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 659_6i-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:27:03.529 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 08:27:03 GMT 2026] MarkDuplicates --INPUT 659_6i-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_6i-T1-TRNA-1_B23WHTKLT4_1.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 08:27:03 GMT 2026] Executing as ?@nf-19455c82d48c8981709b731bd1143182-70320-ddjl5 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 08:27:03 MarkDuplicates Start of doWork freeMemory: 105828216; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:27:03 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:27:03 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:27:07 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,489,228
INFO 2026-06-08 08:27:07 MarkDuplicates Tracking 1667 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 08:27:09 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr1:6,580,643
INFO 2026-06-08 08:27:09 MarkDuplicates Tracking 3231 as yet unmatched pairs. 27 records in RAM.
INFO 2026-06-08 08:27:10 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr1:10,419,519
INFO 2026-06-08 08:27:10 MarkDuplicates Tracking 4691 as yet unmatched pairs. 113 records in RAM.
INFO 2026-06-08 08:27:12 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr1:13,780,595
INFO 2026-06-08 08:27:12 MarkDuplicates Tracking 6188 as yet unmatched pairs. 219 records in RAM.
INFO 2026-06-08 08:27:14 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr1:19,141,415
INFO 2026-06-08 08:27:14 MarkDuplicates Tracking 7410 as yet unmatched pairs. 90 records in RAM.
INFO 2026-06-08 08:27:15 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:21,831,684
INFO 2026-06-08 08:27:15 MarkDuplicates Tracking 8806 as yet unmatched pairs. 120 records in RAM.
INFO 2026-06-08 08:27:17 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:23,692,626
INFO 2026-06-08 08:27:17 MarkDuplicates Tracking 11036 as yet unmatched pairs. 1196 records in RAM.
INFO 2026-06-08 08:27:18 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr1:26,886,073
INFO 2026-06-08 08:27:18 MarkDuplicates Tracking 11239 as yet unmatched pairs. 62 records in RAM.
INFO 2026-06-08 08:27:20 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:31,367,446
INFO 2026-06-08 08:27:20 MarkDuplicates Tracking 12352 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:27:22 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:32,826,544
INFO 2026-06-08 08:27:22 MarkDuplicates Tracking 13762 as yet unmatched pairs. 102 records in RAM.
INFO 2026-06-08 08:27:24 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:37,806,963
INFO 2026-06-08 08:27:24 MarkDuplicates Tracking 15036 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:27:25 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:40,060,115
INFO 2026-06-08 08:27:25 MarkDuplicates Tracking 16292 as yet unmatched pairs. 113 records in RAM.
INFO 2026-06-08 08:27:27 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:43,591,812
INFO 2026-06-08 08:27:27 MarkDuplicates Tracking 17858 as yet unmatched pairs. 165 records in RAM.
INFO 2026-06-08 08:27:29 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:46,286,167
INFO 2026-06-08 08:27:29 MarkDuplicates Tracking 19324 as yet unmatched pairs. 371 records in RAM.
INFO 2026-06-08 08:27:30 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:54,607,126
INFO 2026-06-08 08:27:30 MarkDuplicates Tracking 20450 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:27:32 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:67,430,066
INFO 2026-06-08 08:27:32 MarkDuplicates Tracking 21777 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 08:27:33 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:91,683,848
INFO 2026-06-08 08:27:33 MarkDuplicates Tracking 22774 as yet unmatched pairs. 59 records in RAM.
INFO 2026-06-08 08:27:35 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:109,188,213
INFO 2026-06-08 08:27:35 MarkDuplicates Tracking 23956 as yet unmatched pairs. 171 records in RAM.
INFO 2026-06-08 08:27:36 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:113,900,001
INFO 2026-06-08 08:27:36 MarkDuplicates Tracking 25132 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 08:27:37 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:119,915,891
INFO 2026-06-08 08:27:37 MarkDuplicates Tracking 27135 as yet unmatched pairs. 945 records in RAM.
INFO 2026-06-08 08:27:39 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:121,181,315
INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 26935 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:27:40 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:147,275,396
INFO 2026-06-08 08:27:40 MarkDuplicates Tracking 27753 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:27:41 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:149,842,558
INFO 2026-06-08 08:27:41 MarkDuplicates Tracking 28286 as yet unmatched pairs. 146 records in RAM.
INFO 2026-06-08 08:27:43 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:151,404,880
INFO 2026-06-08 08:27:43 MarkDuplicates Tracking 29633 as yet unmatched pairs. 254 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:154,183,012
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 30615 as yet unmatched pairs. 304 records in RAM.
INFO 2026-06-08 08:27:46 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:155,250,356
INFO 2026-06-08 08:27:46 MarkDuplicates Tracking 31673 as yet unmatched pairs. 68 records in RAM.
INFO 2026-06-08 08:27:48 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:156,212,993
INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 33039 as yet unmatched pairs. 6 records in RAM.
INFO 2026-06-08 08:27:49 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:160,541,628
INFO 2026-06-08 08:27:49 MarkDuplicates Tracking 34533 as yet unmatched pairs. 106 records in RAM.
INFO 2026-06-08 08:27:51 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:168,226,112
INFO 2026-06-08 08:27:51 MarkDuplicates Tracking 35794 as yet unmatched pairs. 173 records in RAM.
INFO 2026-06-08 08:27:52 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:180,094,187
INFO 2026-06-08 08:27:52 MarkDuplicates Tracking 36897 as yet unmatched pairs. 84 records in RAM.
INFO 2026-06-08 08:27:53 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:186,351,362
INFO 2026-06-08 08:27:53 MarkDuplicates Tracking 38113 as yet unmatched pairs. 191 records in RAM.
INFO 2026-06-08 08:27:55 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:201,874,874
INFO 2026-06-08 08:27:55 MarkDuplicates Tracking 39147 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 08:27:56 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:204,619,689
INFO 2026-06-08 08:27:56 MarkDuplicates Tracking 40231 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 08:27:57 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:208,039,638
INFO 2026-06-08 08:27:57 MarkDuplicates Tracking 41390 as yet unmatched pairs. 28 records in RAM.
INFO 2026-06-08 08:27:59 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:225,412,547
INFO 2026-06-08 08:27:59 MarkDuplicates Tracking 42601 as yet unmatched pairs. 90 records in RAM.
INFO 2026-06-08 08:28:00 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:228,367,154
INFO 2026-06-08 08:28:00 MarkDuplicates Tracking 43911 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:28:01 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:236,831,990
INFO 2026-06-08 08:28:01 MarkDuplicates Tracking 45390 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:28:03 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr2:3,580,202
INFO 2026-06-08 08:28:03 MarkDuplicates Tracking 47558 as yet unmatched pairs. 47497 records in RAM.
INFO 2026-06-08 08:28:05 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr2:20,312,380
INFO 2026-06-08 08:28:05 MarkDuplicates Tracking 47987 as yet unmatched pairs. 47925 records in RAM.
INFO 2026-06-08 08:28:06 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr2:27,083,074
INFO 2026-06-08 08:28:06 MarkDuplicates Tracking 49345 as yet unmatched pairs. 49282 records in RAM.
INFO 2026-06-08 08:28:07 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr2:32,010,194
INFO 2026-06-08 08:28:07 MarkDuplicates Tracking 50685 as yet unmatched pairs. 50619 records in RAM.
INFO 2026-06-08 08:28:09 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:28:09 MarkDuplicates Tracking 327290 as yet unmatched pairs. 36875 records in RAM.
INFO 2026-06-08 08:28:11 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr2:36,476,950
INFO 2026-06-08 08:28:11 MarkDuplicates Tracking 465220 as yet unmatched pairs. 29563 records in RAM.
INFO 2026-06-08 08:28:13 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr2:43,224,624
INFO 2026-06-08 08:28:13 MarkDuplicates Tracking 464074 as yet unmatched pairs. 28416 records in RAM.
INFO 2026-06-08 08:28:15 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr2:53,895,008
INFO 2026-06-08 08:28:15 MarkDuplicates Tracking 462486 as yet unmatched pairs. 26828 records in RAM.
INFO 2026-06-08 08:28:16 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr2:61,314,643
INFO 2026-06-08 08:28:16 MarkDuplicates Tracking 461259 as yet unmatched pairs. 25598 records in RAM.
INFO 2026-06-08 08:28:17 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr2:70,991,850
INFO 2026-06-08 08:28:17 MarkDuplicates Tracking 460051 as yet unmatched pairs. 24390 records in RAM.
INFO 2026-06-08 08:28:19 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr2:74,178,712
INFO 2026-06-08 08:28:19 MarkDuplicates Tracking 458785 as yet unmatched pairs. 23124 records in RAM.
INFO 2026-06-08 08:28:20 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr2:86,753,538
INFO 2026-06-08 08:28:20 MarkDuplicates Tracking 457585 as yet unmatched pairs. 21924 records in RAM.
INFO 2026-06-08 08:28:21 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr2:96,864,025
INFO 2026-06-08 08:28:21 MarkDuplicates Tracking 456645 as yet unmatched pairs. 20982 records in RAM.
INFO 2026-06-08 08:28:23 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr2:105,881,366
INFO 2026-06-08 08:28:23 MarkDuplicates Tracking 455417 as yet unmatched pairs. 19754 records in RAM.
INFO 2026-06-08 08:28:24 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr2:108,771,707
INFO 2026-06-08 08:28:24 MarkDuplicates Tracking 455235 as yet unmatched pairs. 19572 records in RAM.
INFO 2026-06-08 08:28:25 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr2:112,389,924
INFO 2026-06-08 08:28:25 MarkDuplicates Tracking 454367 as yet unmatched pairs. 18703 records in RAM.
INFO 2026-06-08 08:28:27 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr2:128,160,536
INFO 2026-06-08 08:28:27 MarkDuplicates Tracking 453360 as yet unmatched pairs. 17695 records in RAM.
INFO 2026-06-08 08:28:28 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr2:149,570,150
INFO 2026-06-08 08:28:28 MarkDuplicates Tracking 452698 as yet unmatched pairs. 17033 records in RAM.
INFO 2026-06-08 08:28:29 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr2:168,163,785
INFO 2026-06-08 08:28:29 MarkDuplicates Tracking 451485 as yet unmatched pairs. 15820 records in RAM.
INFO 2026-06-08 08:28:31 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr2:178,544,462
INFO 2026-06-08 08:28:31 MarkDuplicates Tracking 450016 as yet unmatched pairs. 14351 records in RAM.
INFO 2026-06-08 08:28:32 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr2:188,995,764
INFO 2026-06-08 08:28:32 MarkDuplicates Tracking 449205 as yet unmatched pairs. 13539 records in RAM.
INFO 2026-06-08 08:28:34 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr2:197,398,465
INFO 2026-06-08 08:28:34 MarkDuplicates Tracking 447878 as yet unmatched pairs. 12211 records in RAM.
INFO 2026-06-08 08:28:36 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr2:206,056,833
INFO 2026-06-08 08:28:36 MarkDuplicates Tracking 446098 as yet unmatched pairs. 10431 records in RAM.
INFO 2026-06-08 08:28:37 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr2:215,382,257
INFO 2026-06-08 08:28:37 MarkDuplicates Tracking 445825 as yet unmatched pairs. 10155 records in RAM.
INFO 2026-06-08 08:28:39 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr2:216,679,014
INFO 2026-06-08 08:28:39 MarkDuplicates Tracking 443985 as yet unmatched pairs. 8315 records in RAM.
INFO 2026-06-08 08:28:40 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:218,108,683
INFO 2026-06-08 08:28:40 MarkDuplicates Tracking 442584 as yet unmatched pairs. 6913 records in RAM.
INFO 2026-06-08 08:28:42 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr2:219,426,000
INFO 2026-06-08 08:28:42 MarkDuplicates Tracking 441957 as yet unmatched pairs. 6286 records in RAM.
INFO 2026-06-08 08:28:43 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:229,814,269
INFO 2026-06-08 08:28:43 MarkDuplicates Tracking 439994 as yet unmatched pairs. 4319 records in RAM.
INFO 2026-06-08 08:28:45 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr2:236,581,492
INFO 2026-06-08 08:28:45 MarkDuplicates Tracking 438387 as yet unmatched pairs. 2712 records in RAM.
INFO 2026-06-08 08:28:46 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:239,961,166
INFO 2026-06-08 08:28:46 MarkDuplicates Tracking 437468 as yet unmatched pairs. 1791 records in RAM.
INFO 2026-06-08 08:28:47 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr2:241,742,527
INFO 2026-06-08 08:28:47 MarkDuplicates Tracking 435846 as yet unmatched pairs. 169 records in RAM.
INFO 2026-06-08 08:28:49 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr3:11,554,791
INFO 2026-06-08 08:28:49 MarkDuplicates Tracking 434579 as yet unmatched pairs. 27694 records in RAM.
INFO 2026-06-08 08:28:50 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr3:20,040,460
INFO 2026-06-08 08:28:50 MarkDuplicates Tracking 433302 as yet unmatched pairs. 26417 records in RAM.
INFO 2026-06-08 08:28:52 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr3:37,251,435
INFO 2026-06-08 08:28:52 MarkDuplicates Tracking 432042 as yet unmatched pairs. 25157 records in RAM.
INFO 2026-06-08 08:28:53 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr3:42,557,606
INFO 2026-06-08 08:28:53 MarkDuplicates Tracking 430940 as yet unmatched pairs. 24055 records in RAM.
INFO 2026-06-08 08:28:55 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr3:46,443,511
INFO 2026-06-08 08:28:55 MarkDuplicates Tracking 431478 as yet unmatched pairs. 24593 records in RAM.
INFO 2026-06-08 08:28:57 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr3:47,123,534
INFO 2026-06-08 08:28:57 MarkDuplicates Tracking 428754 as yet unmatched pairs. 21869 records in RAM.
INFO 2026-06-08 08:28:58 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr3:48,573,110
INFO 2026-06-08 08:28:58 MarkDuplicates Tracking 427291 as yet unmatched pairs. 20406 records in RAM.
INFO 2026-06-08 08:29:00 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr3:49,129,076
INFO 2026-06-08 08:29:00 MarkDuplicates Tracking 426050 as yet unmatched pairs. 19165 records in RAM.
INFO 2026-06-08 08:29:01 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr3:50,617,731
INFO 2026-06-08 08:29:01 MarkDuplicates Tracking 424074 as yet unmatched pairs. 17189 records in RAM.
INFO 2026-06-08 08:29:03 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr3:52,529,160
INFO 2026-06-08 08:29:03 MarkDuplicates Tracking 422797 as yet unmatched pairs. 15911 records in RAM.
INFO 2026-06-08 08:29:04 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr3:58,149,904
INFO 2026-06-08 08:29:04 MarkDuplicates Tracking 421602 as yet unmatched pairs. 14716 records in RAM.
INFO 2026-06-08 08:29:05 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr3:73,404,325
INFO 2026-06-08 08:29:05 MarkDuplicates Tracking 420225 as yet unmatched pairs. 13339 records in RAM.
INFO 2026-06-08 08:29:07 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr3:105,539,990
INFO 2026-06-08 08:29:07 MarkDuplicates Tracking 419171 as yet unmatched pairs. 12284 records in RAM.
INFO 2026-06-08 08:29:08 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr3:119,517,126
INFO 2026-06-08 08:29:08 MarkDuplicates Tracking 418165 as yet unmatched pairs. 11278 records in RAM.
INFO 2026-06-08 08:29:09 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr3:123,626,840
INFO 2026-06-08 08:29:09 MarkDuplicates Tracking 417279 as yet unmatched pairs. 10392 records in RAM.
INFO 2026-06-08 08:29:11 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr3:128,486,961
INFO 2026-06-08 08:29:11 MarkDuplicates Tracking 415700 as yet unmatched pairs. 8811 records in RAM.
INFO 2026-06-08 08:29:12 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr3:132,601,270
INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 414424 as yet unmatched pairs. 7528 records in RAM.
INFO 2026-06-08 08:29:14 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr3:143,848,167
INFO 2026-06-08 08:29:14 MarkDuplicates Tracking 413278 as yet unmatched pairs. 6381 records in RAM.
INFO 2026-06-08 08:29:15 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr3:159,764,822
INFO 2026-06-08 08:29:15 MarkDuplicates Tracking 412111 as yet unmatched pairs. 5211 records in RAM.
INFO 2026-06-08 08:29:17 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr3:180,986,964
INFO 2026-06-08 08:29:17 MarkDuplicates Tracking 411020 as yet unmatched pairs. 4119 records in RAM.
INFO 2026-06-08 08:29:19 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: chr3:184,999,717
INFO 2026-06-08 08:29:19 MarkDuplicates Tracking 409547 as yet unmatched pairs. 2644 records in RAM.
INFO 2026-06-08 08:29:20 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr3:194,137,952
INFO 2026-06-08 08:29:20 MarkDuplicates Tracking 409062 as yet unmatched pairs. 2156 records in RAM.
INFO 2026-06-08 08:29:21 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr3:195,977,100
INFO 2026-06-08 08:29:21 MarkDuplicates Tracking 407552 as yet unmatched pairs. 637 records in RAM.
INFO 2026-06-08 08:29:23 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr4:1,236,612
INFO 2026-06-08 08:29:23 MarkDuplicates Tracking 406663 as yet unmatched pairs. 15681 records in RAM.
INFO 2026-06-08 08:29:24 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr4:6,282,482
INFO 2026-06-08 08:29:24 MarkDuplicates Tracking 404434 as yet unmatched pairs. 13451 records in RAM.
INFO 2026-06-08 08:29:25 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr4:20,541,590
INFO 2026-06-08 08:29:25 MarkDuplicates Tracking 403256 as yet unmatched pairs. 12272 records in RAM.
INFO 2026-06-08 08:29:27 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr4:40,502,372
INFO 2026-06-08 08:29:27 MarkDuplicates Tracking 402012 as yet unmatched pairs. 11028 records in RAM.
INFO 2026-06-08 08:29:28 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr4:57,031,310
INFO 2026-06-08 08:29:28 MarkDuplicates Tracking 401525 as yet unmatched pairs. 10541 records in RAM.
INFO 2026-06-08 08:29:29 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr4:76,770,820
INFO 2026-06-08 08:29:30 MarkDuplicates Tracking 399761 as yet unmatched pairs. 8776 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr4:86,758,738
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 398705 as yet unmatched pairs. 7720 records in RAM.
INFO 2026-06-08 08:29:32 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr4:98,995,768
INFO 2026-06-08 08:29:32 MarkDuplicates Tracking 397439 as yet unmatched pairs. 6451 records in RAM.
INFO 2026-06-08 08:29:33 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr4:119,026,933
INFO 2026-06-08 08:29:33 MarkDuplicates Tracking 396777 as yet unmatched pairs. 5789 records in RAM.
INFO 2026-06-08 08:29:35 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr4:122,344,440
INFO 2026-06-08 08:29:35 MarkDuplicates Tracking 395144 as yet unmatched pairs. 4155 records in RAM.
INFO 2026-06-08 08:29:36 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr4:145,902,622
INFO 2026-06-08 08:29:36 MarkDuplicates Tracking 393892 as yet unmatched pairs. 2901 records in RAM.
INFO 2026-06-08 08:29:37 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr4:158,708,092
INFO 2026-06-08 08:29:37 MarkDuplicates Tracking 392620 as yet unmatched pairs. 1626 records in RAM.
INFO 2026-06-08 08:29:39 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr4:185,508,469
INFO 2026-06-08 08:29:39 MarkDuplicates Tracking 391625 as yet unmatched pairs. 631 records in RAM.
INFO 2026-06-08 08:29:41 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr5:10,394,769
INFO 2026-06-08 08:29:41 MarkDuplicates Tracking 390620 as yet unmatched pairs. 22710 records in RAM.
INFO 2026-06-08 08:29:42 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr5:31,401,505
INFO 2026-06-08 08:29:42 MarkDuplicates Tracking 388409 as yet unmatched pairs. 20493 records in RAM.
INFO 2026-06-08 08:29:44 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr5:40,834,496
INFO 2026-06-08 08:29:44 MarkDuplicates Tracking 387162 as yet unmatched pairs. 19246 records in RAM.
INFO 2026-06-08 08:29:45 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr5:58,974,648
INFO 2026-06-08 08:29:45 MarkDuplicates Tracking 386011 as yet unmatched pairs. 18094 records in RAM.
INFO 2026-06-08 08:29:46 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr5:71,643,664
INFO 2026-06-08 08:29:46 MarkDuplicates Tracking 385219 as yet unmatched pairs. 17301 records in RAM.
INFO 2026-06-08 08:29:48 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr5:80,070,315
INFO 2026-06-08 08:29:48 MarkDuplicates Tracking 384057 as yet unmatched pairs. 16139 records in RAM.
INFO 2026-06-08 08:29:49 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr5:96,695,880
INFO 2026-06-08 08:29:49 MarkDuplicates Tracking 383097 as yet unmatched pairs. 15168 records in RAM.
INFO 2026-06-08 08:29:50 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr5:119,178,040
INFO 2026-06-08 08:29:50 MarkDuplicates Tracking 381865 as yet unmatched pairs. 13936 records in RAM.
INFO 2026-06-08 08:29:52 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr5:133,022,842
INFO 2026-06-08 08:29:52 MarkDuplicates Tracking 380485 as yet unmatched pairs. 12556 records in RAM.
INFO 2026-06-08 08:29:53 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr5:138,847,026
INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 379629 as yet unmatched pairs. 11700 records in RAM.
INFO 2026-06-08 08:29:54 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr5:141,211,026
INFO 2026-06-08 08:29:54 MarkDuplicates Tracking 377984 as yet unmatched pairs. 10043 records in RAM.
INFO 2026-06-08 08:29:56 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr5:148,425,538
INFO 2026-06-08 08:29:56 MarkDuplicates Tracking 376821 as yet unmatched pairs. 8866 records in RAM.
INFO 2026-06-08 08:29:57 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,201
INFO 2026-06-08 08:29:57 MarkDuplicates Tracking 384511 as yet unmatched pairs. 16556 records in RAM.
INFO 2026-06-08 08:29:58 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr5:150,407,199
INFO 2026-06-08 08:29:58 MarkDuplicates Tracking 376631 as yet unmatched pairs. 8676 records in RAM.
INFO 2026-06-08 08:30:00 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr5:154,793,828
INFO 2026-06-08 08:30:00 MarkDuplicates Tracking 373224 as yet unmatched pairs. 5269 records in RAM.
INFO 2026-06-08 08:30:01 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr5:171,391,758
INFO 2026-06-08 08:30:01 MarkDuplicates Tracking 374237 as yet unmatched pairs. 6280 records in RAM.
INFO 2026-06-08 08:30:02 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr5:177,248,201
INFO 2026-06-08 08:30:02 MarkDuplicates Tracking 371021 as yet unmatched pairs. 3060 records in RAM.
INFO 2026-06-08 08:30:04 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr5:179,722,809
INFO 2026-06-08 08:30:04 MarkDuplicates Tracking 370025 as yet unmatched pairs. 2056 records in RAM.
INFO 2026-06-08 08:30:06 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr5:181,238,101
INFO 2026-06-08 08:30:06 MarkDuplicates Tracking 369404 as yet unmatched pairs. 1435 records in RAM.
INFO 2026-06-08 08:30:07 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr6:7,571,470
INFO 2026-06-08 08:30:07 MarkDuplicates Tracking 367315 as yet unmatched pairs. 23297 records in RAM.
INFO 2026-06-08 08:30:09 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr6:24,653,025
INFO 2026-06-08 08:30:09 MarkDuplicates Tracking 365898 as yet unmatched pairs. 21876 records in RAM.
INFO 2026-06-08 08:30:10 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr6:30,198,761
INFO 2026-06-08 08:30:10 MarkDuplicates Tracking 364704 as yet unmatched pairs. 20681 records in RAM.
INFO 2026-06-08 08:30:11 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr6:31,356,414
INFO 2026-06-08 08:30:11 MarkDuplicates Tracking 363364 as yet unmatched pairs. 19341 records in RAM.
INFO 2026-06-08 08:30:13 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr6:31,816,920
INFO 2026-06-08 08:30:13 MarkDuplicates Tracking 362162 as yet unmatched pairs. 18138 records in RAM.
INFO 2026-06-08 08:30:14 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr6:31,997,247
INFO 2026-06-08 08:30:14 MarkDuplicates Tracking 362225 as yet unmatched pairs. 18201 records in RAM.
INFO 2026-06-08 08:30:15 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr6:32,519,395
INFO 2026-06-08 08:30:15 MarkDuplicates Tracking 360146 as yet unmatched pairs. 16122 records in RAM.
INFO 2026-06-08 08:30:17 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr6:33,301,747
INFO 2026-06-08 08:30:17 MarkDuplicates Tracking 360147 as yet unmatched pairs. 16122 records in RAM.
INFO 2026-06-08 08:30:18 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr6:35,468,964
INFO 2026-06-08 08:30:18 MarkDuplicates Tracking 358254 as yet unmatched pairs. 14229 records in RAM.
INFO 2026-06-08 08:30:19 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr6:42,268,908
INFO 2026-06-08 08:30:19 MarkDuplicates Tracking 356645 as yet unmatched pairs. 12618 records in RAM.
INFO 2026-06-08 08:30:21 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr6:44,255,010
INFO 2026-06-08 08:30:21 MarkDuplicates Tracking 355328 as yet unmatched pairs. 11301 records in RAM.
INFO 2026-06-08 08:30:22 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr6:66,484,914
INFO 2026-06-08 08:30:22 MarkDuplicates Tracking 354156 as yet unmatched pairs. 10129 records in RAM.
INFO 2026-06-08 08:30:24 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr6:87,562,660
INFO 2026-06-08 08:30:24 MarkDuplicates Tracking 353107 as yet unmatched pairs. 9075 records in RAM.
INFO 2026-06-08 08:30:25 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr6:108,561,170
INFO 2026-06-08 08:30:25 MarkDuplicates Tracking 352335 as yet unmatched pairs. 8301 records in RAM.
INFO 2026-06-08 08:30:26 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr6:118,960,796
INFO 2026-06-08 08:30:26 MarkDuplicates Tracking 350595 as yet unmatched pairs. 6561 records in RAM.
INFO 2026-06-08 08:30:28 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr6:136,614,159
INFO 2026-06-08 08:30:28 MarkDuplicates Tracking 349463 as yet unmatched pairs. 5429 records in RAM.
INFO 2026-06-08 08:30:29 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr6:144,678,486
INFO 2026-06-08 08:30:29 MarkDuplicates Tracking 348292 as yet unmatched pairs. 4258 records in RAM.
INFO 2026-06-08 08:30:31 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr6:152,329,736
INFO 2026-06-08 08:30:31 MarkDuplicates Tracking 346966 as yet unmatched pairs. 2932 records in RAM.
INFO 2026-06-08 08:30:32 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr6:159,692,562
INFO 2026-06-08 08:30:32 MarkDuplicates Tracking 347056 as yet unmatched pairs. 3022 records in RAM.
INFO 2026-06-08 08:30:33 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr6:170,318,673
INFO 2026-06-08 08:30:33 MarkDuplicates Tracking 344290 as yet unmatched pairs. 256 records in RAM.
INFO 2026-06-08 08:30:35 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr7:5,199,608
INFO 2026-06-08 08:30:35 MarkDuplicates Tracking 342423 as yet unmatched pairs. 22882 records in RAM.
INFO 2026-06-08 08:30:36 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,575
INFO 2026-06-08 08:30:36 MarkDuplicates Tracking 343741 as yet unmatched pairs. 24200 records in RAM.
INFO 2026-06-08 08:30:37 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr7:18,591,509
INFO 2026-06-08 08:30:37 MarkDuplicates Tracking 339817 as yet unmatched pairs. 20276 records in RAM.
INFO 2026-06-08 08:30:39 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr7:35,832,875
INFO 2026-06-08 08:30:39 MarkDuplicates Tracking 338266 as yet unmatched pairs. 18725 records in RAM.
INFO 2026-06-08 08:30:40 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr7:44,386,024
INFO 2026-06-08 08:30:40 MarkDuplicates Tracking 337069 as yet unmatched pairs. 17528 records in RAM.
INFO 2026-06-08 08:30:42 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr7:56,104,341
INFO 2026-06-08 08:30:42 MarkDuplicates Tracking 335490 as yet unmatched pairs. 15948 records in RAM.
INFO 2026-06-08 08:30:43 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr7:73,693,990
INFO 2026-06-08 08:30:43 MarkDuplicates Tracking 334600 as yet unmatched pairs. 15057 records in RAM.
INFO 2026-06-08 08:30:44 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr7:75,497,885
INFO 2026-06-08 08:30:44 MarkDuplicates Tracking 333494 as yet unmatched pairs. 13951 records in RAM.
INFO 2026-06-08 08:30:45 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr7:88,210,029
INFO 2026-06-08 08:30:45 MarkDuplicates Tracking 332525 as yet unmatched pairs. 12981 records in RAM.
INFO 2026-06-08 08:30:47 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr7:94,413,725
INFO 2026-06-08 08:30:47 MarkDuplicates Tracking 331781 as yet unmatched pairs. 12237 records in RAM.
INFO 2026-06-08 08:30:48 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr7:99,670,224
INFO 2026-06-08 08:30:48 MarkDuplicates Tracking 329832 as yet unmatched pairs. 10288 records in RAM.
INFO 2026-06-08 08:30:49 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr7:100,813,683
INFO 2026-06-08 08:30:49 MarkDuplicates Tracking 328634 as yet unmatched pairs. 9088 records in RAM.
INFO 2026-06-08 08:30:51 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr7:102,201,725
INFO 2026-06-08 08:30:51 MarkDuplicates Tracking 327623 as yet unmatched pairs. 8076 records in RAM.
INFO 2026-06-08 08:30:52 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr7:107,951,129
INFO 2026-06-08 08:30:52 MarkDuplicates Tracking 326738 as yet unmatched pairs. 7189 records in RAM.
INFO 2026-06-08 08:30:54 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr7:128,074,613
INFO 2026-06-08 08:30:54 MarkDuplicates Tracking 326191 as yet unmatched pairs. 6641 records in RAM.
INFO 2026-06-08 08:30:55 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr7:134,928,818
INFO 2026-06-08 08:30:55 MarkDuplicates Tracking 324987 as yet unmatched pairs. 5437 records in RAM.
INFO 2026-06-08 08:30:56 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr7:139,596,730
INFO 2026-06-08 08:30:56 MarkDuplicates Tracking 323577 as yet unmatched pairs. 4026 records in RAM.
INFO 2026-06-08 08:30:58 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr7:144,284,739
INFO 2026-06-08 08:30:58 MarkDuplicates Tracking 322203 as yet unmatched pairs. 2652 records in RAM.
INFO 2026-06-08 08:30:59 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr7:151,218,099
INFO 2026-06-08 08:30:59 MarkDuplicates Tracking 320770 as yet unmatched pairs. 1216 records in RAM.
INFO 2026-06-08 08:31:00 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr8:7,266,811
INFO 2026-06-08 08:31:00 MarkDuplicates Tracking 319440 as yet unmatched pairs. 19622 records in RAM.
INFO 2026-06-08 08:31:02 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr8:22,080,821
INFO 2026-06-08 08:31:02 MarkDuplicates Tracking 318324 as yet unmatched pairs. 18505 records in RAM.
INFO 2026-06-08 08:31:03 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr8:25,323,848
INFO 2026-06-08 08:31:03 MarkDuplicates Tracking 317111 as yet unmatched pairs. 17292 records in RAM.
INFO 2026-06-08 08:31:05 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr8:37,837,766
INFO 2026-06-08 08:31:05 MarkDuplicates Tracking 315957 as yet unmatched pairs. 16137 records in RAM.
INFO 2026-06-08 08:31:06 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr8:39,090,146
INFO 2026-06-08 08:31:06 MarkDuplicates Tracking 314705 as yet unmatched pairs. 14884 records in RAM.
INFO 2026-06-08 08:31:07 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr8:53,988,162
INFO 2026-06-08 08:31:07 MarkDuplicates Tracking 312876 as yet unmatched pairs. 13044 records in RAM.
INFO 2026-06-08 08:31:09 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr8:70,586,903
INFO 2026-06-08 08:31:09 MarkDuplicates Tracking 311985 as yet unmatched pairs. 12153 records in RAM.
INFO 2026-06-08 08:31:10 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr8:94,391,770
INFO 2026-06-08 08:31:10 MarkDuplicates Tracking 310325 as yet unmatched pairs. 10493 records in RAM.
INFO 2026-06-08 08:31:12 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr8:100,709,702
INFO 2026-06-08 08:31:12 MarkDuplicates Tracking 310598 as yet unmatched pairs. 10766 records in RAM.
INFO 2026-06-08 08:31:13 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr8:116,657,215
INFO 2026-06-08 08:31:13 MarkDuplicates Tracking 308430 as yet unmatched pairs. 8598 records in RAM.
INFO 2026-06-08 08:31:15 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr8:133,238,882
INFO 2026-06-08 08:31:15 MarkDuplicates Tracking 307542 as yet unmatched pairs. 7709 records in RAM.
INFO 2026-06-08 08:31:17 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr8:143,538,155
INFO 2026-06-08 08:31:17 MarkDuplicates Tracking 305400 as yet unmatched pairs. 5566 records in RAM.
INFO 2026-06-08 08:31:18 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,915
INFO 2026-06-08 08:31:18 MarkDuplicates Tracking 304353 as yet unmatched pairs. 4519 records in RAM.
INFO 2026-06-08 08:31:19 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,879
INFO 2026-06-08 08:31:19 MarkDuplicates Tracking 303699 as yet unmatched pairs. 3865 records in RAM.
INFO 2026-06-08 08:31:20 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr8:143,923,782
INFO 2026-06-08 08:31:20 MarkDuplicates Tracking 302483 as yet unmatched pairs. 2649 records in RAM.
INFO 2026-06-08 08:31:22 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr8:144,397,269
INFO 2026-06-08 08:31:22 MarkDuplicates Tracking 300968 as yet unmatched pairs. 1132 records in RAM.
INFO 2026-06-08 08:31:23 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr9:4,662,640
INFO 2026-06-08 08:31:23 MarkDuplicates Tracking 299467 as yet unmatched pairs. 21036 records in RAM.
INFO 2026-06-08 08:31:25 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr9:19,378,905
INFO 2026-06-08 08:31:25 MarkDuplicates Tracking 298915 as yet unmatched pairs. 20484 records in RAM.
INFO 2026-06-08 08:31:26 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr9:35,101,526
INFO 2026-06-08 08:31:26 MarkDuplicates Tracking 296898 as yet unmatched pairs. 18466 records in RAM.
INFO 2026-06-08 08:31:28 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr9:36,204,098
INFO 2026-06-08 08:31:28 MarkDuplicates Tracking 295818 as yet unmatched pairs. 17386 records in RAM.
INFO 2026-06-08 08:31:29 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr9:76,705,630
INFO 2026-06-08 08:31:29 MarkDuplicates Tracking 294811 as yet unmatched pairs. 16379 records in RAM.
INFO 2026-06-08 08:31:31 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr9:89,002,241
INFO 2026-06-08 08:31:31 MarkDuplicates Tracking 293435 as yet unmatched pairs. 15003 records in RAM.
INFO 2026-06-08 08:31:32 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr9:95,447,077
INFO 2026-06-08 08:31:32 MarkDuplicates Tracking 292139 as yet unmatched pairs. 13706 records in RAM.
INFO 2026-06-08 08:31:33 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr9:107,306,392
INFO 2026-06-08 08:31:33 MarkDuplicates Tracking 291228 as yet unmatched pairs. 12795 records in RAM.
INFO 2026-06-08 08:31:35 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr9:114,357,987
INFO 2026-06-08 08:31:35 MarkDuplicates Tracking 289503 as yet unmatched pairs. 11070 records in RAM.
INFO 2026-06-08 08:31:36 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr9:121,341,188
INFO 2026-06-08 08:31:36 MarkDuplicates Tracking 288348 as yet unmatched pairs. 9915 records in RAM.
INFO 2026-06-08 08:31:38 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr9:127,807,677
INFO 2026-06-08 08:31:38 MarkDuplicates Tracking 287069 as yet unmatched pairs. 8634 records in RAM.
INFO 2026-06-08 08:31:39 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr9:129,001,543
INFO 2026-06-08 08:31:39 MarkDuplicates Tracking 285649 as yet unmatched pairs. 7214 records in RAM.
INFO 2026-06-08 08:31:40 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr9:131,146,200
INFO 2026-06-08 08:31:40 MarkDuplicates Tracking 284548 as yet unmatched pairs. 6107 records in RAM.
INFO 2026-06-08 08:31:42 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr9:133,350,286
INFO 2026-06-08 08:31:42 MarkDuplicates Tracking 283715 as yet unmatched pairs. 5273 records in RAM.
INFO 2026-06-08 08:31:44 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr9:136,474,266
INFO 2026-06-08 08:31:44 MarkDuplicates Tracking 281914 as yet unmatched pairs. 3471 records in RAM.
INFO 2026-06-08 08:31:45 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr9:137,039,971
INFO 2026-06-08 08:31:45 MarkDuplicates Tracking 280823 as yet unmatched pairs. 2379 records in RAM.
INFO 2026-06-08 08:31:47 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr10:472,494
INFO 2026-06-08 08:31:47 MarkDuplicates Tracking 278479 as yet unmatched pairs. 16824 records in RAM.
INFO 2026-06-08 08:31:48 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr10:15,128,429
INFO 2026-06-08 08:31:48 MarkDuplicates Tracking 277227 as yet unmatched pairs. 15572 records in RAM.
INFO 2026-06-08 08:31:50 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr10:28,616,277
INFO 2026-06-08 08:31:50 MarkDuplicates Tracking 276257 as yet unmatched pairs. 14602 records in RAM.
INFO 2026-06-08 08:31:51 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr10:33,256,409
INFO 2026-06-08 08:31:51 MarkDuplicates Tracking 275161 as yet unmatched pairs. 13506 records in RAM.
INFO 2026-06-08 08:31:52 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr10:46,039,024
INFO 2026-06-08 08:31:52 MarkDuplicates Tracking 275438 as yet unmatched pairs. 13783 records in RAM.
INFO 2026-06-08 08:31:54 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr10:60,083,562
INFO 2026-06-08 08:31:54 MarkDuplicates Tracking 273392 as yet unmatched pairs. 11736 records in RAM.
INFO 2026-06-08 08:31:55 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr10:72,196,813
INFO 2026-06-08 08:31:55 MarkDuplicates Tracking 271446 as yet unmatched pairs. 9784 records in RAM.
INFO 2026-06-08 08:31:57 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr10:76,949,196
INFO 2026-06-08 08:31:57 MarkDuplicates Tracking 270507 as yet unmatched pairs. 8845 records in RAM.
INFO 2026-06-08 08:31:58 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr10:87,009,798
INFO 2026-06-08 08:31:58 MarkDuplicates Tracking 269185 as yet unmatched pairs. 7523 records in RAM.
INFO 2026-06-08 08:32:00 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr10:93,452,069
INFO 2026-06-08 08:32:00 MarkDuplicates Tracking 268190 as yet unmatched pairs. 6528 records in RAM.
INFO 2026-06-08 08:32:01 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr10:99,698,590
INFO 2026-06-08 08:32:01 MarkDuplicates Tracking 266882 as yet unmatched pairs. 5220 records in RAM.
INFO 2026-06-08 08:32:03 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr10:102,657,321
INFO 2026-06-08 08:32:03 MarkDuplicates Tracking 265352 as yet unmatched pairs. 3690 records in RAM.
INFO 2026-06-08 08:32:04 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr10:116,940,487
INFO 2026-06-08 08:32:04 MarkDuplicates Tracking 264565 as yet unmatched pairs. 2900 records in RAM.
INFO 2026-06-08 08:32:06 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr10:124,789,042
INFO 2026-06-08 08:32:06 MarkDuplicates Tracking 262852 as yet unmatched pairs. 1187 records in RAM.
INFO 2026-06-08 08:32:07 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr11:315,070
INFO 2026-06-08 08:32:07 MarkDuplicates Tracking 261843 as yet unmatched pairs. 32826 records in RAM.
INFO 2026-06-08 08:32:09 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr11:925,989
INFO 2026-06-08 08:32:09 MarkDuplicates Tracking 259459 as yet unmatched pairs. 30441 records in RAM.
INFO 2026-06-08 08:32:11 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr11:5,664,956
INFO 2026-06-08 08:32:11 MarkDuplicates Tracking 258176 as yet unmatched pairs. 29158 records in RAM.
INFO 2026-06-08 08:32:12 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr11:9,059,308
INFO 2026-06-08 08:32:12 MarkDuplicates Tracking 256940 as yet unmatched pairs. 27921 records in RAM.
INFO 2026-06-08 08:32:14 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr11:14,481,024
INFO 2026-06-08 08:32:14 MarkDuplicates Tracking 255638 as yet unmatched pairs. 26619 records in RAM.
INFO 2026-06-08 08:32:15 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr11:33,353,319
INFO 2026-06-08 08:32:15 MarkDuplicates Tracking 254760 as yet unmatched pairs. 25741 records in RAM.
INFO 2026-06-08 08:32:17 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr11:46,320,331
INFO 2026-06-08 08:32:17 MarkDuplicates Tracking 253467 as yet unmatched pairs. 24447 records in RAM.
INFO 2026-06-08 08:32:19 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr11:57,313,034
INFO 2026-06-08 08:32:19 MarkDuplicates Tracking 252090 as yet unmatched pairs. 23070 records in RAM.
INFO 2026-06-08 08:32:20 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr11:61,131,865
INFO 2026-06-08 08:32:20 MarkDuplicates Tracking 250648 as yet unmatched pairs. 21627 records in RAM.
INFO 2026-06-08 08:32:22 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr11:62,522,931
INFO 2026-06-08 08:32:22 MarkDuplicates Tracking 250021 as yet unmatched pairs. 21000 records in RAM.
INFO 2026-06-08 08:32:23 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr11:62,533,198
INFO 2026-06-08 08:32:23 MarkDuplicates Tracking 248497 as yet unmatched pairs. 19476 records in RAM.
INFO 2026-06-08 08:32:25 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr11:63,818,826
INFO 2026-06-08 08:32:25 MarkDuplicates Tracking 246950 as yet unmatched pairs. 17929 records in RAM.
INFO 2026-06-08 08:32:26 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr11:65,120,635
INFO 2026-06-08 08:32:26 MarkDuplicates Tracking 245704 as yet unmatched pairs. 16683 records in RAM.
INFO 2026-06-08 08:32:28 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr11:65,646,573
INFO 2026-06-08 08:32:28 MarkDuplicates Tracking 244067 as yet unmatched pairs. 15046 records in RAM.
INFO 2026-06-08 08:32:29 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr11:66,669,266
INFO 2026-06-08 08:32:29 MarkDuplicates Tracking 242646 as yet unmatched pairs. 13624 records in RAM.
INFO 2026-06-08 08:32:31 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr11:68,158,694
INFO 2026-06-08 08:32:31 MarkDuplicates Tracking 241111 as yet unmatched pairs. 12087 records in RAM.
INFO 2026-06-08 08:32:32 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr11:72,007,289
INFO 2026-06-08 08:32:32 MarkDuplicates Tracking 240005 as yet unmatched pairs. 10981 records in RAM.
INFO 2026-06-08 08:32:34 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr11:73,362,664
INFO 2026-06-08 08:32:34 MarkDuplicates Tracking 238391 as yet unmatched pairs. 9367 records in RAM.
INFO 2026-06-08 08:32:35 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr11:78,280,808
INFO 2026-06-08 08:32:35 MarkDuplicates Tracking 237026 as yet unmatched pairs. 8002 records in RAM.
INFO 2026-06-08 08:32:37 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr11:102,114,253
INFO 2026-06-08 08:32:37 MarkDuplicates Tracking 236654 as yet unmatched pairs. 7628 records in RAM.
INFO 2026-06-08 08:32:38 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr11:114,062,402
INFO 2026-06-08 08:32:38 MarkDuplicates Tracking 235439 as yet unmatched pairs. 6413 records in RAM.
INFO 2026-06-08 08:32:40 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr11:117,986,418
INFO 2026-06-08 08:32:40 MarkDuplicates Tracking 233160 as yet unmatched pairs. 4134 records in RAM.
INFO 2026-06-08 08:32:41 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr11:119,052,089
INFO 2026-06-08 08:32:41 MarkDuplicates Tracking 231796 as yet unmatched pairs. 2770 records in RAM.
INFO 2026-06-08 08:32:43 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr11:125,609,532
INFO 2026-06-08 08:32:43 MarkDuplicates Tracking 230645 as yet unmatched pairs. 1619 records in RAM.
INFO 2026-06-08 08:32:44 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr11:134,216,968
INFO 2026-06-08 08:32:44 MarkDuplicates Tracking 229945 as yet unmatched pairs. 918 records in RAM.
INFO 2026-06-08 08:32:46 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr12:4,911,618
INFO 2026-06-08 08:32:46 MarkDuplicates Tracking 228011 as yet unmatched pairs. 26483 records in RAM.
INFO 2026-06-08 08:32:47 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr12:6,937,268
INFO 2026-06-08 08:32:47 MarkDuplicates Tracking 226940 as yet unmatched pairs. 25412 records in RAM.
INFO 2026-06-08 08:32:49 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr12:9,068,754
INFO 2026-06-08 08:32:49 MarkDuplicates Tracking 226064 as yet unmatched pairs. 24536 records in RAM.
INFO 2026-06-08 08:32:50 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr12:14,424,527
INFO 2026-06-08 08:32:50 MarkDuplicates Tracking 224423 as yet unmatched pairs. 22893 records in RAM.
INFO 2026-06-08 08:32:52 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr12:30,661,162
INFO 2026-06-08 08:32:52 MarkDuplicates Tracking 222866 as yet unmatched pairs. 21336 records in RAM.
INFO 2026-06-08 08:32:54 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr12:48,667,693
INFO 2026-06-08 08:32:54 MarkDuplicates Tracking 221692 as yet unmatched pairs. 20162 records in RAM.
INFO 2026-06-08 08:32:55 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr12:49,631,886
INFO 2026-06-08 08:32:55 MarkDuplicates Tracking 220546 as yet unmatched pairs. 19016 records in RAM.
INFO 2026-06-08 08:32:57 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr12:52,901,932
INFO 2026-06-08 08:32:57 MarkDuplicates Tracking 219371 as yet unmatched pairs. 17841 records in RAM.
INFO 2026-06-08 08:32:59 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr12:53,665,398
INFO 2026-06-08 08:32:59 MarkDuplicates Tracking 218717 as yet unmatched pairs. 17187 records in RAM.
INFO 2026-06-08 08:33:00 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr12:56,080,260
INFO 2026-06-08 08:33:00 MarkDuplicates Tracking 217059 as yet unmatched pairs. 15529 records in RAM.
INFO 2026-06-08 08:33:02 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr12:56,664,776
INFO 2026-06-08 08:33:02 MarkDuplicates Tracking 216074 as yet unmatched pairs. 14544 records in RAM.
INFO 2026-06-08 08:33:03 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr12:57,184,348
INFO 2026-06-08 08:33:03 MarkDuplicates Tracking 214688 as yet unmatched pairs. 13157 records in RAM.
INFO 2026-06-08 08:33:05 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr12:58,919,949
INFO 2026-06-08 08:33:05 MarkDuplicates Tracking 213345 as yet unmatched pairs. 11814 records in RAM.
INFO 2026-06-08 08:33:06 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr12:76,030,818
INFO 2026-06-08 08:33:06 MarkDuplicates Tracking 212356 as yet unmatched pairs. 10824 records in RAM.
INFO 2026-06-08 08:33:58 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 51s. Last read position: chr12:96,035,409
INFO 2026-06-08 08:33:58 MarkDuplicates Tracking 211143 as yet unmatched pairs. 9605 records in RAM.
INFO 2026-06-08 08:34:00 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr12:106,138,439
INFO 2026-06-08 08:34:00 MarkDuplicates Tracking 209705 as yet unmatched pairs. 8166 records in RAM.
INFO 2026-06-08 08:34:01 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr12:111,598,924
INFO 2026-06-08 08:34:01 MarkDuplicates Tracking 208356 as yet unmatched pairs. 6816 records in RAM.
INFO 2026-06-08 08:34:03 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr12:113,948,911
INFO 2026-06-08 08:34:03 MarkDuplicates Tracking 207024 as yet unmatched pairs. 5484 records in RAM.
INFO 2026-06-08 08:34:04 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr12:120,534,738
INFO 2026-06-08 08:34:04 MarkDuplicates Tracking 205986 as yet unmatched pairs. 4445 records in RAM.
INFO 2026-06-08 08:34:06 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr12:122,982,498
INFO 2026-06-08 08:34:06 MarkDuplicates Tracking 204392 as yet unmatched pairs. 2851 records in RAM.
INFO 2026-06-08 08:34:07 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr12:130,875,888
INFO 2026-06-08 08:34:07 MarkDuplicates Tracking 203268 as yet unmatched pairs. 1727 records in RAM.
INFO 2026-06-08 08:34:09 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr13:19,734,404
INFO 2026-06-08 08:34:09 MarkDuplicates Tracking 201522 as yet unmatched pairs. 7246 records in RAM.
INFO 2026-06-08 08:34:10 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr13:30,631,318
INFO 2026-06-08 08:34:10 MarkDuplicates Tracking 200589 as yet unmatched pairs. 6312 records in RAM.
INFO 2026-06-08 08:34:12 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr13:44,545,145
INFO 2026-06-08 08:34:12 MarkDuplicates Tracking 199480 as yet unmatched pairs. 5201 records in RAM.
INFO 2026-06-08 08:34:13 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 1s. Last read position: chr13:51,365,742
INFO 2026-06-08 08:34:13 MarkDuplicates Tracking 198324 as yet unmatched pairs. 4045 records in RAM.
INFO 2026-06-08 08:34:15 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr13:95,161,334
INFO 2026-06-08 08:34:15 MarkDuplicates Tracking 197746 as yet unmatched pairs. 3458 records in RAM.
INFO 2026-06-08 08:34:16 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr13:110,176,456
INFO 2026-06-08 08:34:16 MarkDuplicates Tracking 196007 as yet unmatched pairs. 1717 records in RAM.
INFO 2026-06-08 08:34:18 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr13:113,495,738
INFO 2026-06-08 08:34:18 MarkDuplicates Tracking 194696 as yet unmatched pairs. 406 records in RAM.
INFO 2026-06-08 08:34:19 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr14:21,431,538
INFO 2026-06-08 08:34:19 MarkDuplicates Tracking 193629 as yet unmatched pairs. 16579 records in RAM.
INFO 2026-06-08 08:34:21 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr14:24,150,194
INFO 2026-06-08 08:34:21 MarkDuplicates Tracking 192186 as yet unmatched pairs. 15135 records in RAM.
INFO 2026-06-08 08:34:23 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr14:33,925,908
INFO 2026-06-08 08:34:23 MarkDuplicates Tracking 190959 as yet unmatched pairs. 13908 records in RAM.
INFO 2026-06-08 08:34:24 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 1s. Last read position: chr14:49,862,675
INFO 2026-06-08 08:34:24 MarkDuplicates Tracking 190072 as yet unmatched pairs. 13020 records in RAM.
INFO 2026-06-08 08:34:26 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr14:60,118,481
INFO 2026-06-08 08:34:26 MarkDuplicates Tracking 188422 as yet unmatched pairs. 11370 records in RAM.
INFO 2026-06-08 08:34:27 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 1s. Last read position: chr14:68,594,557
INFO 2026-06-08 08:34:27 MarkDuplicates Tracking 186848 as yet unmatched pairs. 9796 records in RAM.
INFO 2026-06-08 08:34:29 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr14:73,277,059
INFO 2026-06-08 08:34:29 MarkDuplicates Tracking 185687 as yet unmatched pairs. 8635 records in RAM.
INFO 2026-06-08 08:34:30 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 1s. Last read position: chr14:77,026,335
INFO 2026-06-08 08:34:30 MarkDuplicates Tracking 184467 as yet unmatched pairs. 7415 records in RAM.
INFO 2026-06-08 08:34:32 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr14:93,246,033
INFO 2026-06-08 08:34:32 MarkDuplicates Tracking 183052 as yet unmatched pairs. 6000 records in RAM.
INFO 2026-06-08 08:34:33 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr14:100,538,397
INFO 2026-06-08 08:34:33 MarkDuplicates Tracking 181799 as yet unmatched pairs. 4745 records in RAM.
INFO 2026-06-08 08:34:35 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr14:103,340,977
INFO 2026-06-08 08:34:35 MarkDuplicates Tracking 180330 as yet unmatched pairs. 3276 records in RAM.
INFO 2026-06-08 08:34:37 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 1s. Last read position: chr14:105,368,455
INFO 2026-06-08 08:34:37 MarkDuplicates Tracking 178981 as yet unmatched pairs. 1927 records in RAM.
INFO 2026-06-08 08:34:38 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr14:105,741,565
INFO 2026-06-08 08:34:38 MarkDuplicates Tracking 180136 as yet unmatched pairs. 3082 records in RAM.
INFO 2026-06-08 08:34:39 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 1s. Last read position: chr14:105,855,642
INFO 2026-06-08 08:34:39 MarkDuplicates Tracking 177363 as yet unmatched pairs. 309 records in RAM.
INFO 2026-06-08 08:34:41 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 1s. Last read position: chr15:29,720,416
INFO 2026-06-08 08:34:41 MarkDuplicates Tracking 176147 as yet unmatched pairs. 14354 records in RAM.
INFO 2026-06-08 08:34:42 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 1s. Last read position: chr15:39,594,101
INFO 2026-06-08 08:34:42 MarkDuplicates Tracking 175335 as yet unmatched pairs. 13542 records in RAM.
INFO 2026-06-08 08:34:44 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr15:42,528,304
INFO 2026-06-08 08:34:44 MarkDuplicates Tracking 173907 as yet unmatched pairs. 12114 records in RAM.
INFO 2026-06-08 08:34:45 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 1s. Last read position: chr15:44,715,553
INFO 2026-06-08 08:34:45 MarkDuplicates Tracking 173676 as yet unmatched pairs. 11882 records in RAM.
INFO 2026-06-08 08:34:47 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 1s. Last read position: chr15:56,007,058
INFO 2026-06-08 08:34:47 MarkDuplicates Tracking 171722 as yet unmatched pairs. 9927 records in RAM.
INFO 2026-06-08 08:34:48 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 1s. Last read position: chr15:63,042,941
INFO 2026-06-08 08:34:48 MarkDuplicates Tracking 171238 as yet unmatched pairs. 9443 records in RAM.
INFO 2026-06-08 08:34:50 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 1s. Last read position: chr15:65,715,477
INFO 2026-06-08 08:34:50 MarkDuplicates Tracking 169313 as yet unmatched pairs. 7518 records in RAM.
INFO 2026-06-08 08:34:52 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 1s. Last read position: chr15:72,256,560
INFO 2026-06-08 08:34:52 MarkDuplicates Tracking 168201 as yet unmatched pairs. 6406 records in RAM.
INFO 2026-06-08 08:34:53 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr15:75,361,174
INFO 2026-06-08 08:34:53 MarkDuplicates Tracking 167045 as yet unmatched pairs. 5249 records in RAM.
INFO 2026-06-08 08:34:55 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr15:82,849,718
INFO 2026-06-08 08:34:55 MarkDuplicates Tracking 165544 as yet unmatched pairs. 3725 records in RAM.
INFO 2026-06-08 08:34:56 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 1s. Last read position: chr15:89,835,589
INFO 2026-06-08 08:34:56 MarkDuplicates Tracking 164260 as yet unmatched pairs. 2440 records in RAM.
INFO 2026-06-08 08:34:58 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 1s. Last read position: chr15:99,113,620
INFO 2026-06-08 08:34:58 MarkDuplicates Tracking 163906 as yet unmatched pairs. 2086 records in RAM.
INFO 2026-06-08 08:35:00 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 1s. Last read position: chr16:264,628
INFO 2026-06-08 08:35:00 MarkDuplicates Tracking 161799 as yet unmatched pairs. 30147 records in RAM.
INFO 2026-06-08 08:35:01 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr16:1,344,270
INFO 2026-06-08 08:35:01 MarkDuplicates Tracking 160231 as yet unmatched pairs. 28579 records in RAM.
INFO 2026-06-08 08:35:03 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr16:2,092,551
INFO 2026-06-08 08:35:03 MarkDuplicates Tracking 158455 as yet unmatched pairs. 26803 records in RAM.
INFO 2026-06-08 08:35:05 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr16:2,762,315
INFO 2026-06-08 08:35:05 MarkDuplicates Tracking 156879 as yet unmatched pairs. 25226 records in RAM.
INFO 2026-06-08 08:35:06 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr16:3,728,351
INFO 2026-06-08 08:35:06 MarkDuplicates Tracking 155454 as yet unmatched pairs. 23801 records in RAM.
INFO 2026-06-08 08:35:08 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 1s. Last read position: chr16:10,907,187
INFO 2026-06-08 08:35:08 MarkDuplicates Tracking 154258 as yet unmatched pairs. 22604 records in RAM.
INFO 2026-06-08 08:35:09 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 1s. Last read position: chr16:14,919,062
INFO 2026-06-08 08:35:09 MarkDuplicates Tracking 153115 as yet unmatched pairs. 21461 records in RAM.
INFO 2026-06-08 08:35:10 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr16:15,133,852
INFO 2026-06-08 08:35:10 MarkDuplicates Tracking 152511 as yet unmatched pairs. 20857 records in RAM.
INFO 2026-06-08 08:35:12 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 1s. Last read position: chr16:15,720,929
INFO 2026-06-08 08:35:12 MarkDuplicates Tracking 152349 as yet unmatched pairs. 20695 records in RAM.
INFO 2026-06-08 08:35:14 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr16:15,750,240
INFO 2026-06-08 08:35:14 MarkDuplicates Tracking 150711 as yet unmatched pairs. 19057 records in RAM.
INFO 2026-06-08 08:35:16 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr16:16,273,992
INFO 2026-06-08 08:35:16 MarkDuplicates Tracking 148717 as yet unmatched pairs. 17063 records in RAM.
INFO 2026-06-08 08:35:17 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 1s. Last read position: chr16:16,361,314
INFO 2026-06-08 08:35:17 MarkDuplicates Tracking 148628 as yet unmatched pairs. 16974 records in RAM.
INFO 2026-06-08 08:35:18 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr16:18,377,599
INFO 2026-06-08 08:35:18 MarkDuplicates Tracking 148437 as yet unmatched pairs. 16782 records in RAM.
INFO 2026-06-08 08:35:19 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr16:19,440,510
INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 147381 as yet unmatched pairs. 15726 records in RAM.
INFO 2026-06-08 08:35:21 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr16:21,467,133
INFO 2026-06-08 08:35:21 MarkDuplicates Tracking 147237 as yet unmatched pairs. 15582 records in RAM.
INFO 2026-06-08 08:35:22 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr16:22,326,140
INFO 2026-06-08 08:35:22 MarkDuplicates Tracking 146271 as yet unmatched pairs. 14616 records in RAM.
INFO 2026-06-08 08:35:23 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr16:23,410,284
INFO 2026-06-08 08:35:23 MarkDuplicates Tracking 145976 as yet unmatched pairs. 14321 records in RAM.
INFO 2026-06-08 08:35:25 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr16:28,714,366
INFO 2026-06-08 08:35:25 MarkDuplicates Tracking 144872 as yet unmatched pairs. 13217 records in RAM.
INFO 2026-06-08 08:35:26 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr16:29,483,709
INFO 2026-06-08 08:35:26 MarkDuplicates Tracking 144691 as yet unmatched pairs. 13036 records in RAM.
INFO 2026-06-08 08:35:27 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr16:30,069,365
INFO 2026-06-08 08:35:27 MarkDuplicates Tracking 143464 as yet unmatched pairs. 11809 records in RAM.
INFO 2026-06-08 08:35:29 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr16:30,664,747
INFO 2026-06-08 08:35:29 MarkDuplicates Tracking 142434 as yet unmatched pairs. 10779 records in RAM.
INFO 2026-06-08 08:35:30 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr16:31,380,288
INFO 2026-06-08 08:35:30 MarkDuplicates Tracking 141421 as yet unmatched pairs. 9766 records in RAM.
INFO 2026-06-08 08:35:32 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr16:55,488,547
INFO 2026-06-08 08:35:32 MarkDuplicates Tracking 140143 as yet unmatched pairs. 8486 records in RAM.
INFO 2026-06-08 08:35:33 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr16:58,583,141
INFO 2026-06-08 08:35:33 MarkDuplicates Tracking 138910 as yet unmatched pairs. 7253 records in RAM.
INFO 2026-06-08 08:35:35 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr16:68,230,389
INFO 2026-06-08 08:35:35 MarkDuplicates Tracking 137387 as yet unmatched pairs. 5729 records in RAM.
INFO 2026-06-08 08:35:36 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr16:70,687,912
INFO 2026-06-08 08:35:36 MarkDuplicates Tracking 136030 as yet unmatched pairs. 4372 records in RAM.
INFO 2026-06-08 08:35:38 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 1s. Last read position: chr16:81,043,802
INFO 2026-06-08 08:35:38 MarkDuplicates Tracking 134793 as yet unmatched pairs. 3135 records in RAM.
INFO 2026-06-08 08:35:39 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr16:88,643,493
INFO 2026-06-08 08:35:39 MarkDuplicates Tracking 133717 as yet unmatched pairs. 2058 records in RAM.
INFO 2026-06-08 08:35:41 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr16:89,887,655
INFO 2026-06-08 08:35:41 MarkDuplicates Tracking 131926 as yet unmatched pairs. 266 records in RAM.
INFO 2026-06-08 08:35:43 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 2s. Last read position: chr17:1,752,685
INFO 2026-06-08 08:35:43 MarkDuplicates Tracking 130581 as yet unmatched pairs. 34755 records in RAM.
INFO 2026-06-08 08:35:44 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr17:4,891,060
INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 129315 as yet unmatched pairs. 33489 records in RAM.
INFO 2026-06-08 08:35:46 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr17:7,346,366
INFO 2026-06-08 08:35:46 MarkDuplicates Tracking 127779 as yet unmatched pairs. 31953 records in RAM.
INFO 2026-06-08 08:35:47 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr17:7,910,434
INFO 2026-06-08 08:35:47 MarkDuplicates Tracking 127059 as yet unmatched pairs. 31233 records in RAM.
INFO 2026-06-08 08:35:49 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr17:16,101,570
INFO 2026-06-08 08:35:49 MarkDuplicates Tracking 125595 as yet unmatched pairs. 29769 records in RAM.
INFO 2026-06-08 08:35:50 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr17:18,263,175
INFO 2026-06-08 08:35:50 MarkDuplicates Tracking 123998 as yet unmatched pairs. 28172 records in RAM.
INFO 2026-06-08 08:35:52 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr17:28,676,303
INFO 2026-06-08 08:35:52 MarkDuplicates Tracking 122857 as yet unmatched pairs. 27031 records in RAM.
INFO 2026-06-08 08:35:53 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr17:31,249,003
INFO 2026-06-08 08:35:53 MarkDuplicates Tracking 121599 as yet unmatched pairs. 25773 records in RAM.
INFO 2026-06-08 08:35:55 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr17:36,450,253
INFO 2026-06-08 08:35:55 MarkDuplicates Tracking 120475 as yet unmatched pairs. 24649 records in RAM.
INFO 2026-06-08 08:35:56 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr17:38,755,933
INFO 2026-06-08 08:35:56 MarkDuplicates Tracking 119580 as yet unmatched pairs. 23754 records in RAM.
INFO 2026-06-08 08:35:58 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr17:39,723,647
INFO 2026-06-08 08:35:58 MarkDuplicates Tracking 118425 as yet unmatched pairs. 22599 records in RAM.
INFO 2026-06-08 08:35:59 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr17:41,873,889
INFO 2026-06-08 08:35:59 MarkDuplicates Tracking 116659 as yet unmatched pairs. 20832 records in RAM.
INFO 2026-06-08 08:36:01 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr17:42,991,014
INFO 2026-06-08 08:36:01 MarkDuplicates Tracking 115368 as yet unmatched pairs. 19541 records in RAM.
INFO 2026-06-08 08:36:02 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr17:45,514,835
INFO 2026-06-08 08:36:02 MarkDuplicates Tracking 114119 as yet unmatched pairs. 18292 records in RAM.
INFO 2026-06-08 08:36:04 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr17:48,058,363
INFO 2026-06-08 08:36:04 MarkDuplicates Tracking 113437 as yet unmatched pairs. 17610 records in RAM.
INFO 2026-06-08 08:36:05 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,916
INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 114258 as yet unmatched pairs. 18431 records in RAM.
INFO 2026-06-08 08:36:07 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,012
INFO 2026-06-08 08:36:07 MarkDuplicates Tracking 112906 as yet unmatched pairs. 17079 records in RAM.
INFO 2026-06-08 08:36:09 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,880
INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 109655 as yet unmatched pairs. 13828 records in RAM.
INFO 2026-06-08 08:36:11 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr17:58,508,485
INFO 2026-06-08 08:36:11 MarkDuplicates Tracking 107920 as yet unmatched pairs. 12093 records in RAM.
INFO 2026-06-08 08:36:12 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr17:62,688,890
INFO 2026-06-08 08:36:12 MarkDuplicates Tracking 106659 as yet unmatched pairs. 10832 records in RAM.
INFO 2026-06-08 08:36:14 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr17:67,109,610
INFO 2026-06-08 08:36:14 MarkDuplicates Tracking 105582 as yet unmatched pairs. 9745 records in RAM.
INFO 2026-06-08 08:36:15 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr17:74,955,907
INFO 2026-06-08 08:36:15 MarkDuplicates Tracking 104281 as yet unmatched pairs. 8444 records in RAM.
INFO 2026-06-08 08:36:17 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr17:76,009,394
INFO 2026-06-08 08:36:17 MarkDuplicates Tracking 102706 as yet unmatched pairs. 6869 records in RAM.
INFO 2026-06-08 08:36:19 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr17:78,821,011
INFO 2026-06-08 08:36:19 MarkDuplicates Tracking 101419 as yet unmatched pairs. 5582 records in RAM.
INFO 2026-06-08 08:36:20 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr17:80,386,315
INFO 2026-06-08 08:36:20 MarkDuplicates Tracking 100097 as yet unmatched pairs. 4260 records in RAM.
INFO 2026-06-08 08:36:21 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr17:81,868,746
INFO 2026-06-08 08:36:21 MarkDuplicates Tracking 98653 as yet unmatched pairs. 2816 records in RAM.
INFO 2026-06-08 08:36:23 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr17:82,087,225
INFO 2026-06-08 08:36:23 MarkDuplicates Tracking 97882 as yet unmatched pairs. 2045 records in RAM.
INFO 2026-06-08 08:36:25 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr18:348,078
INFO 2026-06-08 08:36:25 MarkDuplicates Tracking 95768 as yet unmatched pairs. 4501 records in RAM.
INFO 2026-06-08 08:36:26 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr18:21,008,143
INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 94886 as yet unmatched pairs. 3619 records in RAM.
INFO 2026-06-08 08:36:27 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr18:44,952,473
INFO 2026-06-08 08:36:27 MarkDuplicates Tracking 93944 as yet unmatched pairs. 2677 records in RAM.
INFO 2026-06-08 08:36:29 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr18:58,709,435
INFO 2026-06-08 08:36:29 MarkDuplicates Tracking 92694 as yet unmatched pairs. 1427 records in RAM.
INFO 2026-06-08 08:36:30 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr18:79,715,419
INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 91360 as yet unmatched pairs. 93 records in RAM.
INFO 2026-06-08 08:36:32 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr19:1,112,026
INFO 2026-06-08 08:36:32 MarkDuplicates Tracking 90064 as yet unmatched pairs. 38383 records in RAM.
INFO 2026-06-08 08:36:34 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr19:2,037,734
INFO 2026-06-08 08:36:34 MarkDuplicates Tracking 88334 as yet unmatched pairs. 36653 records in RAM.
INFO 2026-06-08 08:36:35 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr19:3,573,331
INFO 2026-06-08 08:36:35 MarkDuplicates Tracking 86732 as yet unmatched pairs. 35050 records in RAM.
INFO 2026-06-08 08:36:37 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr19:5,223,198
INFO 2026-06-08 08:36:37 MarkDuplicates Tracking 85045 as yet unmatched pairs. 33363 records in RAM.
INFO 2026-06-08 08:36:38 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr19:6,711,039
INFO 2026-06-08 08:36:38 MarkDuplicates Tracking 83566 as yet unmatched pairs. 31884 records in RAM.
INFO 2026-06-08 08:36:40 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr19:8,490,176
INFO 2026-06-08 08:36:40 MarkDuplicates Tracking 81775 as yet unmatched pairs. 30093 records in RAM.
INFO 2026-06-08 08:36:41 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 1s. Last read position: chr19:10,829,132
INFO 2026-06-08 08:36:41 MarkDuplicates Tracking 80709 as yet unmatched pairs. 29026 records in RAM.
INFO 2026-06-08 08:36:43 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 1s. Last read position: chr19:12,646,603
INFO 2026-06-08 08:36:43 MarkDuplicates Tracking 79342 as yet unmatched pairs. 27659 records in RAM.
INFO 2026-06-08 08:36:44 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr19:14,093,140
INFO 2026-06-08 08:36:44 MarkDuplicates Tracking 77765 as yet unmatched pairs. 26082 records in RAM.
INFO 2026-06-08 08:36:46 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr19:15,265,452
INFO 2026-06-08 08:36:46 MarkDuplicates Tracking 76793 as yet unmatched pairs. 25110 records in RAM.
INFO 2026-06-08 08:36:47 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr19:17,405,415
INFO 2026-06-08 08:36:47 MarkDuplicates Tracking 74941 as yet unmatched pairs. 23258 records in RAM.
INFO 2026-06-08 08:36:49 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr19:18,774,919
INFO 2026-06-08 08:36:49 MarkDuplicates Tracking 73587 as yet unmatched pairs. 21904 records in RAM.
INFO 2026-06-08 08:36:50 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr19:33,002,341
INFO 2026-06-08 08:36:50 MarkDuplicates Tracking 72224 as yet unmatched pairs. 20540 records in RAM.
INFO 2026-06-08 08:36:52 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr19:35,756,853
INFO 2026-06-08 08:36:52 MarkDuplicates Tracking 70593 as yet unmatched pairs. 18909 records in RAM.
INFO 2026-06-08 08:36:53 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr19:38,847,345
INFO 2026-06-08 08:36:53 MarkDuplicates Tracking 69138 as yet unmatched pairs. 17454 records in RAM.
INFO 2026-06-08 08:36:54 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr19:40,235,078
INFO 2026-06-08 08:36:54 MarkDuplicates Tracking 68530 as yet unmatched pairs. 16846 records in RAM.
INFO 2026-06-08 08:36:56 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr19:41,302,847
INFO 2026-06-08 08:36:56 MarkDuplicates Tracking 66719 as yet unmatched pairs. 15035 records in RAM.
INFO 2026-06-08 08:36:58 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr19:42,293,136
INFO 2026-06-08 08:36:58 MarkDuplicates Tracking 65653 as yet unmatched pairs. 13969 records in RAM.
INFO 2026-06-08 08:36:59 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr19:45,090,142
INFO 2026-06-08 08:36:59 MarkDuplicates Tracking 63611 as yet unmatched pairs. 11924 records in RAM.
INFO 2026-06-08 08:37:00 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr19:46,838,407
INFO 2026-06-08 08:37:00 MarkDuplicates Tracking 62071 as yet unmatched pairs. 10384 records in RAM.
INFO 2026-06-08 08:37:02 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr19:48,797,256
INFO 2026-06-08 08:37:02 MarkDuplicates Tracking 60764 as yet unmatched pairs. 9077 records in RAM.
INFO 2026-06-08 08:37:04 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr19:49,543,157
INFO 2026-06-08 08:37:04 MarkDuplicates Tracking 59408 as yet unmatched pairs. 7721 records in RAM.
INFO 2026-06-08 08:37:05 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr19:50,482,576
INFO 2026-06-08 08:37:05 MarkDuplicates Tracking 57749 as yet unmatched pairs. 6062 records in RAM.
INFO 2026-06-08 08:37:06 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr19:50,876,453
INFO 2026-06-08 08:37:06 MarkDuplicates Tracking 58061 as yet unmatched pairs. 6374 records in RAM.
INFO 2026-06-08 08:37:08 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr19:52,949,978
INFO 2026-06-08 08:37:08 MarkDuplicates Tracking 55168 as yet unmatched pairs. 3481 records in RAM.
INFO 2026-06-08 08:37:10 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr19:55,091,649
INFO 2026-06-08 08:37:10 MarkDuplicates Tracking 54132 as yet unmatched pairs. 2445 records in RAM.
INFO 2026-06-08 08:37:11 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr19:57,808,678
INFO 2026-06-08 08:37:11 MarkDuplicates Tracking 52905 as yet unmatched pairs. 1218 records in RAM.
INFO 2026-06-08 08:37:12 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr20:1,921,545
INFO 2026-06-08 08:37:12 MarkDuplicates Tracking 51316 as yet unmatched pairs. 12437 records in RAM.
INFO 2026-06-08 08:37:14 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr20:13,787,317
INFO 2026-06-08 08:37:14 MarkDuplicates Tracking 49707 as yet unmatched pairs. 10828 records in RAM.
INFO 2026-06-08 08:37:15 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr20:25,248,245
INFO 2026-06-08 08:37:15 MarkDuplicates Tracking 48857 as yet unmatched pairs. 9978 records in RAM.
INFO 2026-06-08 08:37:17 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr20:34,996,570
INFO 2026-06-08 08:37:17 MarkDuplicates Tracking 47420 as yet unmatched pairs. 8541 records in RAM.
INFO 2026-06-08 08:37:18 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr20:37,204,784
INFO 2026-06-08 08:37:18 MarkDuplicates Tracking 46224 as yet unmatched pairs. 7345 records in RAM.
INFO 2026-06-08 08:37:20 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr20:43,463,324
INFO 2026-06-08 08:37:20 MarkDuplicates Tracking 45032 as yet unmatched pairs. 6153 records in RAM.
INFO 2026-06-08 08:37:21 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr20:48,985,576
INFO 2026-06-08 08:37:21 MarkDuplicates Tracking 43553 as yet unmatched pairs. 4674 records in RAM.
INFO 2026-06-08 08:37:23 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr20:57,659,478
INFO 2026-06-08 08:37:23 MarkDuplicates Tracking 43084 as yet unmatched pairs. 4205 records in RAM.
INFO 2026-06-08 08:37:24 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr20:62,346,783
INFO 2026-06-08 08:37:24 MarkDuplicates Tracking 40837 as yet unmatched pairs. 1958 records in RAM.
INFO 2026-06-08 08:37:25 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr20:63,931,494
INFO 2026-06-08 08:37:25 MarkDuplicates Tracking 39235 as yet unmatched pairs. 356 records in RAM.
INFO 2026-06-08 08:37:27 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,299
INFO 2026-06-08 08:37:27 MarkDuplicates Tracking 38371 as yet unmatched pairs. 7467 records in RAM.
INFO 2026-06-08 08:37:28 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr21:32,337,506
INFO 2026-06-08 08:37:28 MarkDuplicates Tracking 37299 as yet unmatched pairs. 6394 records in RAM.
INFO 2026-06-08 08:37:30 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr21:36,747,681
INFO 2026-06-08 08:37:30 MarkDuplicates Tracking 36038 as yet unmatched pairs. 5133 records in RAM.
INFO 2026-06-08 08:37:31 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr21:41,473,352
INFO 2026-06-08 08:37:31 MarkDuplicates Tracking 35207 as yet unmatched pairs. 4302 records in RAM.
INFO 2026-06-08 08:37:32 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr21:44,330,203
INFO 2026-06-08 08:37:32 MarkDuplicates Tracking 33394 as yet unmatched pairs. 2489 records in RAM.
INFO 2026-06-08 08:37:34 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr21:46,119,810
INFO 2026-06-08 08:37:34 MarkDuplicates Tracking 32169 as yet unmatched pairs. 1264 records in RAM.
INFO 2026-06-08 08:37:35 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr22:18,088,037
INFO 2026-06-08 08:37:35 MarkDuplicates Tracking 30469 as yet unmatched pairs. 13671 records in RAM.
INFO 2026-06-08 08:37:37 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr22:21,939,548
INFO 2026-06-08 08:37:37 MarkDuplicates Tracking 29320 as yet unmatched pairs. 12522 records in RAM.
INFO 2026-06-08 08:37:38 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr22:24,645,667
INFO 2026-06-08 08:37:38 MarkDuplicates Tracking 27952 as yet unmatched pairs. 11154 records in RAM.
INFO 2026-06-08 08:37:39 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr22:29,308,476
INFO 2026-06-08 08:37:39 MarkDuplicates Tracking 26639 as yet unmatched pairs. 9841 records in RAM.
INFO 2026-06-08 08:37:41 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr22:31,956,687
INFO 2026-06-08 08:37:41 MarkDuplicates Tracking 25527 as yet unmatched pairs. 8729 records in RAM.
INFO 2026-06-08 08:37:42 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr22:37,019,764
INFO 2026-06-08 08:37:42 MarkDuplicates Tracking 24068 as yet unmatched pairs. 7270 records in RAM.
INFO 2026-06-08 08:37:44 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr22:38,726,069
INFO 2026-06-08 08:37:44 MarkDuplicates Tracking 22739 as yet unmatched pairs. 5941 records in RAM.
INFO 2026-06-08 08:37:45 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr22:41,176,247
INFO 2026-06-08 08:37:45 MarkDuplicates Tracking 21473 as yet unmatched pairs. 4675 records in RAM.
INFO 2026-06-08 08:37:46 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr22:43,063,886
INFO 2026-06-08 08:37:46 MarkDuplicates Tracking 20310 as yet unmatched pairs. 3512 records in RAM.
INFO 2026-06-08 08:37:48 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr22:50,221,677
INFO 2026-06-08 08:37:48 MarkDuplicates Tracking 18801 as yet unmatched pairs. 2003 records in RAM.
INFO 2026-06-08 08:37:49 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr22:50,603,170
INFO 2026-06-08 08:37:49 MarkDuplicates Tracking 17101 as yet unmatched pairs. 303 records in RAM.
INFO 2026-06-08 08:37:51 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chrX:14,873,707
INFO 2026-06-08 08:37:51 MarkDuplicates Tracking 15736 as yet unmatched pairs. 13587 records in RAM.
INFO 2026-06-08 08:37:52 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chrX:40,071,119
INFO 2026-06-08 08:37:52 MarkDuplicates Tracking 14829 as yet unmatched pairs. 12678 records in RAM.
INFO 2026-06-08 08:37:53 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chrX:47,586,678
INFO 2026-06-08 08:37:53 MarkDuplicates Tracking 13583 as yet unmatched pairs. 11432 records in RAM.
INFO 2026-06-08 08:37:55 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chrX:53,250,582
INFO 2026-06-08 08:37:55 MarkDuplicates Tracking 12149 as yet unmatched pairs. 9998 records in RAM.
INFO 2026-06-08 08:37:56 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chrX:67,546,576
INFO 2026-06-08 08:37:56 MarkDuplicates Tracking 11016 as yet unmatched pairs. 8865 records in RAM.
INFO 2026-06-08 08:37:57 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chrX:74,591,993
INFO 2026-06-08 08:37:57 MarkDuplicates Tracking 9821 as yet unmatched pairs. 7670 records in RAM.
INFO 2026-06-08 08:37:59 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chrX:103,586,966
INFO 2026-06-08 08:37:59 MarkDuplicates Tracking 8871 as yet unmatched pairs. 6720 records in RAM.
INFO 2026-06-08 08:38:00 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chrX:124,094,116
INFO 2026-06-08 08:38:00 MarkDuplicates Tracking 7692 as yet unmatched pairs. 5541 records in RAM.
INFO 2026-06-08 08:38:02 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chrX:153,690,496
INFO 2026-06-08 08:38:02 MarkDuplicates Tracking 6214 as yet unmatched pairs. 4063 records in RAM.
INFO 2026-06-08 08:38:03 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chrX:154,352,631
INFO 2026-06-08 08:38:03 MarkDuplicates Tracking 5971 as yet unmatched pairs. 3820 records in RAM.
INFO 2026-06-08 08:38:04 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chrX:154,364,547
INFO 2026-06-08 08:38:04 MarkDuplicates Tracking 4371 as yet unmatched pairs. 2216 records in RAM.
INFO 2026-06-08 08:38:06 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chrX:154,887,436
INFO 2026-06-08 08:38:06 MarkDuplicates Tracking 2207 as yet unmatched pairs. 52 records in RAM.
INFO 2026-06-08 08:38:07 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,543
INFO 2026-06-08 08:38:07 MarkDuplicates Tracking 1187 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:38:08 MarkDuplicates Read 415660631 records. 0 pairs never matched.
INFO 2026-06-08 08:38:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 36667580824; totalMemory: 52344913920; maxMemory: 63585648640
INFO 2026-06-08 08:38:45 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:38:46 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:39:04 OpticalDuplicateFinder Large duplicate set. size = 1208
INFO 2026-06-08 08:39:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,455
INFO 2026-06-08 08:39:44 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:39:44 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:40:22 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:40:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 204032264; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:40:26 MarkDuplicates Marking 333158128 records as duplicates.
INFO 2026-06-08 08:40:26 MarkDuplicates Found 8056511 optical duplicate clusters.
INFO 2026-06-08 08:40:26 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:40:42 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:32,826,544
INFO 2026-06-08 08:40:58 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 15s. Last read position: chr1:119,915,891
INFO 2026-06-08 08:41:14 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:47s. Time for last 10,000,000: 15s. Last read position: chr1:180,094,187
INFO 2026-06-08 08:41:30 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:04s. Time for last 10,000,000: 16s. Last read position: chr2:27,083,074
INFO 2026-06-08 08:41:47 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:20s. Time for last 10,000,000: 16s. Last read position: chr2:96,864,025
INFO 2026-06-08 08:42:03 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:37s. Time for last 10,000,000: 16s. Last read position: chr2:206,056,833
INFO 2026-06-08 08:42:22 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:56s. Time for last 10,000,000: 19s. Last read position: chr3:20,040,460
INFO 2026-06-08 08:42:45 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:19s. Time for last 10,000,000: 22s. Last read position: chr3:73,404,325
INFO 2026-06-08 08:43:09 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:42s. Time for last 10,000,000: 23s. Last read position: chr3:194,137,952
INFO 2026-06-08 08:43:30 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:04s. Time for last 10,000,000: 21s. Last read position: chr4:119,026,933
INFO 2026-06-08 08:43:55 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:29s. Time for last 10,000,000: 25s. Last read position: chr5:80,070,315
INFO 2026-06-08 08:44:17 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:51s. Time for last 10,000,000: 22s. Last read position: chr5:171,391,758
INFO 2026-06-08 08:44:43 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:17s. Time for last 10,000,000: 26s. Last read position: chr6:32,519,395
INFO 2026-06-08 08:45:09 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:43s. Time for last 10,000,000: 25s. Last read position: chr6:144,678,486
INFO 2026-06-08 08:45:30 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:04s. Time for last 10,000,000: 21s. Last read position: chr7:73,693,990
INFO 2026-06-08 08:45:53 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:27s. Time for last 10,000,000: 23s. Last read position: chr7:139,596,730
INFO 2026-06-08 08:46:18 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:52s. Time for last 10,000,000: 25s. Last read position: chr8:94,391,770
INFO 2026-06-08 08:46:42 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:06:15s. Time for last 10,000,000: 23s. Last read position: chr9:19,378,905
INFO 2026-06-08 08:47:04 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:06:38s. Time for last 10,000,000: 22s. Last read position: chr9:129,001,543
INFO 2026-06-08 08:47:26 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:07:00s. Time for last 10,000,000: 22s. Last read position: chr10:60,083,562
INFO 2026-06-08 08:47:47 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:07:21s. Time for last 10,000,000: 20s. Last read position: chr11:925,989
INFO 2026-06-08 08:48:08 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:07:41s. Time for last 10,000,000: 20s. Last read position: chr11:63,818,826
INFO 2026-06-08 08:48:29 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:08:02s. Time for last 10,000,000: 20s. Last read position: chr11:117,986,418
INFO 2026-06-08 08:48:51 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:08:25s. Time for last 10,000,000: 22s. Last read position: chr12:49,631,886
INFO 2026-06-08 08:49:12 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:08:45s. Time for last 10,000,000: 20s. Last read position: chr12:111,598,924
INFO 2026-06-08 08:49:33 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:09:06s. Time for last 10,000,000: 20s. Last read position: chr13:110,176,456
INFO 2026-06-08 08:49:53 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:09:26s. Time for last 10,000,000: 20s. Last read position: chr14:93,246,033
INFO 2026-06-08 08:50:14 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:09:48s. Time for last 10,000,000: 21s. Last read position: chr15:56,007,058
INFO 2026-06-08 08:50:36 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:10:09s. Time for last 10,000,000: 21s. Last read position: chr16:2,092,551
INFO 2026-06-08 08:50:56 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:10:30s. Time for last 10,000,000: 20s. Last read position: chr16:18,377,599
INFO 2026-06-08 08:51:19 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:10:53s. Time for last 10,000,000: 22s. Last read position: chr16:55,488,547
INFO 2026-06-08 08:51:40 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:11:13s. Time for last 10,000,000: 20s. Last read position: chr17:7,910,434
INFO 2026-06-08 08:51:59 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:11:32s. Time for last 10,000,000: 19s. Last read position: chr17:45,514,835
INFO 2026-06-08 08:52:18 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:11:51s. Time for last 10,000,000: 18s. Last read position: chr17:78,821,011
INFO 2026-06-08 08:52:36 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:12:09s. Time for last 10,000,000: 18s. Last read position: chr19:2,037,734
INFO 2026-06-08 08:52:53 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:12:27s. Time for last 10,000,000: 17s. Last read position: chr19:18,774,919
INFO 2026-06-08 08:53:09 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:12:43s. Time for last 10,000,000: 16s. Last read position: chr19:49,543,157
INFO 2026-06-08 08:53:25 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:12:59s. Time for last 10,000,000: 16s. Last read position: chr20:37,204,784
INFO 2026-06-08 08:53:41 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:13:15s. Time for last 10,000,000: 15s. Last read position: chr21:44,330,203
INFO 2026-06-08 08:53:57 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:13:30s. Time for last 10,000,000: 15s. Last read position: chr22:43,063,886
INFO 2026-06-08 08:54:12 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:13:46s. Time for last 10,000,000: 15s. Last read position: chrX:124,094,116
INFO 2026-06-08 08:54:26 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:54:26 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:54:26 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:54:26 MarkDuplicates Before output close freeMemory: 204026816; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:54:26 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:54:26 MarkDuplicates After output close freeMemory: 104250120; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:54:26 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 27.39 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory