatched pairs. 48742 records in RAM.
INFO 2026-06-08 08:45:56 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr17:50,198,179
INFO 2026-06-08 08:45:56 MarkDuplicates Tracking 196545 as yet unmatched pairs. 39239 records in RAM.
INFO 2026-06-08 08:45:58 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,441
INFO 2026-06-08 08:45:58 MarkDuplicates Tracking 189975 as yet unmatched pairs. 32669 records in RAM.
INFO 2026-06-08 08:45:59 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr17:50,356,655
INFO 2026-06-08 08:45:59 MarkDuplicates Tracking 182883 as yet unmatched pairs. 25577 records in RAM.
INFO 2026-06-08 08:46:00 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr17:59,088,298
INFO 2026-06-08 08:46:00 MarkDuplicates Tracking 180552 as yet unmatched pairs. 23246 records in RAM.
INFO 2026-06-08 08:46:02 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr17:61,956,428
INFO 2026-06-08 08:46:02 MarkDuplicates Tracking 178307 as yet unmatched pairs. 21001 records in RAM.
INFO 2026-06-08 08:46:03 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr17:64,390,640
INFO 2026-06-08 08:46:03 MarkDuplicates Tracking 175689 as yet unmatched pairs. 18383 records in RAM.
INFO 2026-06-08 08:46:05 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr17:68,251,139
INFO 2026-06-08 08:46:05 MarkDuplicates Tracking 173869 as yet unmatched pairs. 16562 records in RAM.
INFO 2026-06-08 08:46:06 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr17:74,771,835
INFO 2026-06-08 08:46:06 MarkDuplicates Tracking 171211 as yet unmatched pairs. 13902 records in RAM.
INFO 2026-06-08 08:46:08 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr17:76,007,026
INFO 2026-06-08 08:46:08 MarkDuplicates Tracking 168490 as yet unmatched pairs. 11181 records in RAM.
INFO 2026-06-08 08:46:09 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr17:78,976,042
INFO 2026-06-08 08:46:09 MarkDuplicates Tracking 165806 as yet unmatched pairs. 8497 records in RAM.
INFO 2026-06-08 08:46:10 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr17:80,347,726
INFO 2026-06-08 08:46:10 MarkDuplicates Tracking 163534 as yet unmatched pairs. 6220 records in RAM.
INFO 2026-06-08 08:46:12 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr17:81,843,969
INFO 2026-06-08 08:46:12 MarkDuplicates Tracking 161078 as yet unmatched pairs. 3764 records in RAM.
INFO 2026-06-08 08:46:13 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr17:82,236,032
INFO 2026-06-08 08:46:13 MarkDuplicates Tracking 158617 as yet unmatched pairs. 1303 records in RAM.
INFO 2026-06-08 08:46:14 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr18:9,588,213
INFO 2026-06-08 08:46:14 MarkDuplicates Tracking 156093 as yet unmatched pairs. 6784 records in RAM.
INFO 2026-06-08 08:46:16 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr18:32,412,928
INFO 2026-06-08 08:46:16 MarkDuplicates Tracking 153975 as yet unmatched pairs. 4664 records in RAM.
INFO 2026-06-08 08:46:18 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr18:57,573,275
INFO 2026-06-08 08:46:18 MarkDuplicates Tracking 151693 as yet unmatched pairs. 2372 records in RAM.
INFO 2026-06-08 08:46:19 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr19:281,404
INFO 2026-06-08 08:46:19 MarkDuplicates Tracking 149333 as yet unmatched pairs. 59666 records in RAM.
INFO 2026-06-08 08:46:21 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr19:1,632,339
INFO 2026-06-08 08:46:21 MarkDuplicates Tracking 146466 as yet unmatched pairs. 56799 records in RAM.
INFO 2026-06-08 08:46:23 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr19:4,446,847
INFO 2026-06-08 08:46:23 MarkDuplicates Tracking 143640 as yet unmatched pairs. 53972 records in RAM.
INFO 2026-06-08 08:46:24 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr19:6,733,658
INFO 2026-06-08 08:46:24 MarkDuplicates Tracking 141062 as yet unmatched pairs. 51392 records in RAM.
INFO 2026-06-08 08:46:26 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 2s. Last read position: chr19:10,107,989
INFO 2026-06-08 08:46:26 MarkDuplicates Tracking 138474 as yet unmatched pairs. 48803 records in RAM.
INFO 2026-06-08 08:46:28 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr19:11,405,168
INFO 2026-06-08 08:46:28 MarkDuplicates Tracking 136003 as yet unmatched pairs. 46332 records in RAM.
INFO 2026-06-08 08:46:30 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 1s. Last read position: chr19:13,918,913
INFO 2026-06-08 08:46:30 MarkDuplicates Tracking 133678 as yet unmatched pairs. 44007 records in RAM.
INFO 2026-06-08 08:46:31 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr19:15,244,533
INFO 2026-06-08 08:46:31 MarkDuplicates Tracking 131032 as yet unmatched pairs. 41359 records in RAM.
INFO 2026-06-08 08:46:33 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr19:17,422,334
INFO 2026-06-08 08:46:33 MarkDuplicates Tracking 127986 as yet unmatched pairs. 38312 records in RAM.
INFO 2026-06-08 08:46:34 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr19:19,024,945
INFO 2026-06-08 08:46:34 MarkDuplicates Tracking 125429 as yet unmatched pairs. 35754 records in RAM.
INFO 2026-06-08 08:46:36 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr19:35,013,626
INFO 2026-06-08 08:46:36 MarkDuplicates Tracking 123386 as yet unmatched pairs. 33710 records in RAM.
INFO 2026-06-08 08:46:37 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr19:37,564,942
INFO 2026-06-08 08:46:37 MarkDuplicates Tracking 120657 as yet unmatched pairs. 30981 records in RAM.
INFO 2026-06-08 08:46:39 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr19:39,433,386
INFO 2026-06-08 08:46:39 MarkDuplicates Tracking 118765 as yet unmatched pairs. 29087 records in RAM.
INFO 2026-06-08 08:46:40 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr19:40,235,884
INFO 2026-06-08 08:46:40 MarkDuplicates Tracking 116410 as yet unmatched pairs. 26732 records in RAM.
INFO 2026-06-08 08:46:41 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr19:41,761,331
INFO 2026-06-08 08:46:41 MarkDuplicates Tracking 114443 as yet unmatched pairs. 24765 records in RAM.
INFO 2026-06-08 08:46:43 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr19:43,552,074
INFO 2026-06-08 08:46:43 MarkDuplicates Tracking 111225 as yet unmatched pairs. 21540 records in RAM.
INFO 2026-06-08 08:46:44 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr19:45,306,916
INFO 2026-06-08 08:46:44 MarkDuplicates Tracking 108658 as yet unmatched pairs. 18973 records in RAM.
INFO 2026-06-08 08:46:46 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr19:46,921,069
INFO 2026-06-08 08:46:46 MarkDuplicates Tracking 106553 as yet unmatched pairs. 16867 records in RAM.
INFO 2026-06-08 08:46:47 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr19:48,913,519
INFO 2026-06-08 08:46:47 MarkDuplicates Tracking 103395 as yet unmatched pairs. 13709 records in RAM.
INFO 2026-06-08 08:46:49 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr19:49,651,948
INFO 2026-06-08 08:46:49 MarkDuplicates Tracking 100853 as yet unmatched pairs. 11167 records in RAM.
INFO 2026-06-08 08:46:50 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr19:52,613,463
INFO 2026-06-08 08:46:50 MarkDuplicates Tracking 98249 as yet unmatched pairs. 8563 records in RAM.
INFO 2026-06-08 08:46:51 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr19:54,665,136
INFO 2026-06-08 08:46:51 MarkDuplicates Tracking 96013 as yet unmatched pairs. 6318 records in RAM.
INFO 2026-06-08 08:46:53 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr19:55,692,685
INFO 2026-06-08 08:46:53 MarkDuplicates Tracking 93018 as yet unmatched pairs. 3323 records in RAM.
INFO 2026-06-08 08:46:54 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 1s. Last read position: chr19:57,909,955
INFO 2026-06-08 08:46:54 MarkDuplicates Tracking 91122 as yet unmatched pairs. 1427 records in RAM.
INFO 2026-06-08 08:46:56 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr20:2,835,486
INFO 2026-06-08 08:46:56 MarkDuplicates Tracking 88473 as yet unmatched pairs. 21592 records in RAM.
INFO 2026-06-08 08:46:57 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 1s. Last read position: chr20:16,312,335
INFO 2026-06-08 08:46:57 MarkDuplicates Tracking 86008 as yet unmatched pairs. 19127 records in RAM.
INFO 2026-06-08 08:46:59 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr20:25,271,382
INFO 2026-06-08 08:46:59 MarkDuplicates Tracking 83685 as yet unmatched pairs. 16804 records in RAM.
INFO 2026-06-08 08:47:00 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr20:34,919,519
INFO 2026-06-08 08:47:00 MarkDuplicates Tracking 81328 as yet unmatched pairs. 14447 records in RAM.
INFO 2026-06-08 08:47:02 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr20:38,013,469
INFO 2026-06-08 08:47:02 MarkDuplicates Tracking 78895 as yet unmatched pairs. 12014 records in RAM.
INFO 2026-06-08 08:47:03 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr20:45,416,258
INFO 2026-06-08 08:47:03 MarkDuplicates Tracking 76677 as yet unmatched pairs. 9796 records in RAM.
INFO 2026-06-08 08:47:05 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr20:50,191,161
INFO 2026-06-08 08:47:05 MarkDuplicates Tracking 74169 as yet unmatched pairs. 7288 records in RAM.
INFO 2026-06-08 08:47:06 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr20:58,995,647
INFO 2026-06-08 08:47:06 MarkDuplicates Tracking 71729 as yet unmatched pairs. 4848 records in RAM.
INFO 2026-06-08 08:47:07 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 1s. Last read position: chr20:63,494,811
INFO 2026-06-08 08:47:07 MarkDuplicates Tracking 69167 as yet unmatched pairs. 2285 records in RAM.
INFO 2026-06-08 08:47:09 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr21:8,214,638
INFO 2026-06-08 08:47:09 MarkDuplicates Tracking 66687 as yet unmatched pairs. 13000 records in RAM.
INFO 2026-06-08 08:47:10 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 0s. Last read position: chr21:8,399,027
INFO 2026-06-08 08:47:10 MarkDuplicates Tracking 65837 as yet unmatched pairs. 12144 records in RAM.
INFO 2026-06-08 08:47:11 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr21:13,353,597
INFO 2026-06-08 08:47:11 MarkDuplicates Tracking 64232 as yet unmatched pairs. 10537 records in RAM.
INFO 2026-06-08 08:47:12 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr21:33,553,863
INFO 2026-06-08 08:47:12 MarkDuplicates Tracking 62013 as yet unmatched pairs. 8317 records in RAM.
INFO 2026-06-08 08:47:14 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 2s. Last read position: chr21:41,452,661
INFO 2026-06-08 08:47:14 MarkDuplicates Tracking 59672 as yet unmatched pairs. 5976 records in RAM.
INFO 2026-06-08 08:47:16 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr21:44,889,368
INFO 2026-06-08 08:47:16 MarkDuplicates Tracking 57381 as yet unmatched pairs. 3685 records in RAM.
INFO 2026-06-08 08:47:17 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr21:46,215,721
INFO 2026-06-08 08:47:17 MarkDuplicates Tracking 54372 as yet unmatched pairs. 676 records in RAM.
INFO 2026-06-08 08:47:19 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr22:20,315,380
INFO 2026-06-08 08:47:19 MarkDuplicates Tracking 51885 as yet unmatched pairs. 22683 records in RAM.
INFO 2026-06-08 08:47:20 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr22:23,781,352
INFO 2026-06-08 08:47:20 MarkDuplicates Tracking 49554 as yet unmatched pairs. 20352 records in RAM.
INFO 2026-06-08 08:47:22 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr22:28,796,072
INFO 2026-06-08 08:47:22 MarkDuplicates Tracking 48658 as yet unmatched pairs. 19456 records in RAM.
INFO 2026-06-08 08:47:24 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr22:31,081,363
INFO 2026-06-08 08:47:24 MarkDuplicates Tracking 44542 as yet unmatched pairs. 15340 records in RAM.
INFO 2026-06-08 08:47:25 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr22:36,289,121
INFO 2026-06-08 08:47:25 MarkDuplicates Tracking 42047 as yet unmatched pairs. 12845 records in RAM.
INFO 2026-06-08 08:47:27 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr22:37,773,824
INFO 2026-06-08 08:47:27 MarkDuplicates Tracking 39496 as yet unmatched pairs. 10294 records in RAM.
INFO 2026-06-08 08:47:29 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr22:39,243,838
INFO 2026-06-08 08:47:29 MarkDuplicates Tracking 37130 as yet unmatched pairs. 7928 records in RAM.
INFO 2026-06-08 08:47:31 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr22:42,081,967
INFO 2026-06-08 08:47:31 MarkDuplicates Tracking 34736 as yet unmatched pairs. 5534 records in RAM.
INFO 2026-06-08 08:47:32 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr22:46,675,471
INFO 2026-06-08 08:47:32 MarkDuplicates Tracking 32146 as yet unmatched pairs. 2944 records in RAM.
INFO 2026-06-08 08:47:34 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chrX:316,936
INFO 2026-06-08 08:47:34 MarkDuplicates Tracking 29175 as yet unmatched pairs. 23518 records in RAM.
INFO 2026-06-08 08:47:35 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chrX:15,551,841
INFO 2026-06-08 08:47:35 MarkDuplicates Tracking 26798 as yet unmatched pairs. 21141 records in RAM.
INFO 2026-06-08 08:47:37 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chrX:40,053,936
INFO 2026-06-08 08:47:37 MarkDuplicates Tracking 24722 as yet unmatched pairs. 19062 records in RAM.
INFO 2026-06-08 08:47:38 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 1s. Last read position: chrX:47,245,436
INFO 2026-06-08 08:47:38 MarkDuplicates Tracking 22316 as yet unmatched pairs. 16655 records in RAM.
INFO 2026-06-08 08:47:40 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chrX:53,403,834
INFO 2026-06-08 08:47:40 MarkDuplicates Tracking 19884 as yet unmatched pairs. 14223 records in RAM.
INFO 2026-06-08 08:47:41 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chrX:69,528,998
INFO 2026-06-08 08:47:41 MarkDuplicates Tracking 17434 as yet unmatched pairs. 11773 records in RAM.
INFO 2026-06-08 08:47:42 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chrX:77,656,569
INFO 2026-06-08 08:47:42 MarkDuplicates Tracking 15205 as yet unmatched pairs. 9544 records in RAM.
INFO 2026-06-08 08:47:44 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chrX:103,676,179
INFO 2026-06-08 08:47:44 MarkDuplicates Tracking 13284 as yet unmatched pairs. 7623 records in RAM.
INFO 2026-06-08 08:47:45 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chrX:124,042,616
INFO 2026-06-08 08:47:45 MarkDuplicates Tracking 10945 as yet unmatched pairs. 5284 records in RAM.
INFO 2026-06-08 08:47:47 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chrX:153,723,153
INFO 2026-06-08 08:47:47 MarkDuplicates Tracking 9022 as yet unmatched pairs. 3360 records in RAM.
INFO 2026-06-08 08:47:48 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chrX:154,446,526
INFO 2026-06-08 08:47:48 MarkDuplicates Tracking 6351 as yet unmatched pairs. 689 records in RAM.
INFO 2026-06-08 08:47:49 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,778
INFO 2026-06-08 08:47:49 MarkDuplicates Tracking 4107 as yet unmatched pairs. 94 records in RAM.
INFO 2026-06-08 08:47:51 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,061
INFO 2026-06-08 08:47:51 MarkDuplicates Tracking 2234 as yet unmatched pairs. 2203 records in RAM.
INFO 2026-06-08 08:47:52 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,697
INFO 2026-06-08 08:47:52 MarkDuplicates Tracking 33 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:47:52 MarkDuplicates Read 432185791 records. 0 pairs never matched.
INFO 2026-06-08 08:48:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 37349882144; totalMemory: 53351546880; maxMemory: 63585648640
INFO 2026-06-08 08:48:36 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:48:52 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:49:10 OpticalDuplicateFinder Large duplicate set. size = 2146
INFO 2026-06-08 08:49:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,652
INFO 2026-06-08 08:49:10 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,651
INFO 2026-06-08 08:49:10 OpticalDuplicateFinder Large duplicate set. size = 1207
INFO 2026-06-08 08:49:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,761
INFO 2026-06-08 08:49:16 OpticalDuplicateFinder Large duplicate set. size = 1087
INFO 2026-06-08 08:49:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,624
INFO 2026-06-08 08:49:16 OpticalDuplicateFinder Large duplicate set. size = 1008
INFO 2026-06-08 08:49:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,248
INFO 2026-06-08 08:49:16 OpticalDuplicateFinder Large duplicate set. size = 1578
INFO 2026-06-08 08:49:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,846
INFO 2026-06-08 08:49:34 OpticalDuplicateFinder Large duplicate set. size = 1132
INFO 2026-06-08 08:49:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,980
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1277
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,224
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1342
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,699
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1196
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,073
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1330
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,528
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1049
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,000
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1650
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,381
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1086
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,726
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1095
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,151
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1078
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,268
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1131
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,342
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder Large duplicate set. size = 1443
INFO 2026-06-08 08:49:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,137
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1089
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,688
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1234
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,761
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1195
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,252
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1044
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,086
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1101
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,209
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1085
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,121
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1728
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,877
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1107
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,254
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1075
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,647
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1240
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,710
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1070
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,318
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1052
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,525
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1409
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,067
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1352
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,093
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder Large duplicate set. size = 1279
INFO 2026-06-08 08:49:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,787
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1085
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,242
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1127
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,853
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1895
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,953
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1016
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,667
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1158
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,592
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1070
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,759
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1038
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,305
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1423
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,863
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1174
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,482
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1076
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,024
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1429
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,930
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1041
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,707
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1850
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,515
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 3078
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,036
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,380
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,680
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1052
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,824
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1616
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,394
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1707
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,986
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1793
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,291
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1886
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,581
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1311
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,837
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1184
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,148
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1250
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,749
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1198
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,939
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1139
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,506
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1026
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,423
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1331
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,335
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1008
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,224
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1054
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,001
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder Large duplicate set. size = 1081
INFO 2026-06-08 08:49:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,543
INFO 2026-06-08 08:49:38 OpticalDuplicateFinder Large duplicate set. size = 1851
INFO 2026-06-08 08:49:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,348
INFO 2026-06-08 08:49:38 OpticalDuplicateFinder Large duplicate set. size = 1591
INFO 2026-06-08 08:49:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,258
INFO 2026-06-08 08:49:58 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:49:59 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:50:40 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:50:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 105278672; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:50:43 MarkDuplicates Marking 315317945 records as duplicates.
INFO 2026-06-08 08:50:43 MarkDuplicates Found 6092611 optical duplicate clusters.
INFO 2026-06-08 08:50:43 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:50:57 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:14s. Time for last 10,000,000: 14s. Last read position: chr1:46,689,659
INFO 2026-06-08 08:51:12 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:29s. Time for last 10,000,000: 14s. Last read position: chr1:149,851,246
INFO 2026-06-08 08:51:25 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:42s. Time for last 10,000,000: 13s. Last read position: chr1:164,807,570
INFO 2026-06-08 08:51:39 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:00:56s. Time for last 10,000,000: 14s. Last read position: chr1:228,408,561
INFO 2026-06-08 08:51:53 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:10s. Time for last 10,000,000: 13s. Last read position: chr2:62,707,167
INFO 2026-06-08 08:52:07 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:24s. Time for last 10,000,000: 13s. Last read position: chr2:173,955,388
INFO 2026-06-08 08:52:21 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:38s. Time for last 10,000,000: 13s. Last read position: chr2:197,416,742
INFO 2026-06-08 08:52:35 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:01:52s. Time for last 10,000,000: 13s. Last read position: chr2:215,433,406
INFO 2026-06-08 08:52:49 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:06s. Time for last 10,000,000: 13s. Last read position: chr3:48,970,686
INFO 2026-06-08 08:53:02 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:19s. Time for last 10,000,000: 13s. Last read position: chr3:150,742,623
INFO 2026-06-08 08:53:17 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:34s. Time for last 10,000,000: 14s. Last read position: chr4:87,614,493
INFO 2026-06-08 08:53:30 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:02:47s. Time for last 10,000,000: 13s. Last read position: chr5:70,440,762
INFO 2026-06-08 08:53:44 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:01s. Time for last 10,000,000: 13s. Last read position: chr5:150,121,882
INFO 2026-06-08 08:53:58 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:15s. Time for last 10,000,000: 13s. Last read position: chr6:30,705,512
INFO 2026-06-08 08:54:12 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:29s. Time for last 10,000,000: 13s. Last read position: chr6:82,957,312
INFO 2026-06-08 08:54:25 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:03:42s. Time for last 10,000,000: 13s. Last read position: chr7:44,114,132
INFO 2026-06-08 08:54:39 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:03:56s. Time for last 10,000,000: 13s. Last read position: chr7:105,063,542
INFO 2026-06-08 08:54:53 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:10s. Time for last 10,000,000: 13s. Last read position: chr8:69,627,212
INFO 2026-06-08 08:55:06 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:23s. Time for last 10,000,000: 13s. Last read position: chr8:144,516,271
INFO 2026-06-08 08:55:20 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:04:37s. Time for last 10,000,000: 13s. Last read position: chr9:132,328,216
INFO 2026-06-08 08:55:33 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:04:50s. Time for last 10,000,000: 13s. Last read position: chr10:79,710,440
INFO 2026-06-08 08:55:47 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:04s. Time for last 10,000,000: 13s. Last read position: chr11:28,113,562
INFO 2026-06-08 08:56:01 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:18s. Time for last 10,000,000: 13s. Last read position: chr11:68,047,443
INFO 2026-06-08 08:56:15 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:05:31s. Time for last 10,000,000: 13s. Last read position: chr12:6,200,430
INFO 2026-06-08 08:56:28 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:05:45s. Time for last 10,000,000: 13s. Last read position: chr12:45,891,840
INFO 2026-06-08 08:56:42 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:05:59s. Time for last 10,000,000: 13s. Last read position: chr12:95,022,272
INFO 2026-06-08 08:56:56 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:13s. Time for last 10,000,000: 13s. Last read position: chr13:75,804,289
INFO 2026-06-08 08:57:09 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:06:26s. Time for last 10,000,000: 13s. Last read position: chr14:89,412,074
INFO 2026-06-08 08:57:23 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:06:40s. Time for last 10,000,000: 13s. Last read position: chr15:63,057,022
INFO 2026-06-08 08:57:37 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:06:54s. Time for last 10,000,000: 13s. Last read position: chr16:8,855,306
INFO 2026-06-08 08:57:51 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:08s. Time for last 10,000,000: 13s. Last read position: chr16:28,830,968
INFO 2026-06-08 08:58:04 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:07:21s. Time for last 10,000,000: 13s. Last read position: chr17:156,317
INFO 2026-06-08 08:58:18 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:07:35s. Time for last 10,000,000: 13s. Last read position: chr17:39,712,359
INFO 2026-06-08 08:58:32 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:07:48s. Time for last 10,000,000: 13s. Last read position: chr17:50,187,483
INFO 2026-06-08 08:58:45 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:08:02s. Time for last 10,000,000: 13s. Last read position: chr17:50,195,313
INFO 2026-06-08 08:58:59 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:08:16s. Time for last 10,000,000: 14s. Last read position: chr17:68,251,139
INFO 2026-06-08 08:59:13 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:08:30s. Time for last 10,000,000: 13s. Last read position: chr19:281,404
INFO 2026-06-08 08:59:27 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:08:44s. Time for last 10,000,000: 13s. Last read position: chr19:35,013,626
INFO 2026-06-08 08:59:41 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:08:58s. Time for last 10,000,000: 13s. Last read position: chr19:52,613,463
INFO 2026-06-08 08:59:55 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:09:11s. Time for last 10,000,000: 13s. Last read position: chr20:50,191,161
INFO 2026-06-08 09:00:08 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:09:25s. Time for last 10,000,000: 13s. Last read position: chr22:20,315,380
INFO 2026-06-08 09:00:22 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:09:39s. Time for last 10,000,000: 13s. Last read position: chrX:15,551,841
INFO 2026-06-08 09:00:36 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:09:52s. Time for last 10,000,000: 13s. Last read position: GL000220.1:116,778
INFO 2026-06-08 09:00:45 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 09:00:45 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 09:00:45 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 09:00:45 MarkDuplicates Before output close freeMemory: 204574064; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 09:00:45 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 09:00:45 MarkDuplicates After output close freeMemory: 104812280; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 09:00:45 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 25.35 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory