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 aih-tih-sc-0fc41c-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0fc41c-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-0fc41c-R1_B23WHYVLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:41:59.835 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 08:41:59 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-0fc41c-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0fc41c-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-0fc41c-R1_B23WHYVLT4_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 08:41:59 GMT 2026] Executing as ?@nf-e878d6ed8c512e1fdc0c41d5d4b36cb8-6c5d2-qjq9z 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 08:41:59 MarkDuplicates Start of doWork freeMemory: 105492360; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:41:59 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:41:59 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:42:04 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,294,588
INFO 2026-06-08 08:42:04 MarkDuplicates Tracking 3426 as yet unmatched pairs. 139 records in RAM.
INFO 2026-06-08 08:42:06 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:2,304,507
INFO 2026-06-08 08:42:06 MarkDuplicates Tracking 6410 as yet unmatched pairs. 120 records in RAM.
INFO 2026-06-08 08:42:07 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:8,359,806
INFO 2026-06-08 08:42:07 MarkDuplicates Tracking 9693 as yet unmatched pairs. 120 records in RAM.
INFO 2026-06-08 08:42:09 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:11,095,757
INFO 2026-06-08 08:42:09 MarkDuplicates Tracking 12381 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 08:42:12 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:15,727,499
INFO 2026-06-08 08:42:12 MarkDuplicates Tracking 15423 as yet unmatched pairs. 119 records in RAM.
INFO 2026-06-08 08:42:13 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:16,992,250
INFO 2026-06-08 08:42:13 MarkDuplicates Tracking 17986 as yet unmatched pairs. 184 records in RAM.
INFO 2026-06-08 08:42:15 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:19,122,936
INFO 2026-06-08 08:42:15 MarkDuplicates Tracking 20833 as yet unmatched pairs. 191 records in RAM.
INFO 2026-06-08 08:42:17 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:21,724,081
INFO 2026-06-08 08:42:17 MarkDuplicates Tracking 23682 as yet unmatched pairs. 323 records in RAM.
INFO 2026-06-08 08:42:19 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:22,638,840
INFO 2026-06-08 08:42:19 MarkDuplicates Tracking 27491 as yet unmatched pairs. 1199 records in RAM.
INFO 2026-06-08 08:42:21 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:25,246,702
INFO 2026-06-08 08:42:21 MarkDuplicates Tracking 29328 as yet unmatched pairs. 343 records in RAM.
INFO 2026-06-08 08:42:23 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr1:27,334,261
INFO 2026-06-08 08:42:23 MarkDuplicates Tracking 31882 as yet unmatched pairs. 150 records in RAM.
INFO 2026-06-08 08:42:24 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:29,325,267
INFO 2026-06-08 08:42:24 MarkDuplicates Tracking 34756 as yet unmatched pairs. 278 records in RAM.
INFO 2026-06-08 08:42:26 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:32,770,934
INFO 2026-06-08 08:42:26 MarkDuplicates Tracking 37667 as yet unmatched pairs. 276 records in RAM.
INFO 2026-06-08 08:42:27 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:35,636,398
INFO 2026-06-08 08:42:27 MarkDuplicates Tracking 40438 as yet unmatched pairs. 134 records in RAM.
INFO 2026-06-08 08:42:29 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:37,483,104
INFO 2026-06-08 08:42:29 MarkDuplicates Tracking 43031 as yet unmatched pairs. 66 records in RAM.
INFO 2026-06-08 08:42:31 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:40,421,972
INFO 2026-06-08 08:42:31 MarkDuplicates Tracking 45830 as yet unmatched pairs. 138 records in RAM.
INFO 2026-06-08 08:42:34 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:43,894,400
INFO 2026-06-08 08:42:34 MarkDuplicates Tracking 48606 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 08:42:36 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:46,716,317
INFO 2026-06-08 08:42:36 MarkDuplicates Tracking 51807 as yet unmatched pairs. 476 records in RAM.
INFO 2026-06-08 08:42:37 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:54,853,445
INFO 2026-06-08 08:42:37 MarkDuplicates Tracking 54304 as yet unmatched pairs. 286 records in RAM.
INFO 2026-06-08 08:42:39 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:67,420,100
INFO 2026-06-08 08:42:39 MarkDuplicates Tracking 56888 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 08:42:41 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:90,010,175
INFO 2026-06-08 08:42:41 MarkDuplicates Tracking 59278 as yet unmatched pairs. 126 records in RAM.
INFO 2026-06-08 08:42:42 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:108,937,077
INFO 2026-06-08 08:42:42 MarkDuplicates Tracking 61692 as yet unmatched pairs. 92 records in RAM.
INFO 2026-06-08 08:42:44 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:112,527,217
INFO 2026-06-08 08:42:44 MarkDuplicates Tracking 64227 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 08:42:46 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:116,384,013
INFO 2026-06-08 08:42:46 MarkDuplicates Tracking 67441 as yet unmatched pairs. 539 records in RAM.
INFO 2026-06-08 08:42:47 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:119,923,887
INFO 2026-06-08 08:42:47 MarkDuplicates Tracking 70042 as yet unmatched pairs. 634 records in RAM.
INFO 2026-06-08 08:42:49 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:144,897,123
INFO 2026-06-08 08:42:49 MarkDuplicates Tracking 71267 as yet unmatched pairs. 176 records in RAM.
INFO 2026-06-08 08:42:51 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:146,964,898
INFO 2026-06-08 08:42:51 MarkDuplicates Tracking 73005 as yet unmatched pairs. 405 records in RAM.
INFO 2026-06-08 08:42:53 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:148,590,757
INFO 2026-06-08 08:42:53 MarkDuplicates Tracking 73986 as yet unmatched pairs. 98 records in RAM.
INFO 2026-06-08 08:42:55 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr1:149,923,433
INFO 2026-06-08 08:42:55 MarkDuplicates Tracking 75411 as yet unmatched pairs. 194 records in RAM.
INFO 2026-06-08 08:42:57 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:150,968,502
INFO 2026-06-08 08:42:57 MarkDuplicates Tracking 78736 as yet unmatched pairs. 932 records in RAM.
INFO 2026-06-08 08:42:58 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:152,032,636
INFO 2026-06-08 08:42:58 MarkDuplicates Tracking 81527 as yet unmatched pairs. 752 records in RAM.
INFO 2026-06-08 08:43:00 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:154,170,428
INFO 2026-06-08 08:43:00 MarkDuplicates Tracking 91466 as yet unmatched pairs. 8112 records in RAM.
INFO 2026-06-08 08:43:02 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:154,945,802
INFO 2026-06-08 08:43:02 MarkDuplicates Tracking 86373 as yet unmatched pairs. 363 records in RAM.
INFO 2026-06-08 08:43:03 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:155,187,366
INFO 2026-06-08 08:43:03 MarkDuplicates Tracking 98218 as yet unmatched pairs. 9335 records in RAM.
INFO 2026-06-08 08:43:05 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:155,192,154
INFO 2026-06-08 08:43:05 MarkDuplicates Tracking 96475 as yet unmatched pairs. 5872 records in RAM.
INFO 2026-06-08 08:43:06 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:155,751,765
INFO 2026-06-08 08:43:06 MarkDuplicates Tracking 93259 as yet unmatched pairs. 206 records in RAM.
INFO 2026-06-08 08:43:08 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:156,160,479
INFO 2026-06-08 08:43:08 MarkDuplicates Tracking 96382 as yet unmatched pairs. 84 records in RAM.
INFO 2026-06-08 08:43:10 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:159,918,877
INFO 2026-06-08 08:43:10 MarkDuplicates Tracking 100600 as yet unmatched pairs. 1654 records in RAM.
INFO 2026-06-08 08:43:11 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:161,171,850
INFO 2026-06-08 08:43:11 MarkDuplicates Tracking 101929 as yet unmatched pairs. 262 records in RAM.
INFO 2026-06-08 08:43:12 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:169,106,754
INFO 2026-06-08 08:43:12 MarkDuplicates Tracking 110604 as yet unmatched pairs. 6264 records in RAM.
INFO 2026-06-08 08:43:14 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:169,130,011
INFO 2026-06-08 08:43:14 MarkDuplicates Tracking 118991 as yet unmatched pairs. 11632 records in RAM.
INFO 2026-06-08 08:43:16 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:171,584,455
INFO 2026-06-08 08:43:16 MarkDuplicates Tracking 110550 as yet unmatched pairs. 608 records in RAM.
INFO 2026-06-08 08:43:17 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr1:180,806,089
INFO 2026-06-08 08:43:17 MarkDuplicates Tracking 112698 as yet unmatched pairs. 117 records in RAM.
INFO 2026-06-08 08:43:19 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:186,320,369
INFO 2026-06-08 08:43:19 MarkDuplicates Tracking 116278 as yet unmatched pairs. 1179 records in RAM.
INFO 2026-06-08 08:43:20 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr1:198,157,249
INFO 2026-06-08 08:43:20 MarkDuplicates Tracking 117605 as yet unmatched pairs. 130 records in RAM.
INFO 2026-06-08 08:43:22 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr1:202,733,819
INFO 2026-06-08 08:43:22 MarkDuplicates Tracking 120526 as yet unmatched pairs. 278 records in RAM.
INFO 2026-06-08 08:43:24 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr1:204,346,773
INFO 2026-06-08 08:43:24 MarkDuplicates Tracking 122765 as yet unmatched pairs. 9 records in RAM.
INFO 2026-06-08 08:43:26 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:207,023,306
INFO 2026-06-08 08:43:26 MarkDuplicates Tracking 125614 as yet unmatched pairs. 286 records in RAM.
INFO 2026-06-08 08:43:28 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr1:207,783,311
INFO 2026-06-08 08:43:28 MarkDuplicates Tracking 131297 as yet unmatched pairs. 3315 records in RAM.
INFO 2026-06-08 08:43:29 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:214,384,336
INFO 2026-06-08 08:43:29 MarkDuplicates Tracking 130919 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:43:31 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr1:223,795,918
INFO 2026-06-08 08:43:31 MarkDuplicates Tracking 133723 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-08 08:43:32 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr1:226,377,185
INFO 2026-06-08 08:43:32 MarkDuplicates Tracking 136334 as yet unmatched pairs. 207 records in RAM.
INFO 2026-06-08 08:43:34 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr1:228,487,548
INFO 2026-06-08 08:43:34 MarkDuplicates Tracking 139514 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 08:43:35 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr1:235,335,257
INFO 2026-06-08 08:43:35 MarkDuplicates Tracking 142752 as yet unmatched pairs. 190 records in RAM.
INFO 2026-06-08 08:43:37 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr1:244,863,758
INFO 2026-06-08 08:43:37 MarkDuplicates Tracking 145235 as yet unmatched pairs. 64 records in RAM.
INFO 2026-06-08 08:43:40 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr2:9,393,540
INFO 2026-06-08 08:43:40 MarkDuplicates Tracking 148274 as yet unmatched pairs. 147714 records in RAM.
INFO 2026-06-08 08:43:41 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr2:20,203,166
INFO 2026-06-08 08:43:41 MarkDuplicates Tracking 154043 as yet unmatched pairs. 153478 records in RAM.
INFO 2026-06-08 08:43:43 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr2:25,387,228
INFO 2026-06-08 08:43:43 MarkDuplicates Tracking 153601 as yet unmatched pairs. 153031 records in RAM.
INFO 2026-06-08 08:43:45 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr2:28,752,149
INFO 2026-06-08 08:43:45 MarkDuplicates Tracking 159096 as yet unmatched pairs. 158517 records in RAM.
INFO 2026-06-08 08:43:48 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,255
INFO 2026-06-08 08:43:48 MarkDuplicates Tracking 208266 as yet unmatched pairs. 152681 records in RAM.
INFO 2026-06-08 08:43:49 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:43:49 MarkDuplicates Tracking 515918 as yet unmatched pairs. 126808 records in RAM.
INFO 2026-06-08 08:43:52 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,397
INFO 2026-06-08 08:43:52 MarkDuplicates Tracking 1024857 as yet unmatched pairs. 84372 records in RAM.
INFO 2026-06-08 08:43:53 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:43:53 MarkDuplicates Tracking 1052411 as yet unmatched pairs. 82100 records in RAM.
INFO 2026-06-08 08:43:55 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:37,227,545
INFO 2026-06-08 08:43:55 MarkDuplicates Tracking 1123448 as yet unmatched pairs. 74962 records in RAM.
INFO 2026-06-08 08:43:56 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:43,947,298
INFO 2026-06-08 08:43:56 MarkDuplicates Tracking 1121205 as yet unmatched pairs. 72714 records in RAM.
INFO 2026-06-08 08:43:58 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:54,626,036
INFO 2026-06-08 08:43:58 MarkDuplicates Tracking 1118415 as yet unmatched pairs. 69895 records in RAM.
INFO 2026-06-08 08:44:00 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:61,872,208
INFO 2026-06-08 08:44:00 MarkDuplicates Tracking 1115903 as yet unmatched pairs. 67373 records in RAM.
INFO 2026-06-08 08:44:02 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr2:70,989,747
INFO 2026-06-08 08:44:02 MarkDuplicates Tracking 1113015 as yet unmatched pairs. 64468 records in RAM.
INFO 2026-06-08 08:44:04 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:74,527,577
INFO 2026-06-08 08:44:04 MarkDuplicates Tracking 1110389 as yet unmatched pairs. 61838 records in RAM.
INFO 2026-06-08 08:44:06 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr2:85,659,671
INFO 2026-06-08 08:44:06 MarkDuplicates Tracking 1117986 as yet unmatched pairs. 69423 records in RAM.
INFO 2026-06-08 08:44:08 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:85,663,431
INFO 2026-06-08 08:44:08 MarkDuplicates Tracking 1116675 as yet unmatched pairs. 68105 records in RAM.
INFO 2026-06-08 08:44:10 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:85,665,355
INFO 2026-06-08 08:44:10 MarkDuplicates Tracking 1143781 as yet unmatched pairs. 95204 records in RAM.
INFO 2026-06-08 08:44:11 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr2:85,666,681
INFO 2026-06-08 08:44:11 MarkDuplicates Tracking 1137940 as yet unmatched pairs. 89361 records in RAM.
INFO 2026-06-08 08:44:13 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:88,857,579
INFO 2026-06-08 08:44:13 MarkDuplicates Tracking 1096264 as yet unmatched pairs. 47672 records in RAM.
INFO 2026-06-08 08:44:15 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:97,796,842
INFO 2026-06-08 08:44:15 MarkDuplicates Tracking 1093639 as yet unmatched pairs. 45037 records in RAM.
INFO 2026-06-08 08:44:16 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr2:107,866,299
INFO 2026-06-08 08:44:16 MarkDuplicates Tracking 1091162 as yet unmatched pairs. 42551 records in RAM.
INFO 2026-06-08 08:44:18 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr2:109,827,854
INFO 2026-06-08 08:44:18 MarkDuplicates Tracking 1089542 as yet unmatched pairs. 40925 records in RAM.
INFO 2026-06-08 08:44:19 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr2:112,388,114
INFO 2026-06-08 08:44:19 MarkDuplicates Tracking 1088500 as yet unmatched pairs. 39879 records in RAM.
INFO 2026-06-08 08:44:21 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:121,430,110
INFO 2026-06-08 08:44:21 MarkDuplicates Tracking 1086249 as yet unmatched pairs. 37616 records in RAM.
INFO 2026-06-08 08:44:22 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr2:138,005,103
INFO 2026-06-08 08:44:22 MarkDuplicates Tracking 1083655 as yet unmatched pairs. 35011 records in RAM.
INFO 2026-06-08 08:44:24 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:159,780,981
INFO 2026-06-08 08:44:24 MarkDuplicates Tracking 1081189 as yet unmatched pairs. 32526 records in RAM.
INFO 2026-06-08 08:44:25 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:173,963,806
INFO 2026-06-08 08:44:25 MarkDuplicates Tracking 1078801 as yet unmatched pairs. 30119 records in RAM.
INFO 2026-06-08 08:44:27 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr2:182,983,303
INFO 2026-06-08 08:44:27 MarkDuplicates Tracking 1076534 as yet unmatched pairs. 27846 records in RAM.
INFO 2026-06-08 08:44:29 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr2:197,392,999
INFO 2026-06-08 08:44:29 MarkDuplicates Tracking 1073911 as yet unmatched pairs. 25208 records in RAM.
INFO 2026-06-08 08:44:31 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr2:203,251,971
INFO 2026-06-08 08:44:31 MarkDuplicates Tracking 1071029 as yet unmatched pairs. 22316 records in RAM.
INFO 2026-06-08 08:44:32 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:210,606,866
INFO 2026-06-08 08:44:32 MarkDuplicates Tracking 1069806 as yet unmatched pairs. 21080 records in RAM.
INFO 2026-06-08 08:44:33 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr2:215,384,104
INFO 2026-06-08 08:44:33 MarkDuplicates Tracking 1067477 as yet unmatched pairs. 18741 records in RAM.
INFO 2026-06-08 08:44:35 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr2:216,499,369
INFO 2026-06-08 08:44:35 MarkDuplicates Tracking 1066051 as yet unmatched pairs. 17311 records in RAM.
INFO 2026-06-08 08:44:38 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr2:219,169,850
INFO 2026-06-08 08:44:38 MarkDuplicates Tracking 1060619 as yet unmatched pairs. 11871 records in RAM.
INFO 2026-06-08 08:44:39 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr2:227,472,454
INFO 2026-06-08 08:44:39 MarkDuplicates Tracking 1058470 as yet unmatched pairs. 9707 records in RAM.
INFO 2026-06-08 08:44:41 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr2:232,567,158
INFO 2026-06-08 08:44:41 MarkDuplicates Tracking 1055429 as yet unmatched pairs. 6656 records in RAM.
INFO 2026-06-08 08:44:43 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr2:238,253,282
INFO 2026-06-08 08:44:43 MarkDuplicates Tracking 1052483 as yet unmatched pairs. 3679 records in RAM.
INFO 2026-06-08 08:44:44 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr2:241,569,035
INFO 2026-06-08 08:44:44 MarkDuplicates Tracking 1049283 as yet unmatched pairs. 468 records in RAM.
INFO 2026-06-08 08:44:47 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr3:12,609,250
INFO 2026-06-08 08:44:47 MarkDuplicates Tracking 1047141 as yet unmatched pairs. 48295 records in RAM.
INFO 2026-06-08 08:44:49 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr3:33,092,824
INFO 2026-06-08 08:44:49 MarkDuplicates Tracking 1044149 as yet unmatched pairs. 45301 records in RAM.
INFO 2026-06-08 08:44:50 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr3:42,658,440
INFO 2026-06-08 08:44:50 MarkDuplicates Tracking 1041123 as yet unmatched pairs. 42266 records in RAM.
INFO 2026-06-08 08:44:52 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr3:47,870,812
INFO 2026-06-08 08:44:52 MarkDuplicates Tracking 1038252 as yet unmatched pairs. 39390 records in RAM.
INFO 2026-06-08 08:44:54 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr3:49,360,359
INFO 2026-06-08 08:44:54 MarkDuplicates Tracking 1036151 as yet unmatched pairs. 37284 records in RAM.
INFO 2026-06-08 08:44:55 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr3:51,420,506
INFO 2026-06-08 08:44:55 MarkDuplicates Tracking 1032565 as yet unmatched pairs. 33697 records in RAM.
INFO 2026-06-08 08:44:57 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr3:57,584,402
INFO 2026-06-08 08:44:57 MarkDuplicates Tracking 1029779 as yet unmatched pairs. 30900 records in RAM.
INFO 2026-06-08 08:44:59 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr3:100,297,983
INFO 2026-06-08 08:44:59 MarkDuplicates Tracking 1027265 as yet unmatched pairs. 28376 records in RAM.
INFO 2026-06-08 08:45:00 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr3:121,690,795
INFO 2026-06-08 08:45:00 MarkDuplicates Tracking 1024960 as yet unmatched pairs. 26065 records in RAM.
INFO 2026-06-08 08:45:02 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr3:128,067,428
INFO 2026-06-08 08:45:02 MarkDuplicates Tracking 1022337 as yet unmatched pairs. 23429 records in RAM.
INFO 2026-06-08 08:45:03 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr3:136,343,937
INFO 2026-06-08 08:45:03 MarkDuplicates Tracking 1019283 as yet unmatched pairs. 20365 records in RAM.
INFO 2026-06-08 08:45:05 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr3:154,284,888
INFO 2026-06-08 08:45:05 MarkDuplicates Tracking 1016758 as yet unmatched pairs. 17830 records in RAM.
INFO 2026-06-08 08:45:06 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr3:182,620,531
INFO 2026-06-08 08:45:06 MarkDuplicates Tracking 1014145 as yet unmatched pairs. 15201 records in RAM.
INFO 2026-06-08 08:45:08 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr3:187,043,068
INFO 2026-06-08 08:45:08 MarkDuplicates Tracking 1011691 as yet unmatched pairs. 12730 records in RAM.
INFO 2026-06-08 08:45:09 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr3:195,747,133
INFO 2026-06-08 08:45:09 MarkDuplicates Tracking 1010642 as yet unmatched pairs. 11668 records in RAM.
INFO 2026-06-08 08:45:11 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr3:195,779,694
INFO 2026-06-08 08:45:11 MarkDuplicates Tracking 1016145 as yet unmatched pairs. 17170 records in RAM.
INFO 2026-06-08 08:45:12 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr3:195,781,099
INFO 2026-06-08 08:45:12 MarkDuplicates Tracking 1015567 as yet unmatched pairs. 16591 records in RAM.
INFO 2026-06-08 08:45:13 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr3:195,782,310
INFO 2026-06-08 08:45:13 MarkDuplicates Tracking 1015207 as yet unmatched pairs. 16231 records in RAM.
INFO 2026-06-08 08:45:15 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr3:195,783,735
INFO 2026-06-08 08:45:15 MarkDuplicates Tracking 1013411 as yet unmatched pairs. 14433 records in RAM.
INFO 2026-06-08 08:45:16 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr3:195,785,251
INFO 2026-06-08 08:45:16 MarkDuplicates Tracking 1013458 as yet unmatched pairs. 14473 records in RAM.
INFO 2026-06-08 08:45:18 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr3:195,786,962
INFO 2026-06-08 08:45:18 MarkDuplicates Tracking 1004315 as yet unmatched pairs. 5325 records in RAM.
INFO 2026-06-08 08:45:19 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr3:195,867,566
INFO 2026-06-08 08:45:19 MarkDuplicates Tracking 1000291 as yet unmatched pairs. 1295 records in RAM.
INFO 2026-06-08 08:45:21 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr4:1,212,990
INFO 2026-06-08 08:45:21 MarkDuplicates Tracking 998156 as yet unmatched pairs. 40845 records in RAM.
INFO 2026-06-08 08:45:23 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr4:2,947,554
INFO 2026-06-08 08:45:23 MarkDuplicates Tracking 994196 as yet unmatched pairs. 36875 records in RAM.
INFO 2026-06-08 08:45:25 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: chr4:7,868,575
INFO 2026-06-08 08:45:25 MarkDuplicates Tracking 992463 as yet unmatched pairs. 35132 records in RAM.
INFO 2026-06-08 08:45:27 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: chr4:25,655,876
INFO 2026-06-08 08:45:27 MarkDuplicates Tracking 990574 as yet unmatched pairs. 33233 records in RAM.
INFO 2026-06-08 08:45:29 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr4:25,669,672
INFO 2026-06-08 08:45:29 MarkDuplicates Tracking 990079 as yet unmatched pairs. 32737 records in RAM.
INFO 2026-06-08 08:45:30 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr4:25,674,332
INFO 2026-06-08 08:45:30 MarkDuplicates Tracking 992922 as yet unmatched pairs. 35579 records in RAM.
INFO 2026-06-08 08:45:32 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr4:25,676,697
INFO 2026-06-08 08:45:32 MarkDuplicates Tracking 985790 as yet unmatched pairs. 28437 records in RAM.
INFO 2026-06-08 08:45:34 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr4:41,661,494
INFO 2026-06-08 08:45:34 MarkDuplicates Tracking 978829 as yet unmatched pairs. 21467 records in RAM.
INFO 2026-06-08 08:45:35 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr4:56,986,372
INFO 2026-06-08 08:45:35 MarkDuplicates Tracking 976327 as yet unmatched pairs. 18952 records in RAM.
INFO 2026-06-08 08:45:37 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr4:76,741,071
INFO 2026-06-08 08:45:37 MarkDuplicates Tracking 973805 as yet unmatched pairs. 16423 records in RAM.
INFO 2026-06-08 08:45:39 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr4:87,114,705
INFO 2026-06-08 08:45:39 MarkDuplicates Tracking 971065 as yet unmatched pairs. 13669 records in RAM.
INFO 2026-06-08 08:45:40 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr4:105,235,570
INFO 2026-06-08 08:45:40 MarkDuplicates Tracking 969080 as yet unmatched pairs. 11677 records in RAM.
INFO 2026-06-08 08:45:42 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr4:113,213,982
INFO 2026-06-08 08:45:42 MarkDuplicates Tracking 966139 as yet unmatched pairs. 8719 records in RAM.
INFO 2026-06-08 08:45:43 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr4:139,703,469
INFO 2026-06-08 08:45:43 MarkDuplicates Tracking 963943 as yet unmatched pairs. 6519 records in RAM.
INFO 2026-06-08 08:45:45 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr4:151,175,156
INFO 2026-06-08 08:45:45 MarkDuplicates Tracking 961613 as yet unmatched pairs. 4169 records in RAM.
INFO 2026-06-08 08:45:46 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr4:169,116,496
INFO 2026-06-08 08:45:46 MarkDuplicates Tracking 959029 as yet unmatched pairs. 1573 records in RAM.
INFO 2026-06-08 08:45:49 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr5:1,474,644
INFO 2026-06-08 08:45:49 MarkDuplicates Tracking 957517 as yet unmatched pairs. 56445 records in RAM.
INFO 2026-06-08 08:45:50 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr5:14,358,189
INFO 2026-06-08 08:45:50 MarkDuplicates Tracking 955090 as yet unmatched pairs. 53980 records in RAM.
INFO 2026-06-08 08:45:52 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr5:17,275,376
INFO 2026-06-08 08:45:52 MarkDuplicates Tracking 950860 as yet unmatched pairs. 49750 records in RAM.
INFO 2026-06-08 08:45:54 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr5:39,202,658
INFO 2026-06-08 08:45:54 MarkDuplicates Tracking 948607 as yet unmatched pairs. 47487 records in RAM.
INFO 2026-06-08 08:45:56 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr5:59,215,824
INFO 2026-06-08 08:45:56 MarkDuplicates Tracking 947222 as yet unmatched pairs. 46091 records in RAM.
INFO 2026-06-08 08:45:57 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr5:70,110,290
INFO 2026-06-08 08:45:57 MarkDuplicates Tracking 943643 as yet unmatched pairs. 42490 records in RAM.
INFO 2026-06-08 08:45:59 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr5:78,510,020
INFO 2026-06-08 08:45:59 MarkDuplicates Tracking 941449 as yet unmatched pairs. 40288 records in RAM.
INFO 2026-06-08 08:46:01 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr5:95,900,959
INFO 2026-06-08 08:46:01 MarkDuplicates Tracking 939112 as yet unmatched pairs. 37934 records in RAM.
INFO 2026-06-08 08:46:03 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr5:115,831,767
INFO 2026-06-08 08:46:03 MarkDuplicates Tracking 936594 as yet unmatched pairs. 35410 records in RAM.
INFO 2026-06-08 08:46:05 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr5:133,400,897
INFO 2026-06-08 08:46:05 MarkDuplicates Tracking 933994 as yet unmatched pairs. 32804 records in RAM.
INFO 2026-06-08 08:46:06 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr5:138,824,644
INFO 2026-06-08 08:46:06 MarkDuplicates Tracking 932010 as yet unmatched pairs. 30813 records in RAM.
INFO 2026-06-08 08:46:08 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr5:141,184,408
INFO 2026-06-08 08:46:08 MarkDuplicates Tracking 928659 as yet unmatched pairs. 27420 records in RAM.
INFO 2026-06-08 08:46:09 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr5:141,422,625
INFO 2026-06-08 08:46:09 MarkDuplicates Tracking 926343 as yet unmatched pairs. 25098 records in RAM.
INFO 2026-06-08 08:46:11 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr5:146,261,527
INFO 2026-06-08 08:46:11 MarkDuplicates Tracking 923067 as yet unmatched pairs. 21818 records in RAM.
INFO 2026-06-08 08:46:12 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,205
INFO 2026-06-08 08:46:12 MarkDuplicates Tracking 943803 as yet unmatched pairs. 42543 records in RAM.
INFO 2026-06-08 08:46:14 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr5:150,406,259
INFO 2026-06-08 08:46:14 MarkDuplicates Tracking 932232 as yet unmatched pairs. 30970 records in RAM.
INFO 2026-06-08 08:46:16 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr5:151,063,711
INFO 2026-06-08 08:46:16 MarkDuplicates Tracking 914209 as yet unmatched pairs. 12939 records in RAM.
INFO 2026-06-08 08:46:17 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr5:163,518,531
INFO 2026-06-08 08:46:17 MarkDuplicates Tracking 911531 as yet unmatched pairs. 10246 records in RAM.
INFO 2026-06-08 08:46:19 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr5:173,953,178
INFO 2026-06-08 08:46:19 MarkDuplicates Tracking 909252 as yet unmatched pairs. 7954 records in RAM.
INFO 2026-06-08 08:46:20 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr5:178,612,445
INFO 2026-06-08 08:46:20 MarkDuplicates Tracking 906346 as yet unmatched pairs. 5031 records in RAM.
INFO 2026-06-08 08:46:22 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr5:179,833,188
INFO 2026-06-08 08:46:22 MarkDuplicates Tracking 904636 as yet unmatched pairs. 3319 records in RAM.
INFO 2026-06-08 08:46:24 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr6:2,835,990
INFO 2026-06-08 08:46:24 MarkDuplicates Tracking 900765 as yet unmatched pairs. 53771 records in RAM.
INFO 2026-06-08 08:46:26 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr6:7,541,861
INFO 2026-06-08 08:46:26 MarkDuplicates Tracking 897728 as yet unmatched pairs. 50721 records in RAM.
INFO 2026-06-08 08:46:27 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr6:17,787,776
INFO 2026-06-08 08:46:27 MarkDuplicates Tracking 895055 as yet unmatched pairs. 48040 records in RAM.
INFO 2026-06-08 08:46:29 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr6:27,838,703
INFO 2026-06-08 08:46:29 MarkDuplicates Tracking 892257 as yet unmatched pairs. 45237 records in RAM.
INFO 2026-06-08 08:46:31 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr6:30,186,451
INFO 2026-06-08 08:46:31 MarkDuplicates Tracking 889834 as yet unmatched pairs. 42810 records in RAM.
INFO 2026-06-08 08:46:33 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr6:30,986,658
INFO 2026-06-08 08:46:33 MarkDuplicates Tracking 887525 as yet unmatched pairs. 40495 records in RAM.
INFO 2026-06-08 08:46:35 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr6:31,627,962
INFO 2026-06-08 08:46:35 MarkDuplicates Tracking 885104 as yet unmatched pairs. 38068 records in RAM.
INFO 2026-06-08 08:46:37 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr6:31,829,102
INFO 2026-06-08 08:46:37 MarkDuplicates Tracking 882570 as yet unmatched pairs. 35533 records in RAM.
INFO 2026-06-08 08:46:38 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr6:32,440,006
INFO 2026-06-08 08:46:38 MarkDuplicates Tracking 880718 as yet unmatched pairs. 33678 records in RAM.
INFO 2026-06-08 08:46:40 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr6:33,292,238
INFO 2026-06-08 08:46:40 MarkDuplicates Tracking 877690 as yet unmatched pairs. 30647 records in RAM.
INFO 2026-06-08 08:46:41 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr6:33,691,066
INFO 2026-06-08 08:46:41 MarkDuplicates Tracking 874436 as yet unmatched pairs. 27389 records in RAM.
INFO 2026-06-08 08:46:43 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr6:38,592,635
INFO 2026-06-08 08:46:43 MarkDuplicates Tracking 871461 as yet unmatched pairs. 24407 records in RAM.
INFO 2026-06-08 08:46:45 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr6:43,213,223
INFO 2026-06-08 08:46:45 MarkDuplicates Tracking 868357 as yet unmatched pairs. 21295 records in RAM.
INFO 2026-06-08 08:46:46 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr6:46,856,729
INFO 2026-06-08 08:46:46 MarkDuplicates Tracking 866771 as yet unmatched pairs. 19705 records in RAM.
INFO 2026-06-08 08:46:48 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr6:63,280,437
INFO 2026-06-08 08:46:48 MarkDuplicates Tracking 863875 as yet unmatched pairs. 16782 records in RAM.
INFO 2026-06-08 08:46:50 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr6:83,893,611
INFO 2026-06-08 08:46:50 MarkDuplicates Tracking 860601 as yet unmatched pairs. 13475 records in RAM.
INFO 2026-06-08 08:46:51 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr6:109,796,817
INFO 2026-06-08 08:46:51 MarkDuplicates Tracking 858058 as yet unmatched pairs. 10914 records in RAM.
INFO 2026-06-08 08:46:53 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr6:136,372,512
INFO 2026-06-08 08:46:53 MarkDuplicates Tracking 855806 as yet unmatched pairs. 8658 records in RAM.
INFO 2026-06-08 08:46:55 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr6:152,136,646
INFO 2026-06-08 08:46:55 MarkDuplicates Tracking 853012 as yet unmatched pairs. 5861 records in RAM.
INFO 2026-06-08 08:46:56 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr6:158,785,490
INFO 2026-06-08 08:46:56 MarkDuplicates Tracking 856556 as yet unmatched pairs. 9401 records in RAM.
INFO 2026-06-08 08:46:58 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr6:170,317,476
INFO 2026-06-08 08:46:58 MarkDuplicates Tracking 847709 as yet unmatched pairs. 550 records in RAM.
INFO 2026-06-08 08:47:00 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr7:2,937,948
INFO 2026-06-08 08:47:00 MarkDuplicates Tracking 843889 as yet unmatched pairs. 54918 records in RAM.
INFO 2026-06-08 08:47:01 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr7:5,388,630
INFO 2026-06-08 08:47:01 MarkDuplicates Tracking 840811 as yet unmatched pairs. 51827 records in RAM.
INFO 2026-06-08 08:47:03 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,576
INFO 2026-06-08 08:47:03 MarkDuplicates Tracking 839197 as yet unmatched pairs. 50207 records in RAM.
INFO 2026-06-08 08:47:06 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr7:20,158,323
INFO 2026-06-08 08:47:06 MarkDuplicates Tracking 835560 as yet unmatched pairs. 46564 records in RAM.
INFO 2026-06-08 08:47:08 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 2s. Last read position: chr7:30,631,450
INFO 2026-06-08 08:47:08 MarkDuplicates Tracking 832847 as yet unmatched pairs. 43841 records in RAM.
INFO 2026-06-08 08:47:09 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr7:44,565,872
INFO 2026-06-08 08:47:09 MarkDuplicates Tracking 830240 as yet unmatched pairs. 41225 records in RAM.
INFO 2026-06-08 08:47:11 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr7:55,912,681
INFO 2026-06-08 08:47:11 MarkDuplicates Tracking 827215 as yet unmatched pairs. 38193 records in RAM.
INFO 2026-06-08 08:47:12 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr7:72,942,542
INFO 2026-06-08 08:47:12 MarkDuplicates Tracking 825137 as yet unmatched pairs. 36104 records in RAM.
INFO 2026-06-08 08:47:13 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr7:74,689,173
INFO 2026-06-08 08:47:13 MarkDuplicates Tracking 824011 as yet unmatched pairs. 34978 records in RAM.
INFO 2026-06-08 08:47:15 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr7:75,881,989
INFO 2026-06-08 08:47:15 MarkDuplicates Tracking 822301 as yet unmatched pairs. 33267 records in RAM.
INFO 2026-06-08 08:47:16 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr7:82,443,248
INFO 2026-06-08 08:47:16 MarkDuplicates Tracking 819248 as yet unmatched pairs. 30205 records in RAM.
INFO 2026-06-08 08:47:18 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr7:92,447,679
INFO 2026-06-08 08:47:18 MarkDuplicates Tracking 816849 as yet unmatched pairs. 27796 records in RAM.
INFO 2026-06-08 08:47:20 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr7:99,386,767
INFO 2026-06-08 08:47:20 MarkDuplicates Tracking 814835 as yet unmatched pairs. 25761 records in RAM.
INFO 2026-06-08 08:47:21 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr7:100,681,712
INFO 2026-06-08 08:47:21 MarkDuplicates Tracking 811500 as yet unmatched pairs. 22424 records in RAM.
INFO 2026-06-08 08:47:23 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr7:102,539,655
INFO 2026-06-08 08:47:23 MarkDuplicates Tracking 809685 as yet unmatched pairs. 20608 records in RAM.
INFO 2026-06-08 08:47:24 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr7:104,669,198
INFO 2026-06-08 08:47:24 MarkDuplicates Tracking 807874 as yet unmatched pairs. 18796 records in RAM.
INFO 2026-06-08 08:47:26 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr7:116,755,397
INFO 2026-06-08 08:47:26 MarkDuplicates Tracking 806330 as yet unmatched pairs. 17245 records in RAM.
INFO 2026-06-08 08:47:27 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr7:127,929,298
INFO 2026-06-08 08:47:27 MarkDuplicates Tracking 803558 as yet unmatched pairs. 14472 records in RAM.
INFO 2026-06-08 08:47:29 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr7:135,672,766
INFO 2026-06-08 08:47:29 MarkDuplicates Tracking 800484 as yet unmatched pairs. 11372 records in RAM.
INFO 2026-06-08 08:47:31 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: chr7:140,456,651
INFO 2026-06-08 08:47:31 MarkDuplicates Tracking 797841 as yet unmatched pairs. 8722 records in RAM.
INFO 2026-06-08 08:47:34 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr7:144,362,925
INFO 2026-06-08 08:47:34 MarkDuplicates Tracking 795564 as yet unmatched pairs. 6445 records in RAM.
INFO 2026-06-08 08:47:35 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr7:151,074,806
INFO 2026-06-08 08:47:35 MarkDuplicates Tracking 792927 as yet unmatched pairs. 3804 records in RAM.
INFO 2026-06-08 08:47:37 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr7:157,256,387
INFO 2026-06-08 08:47:37 MarkDuplicates Tracking 789798 as yet unmatched pairs. 668 records in RAM.
INFO 2026-06-08 08:47:39 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr8:11,845,206
INFO 2026-06-08 08:47:39 MarkDuplicates Tracking 791349 as yet unmatched pairs. 49526 records in RAM.
INFO 2026-06-08 08:47:40 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr8:17,924,728
INFO 2026-06-08 08:47:40 MarkDuplicates Tracking 784531 as yet unmatched pairs. 42702 records in RAM.
INFO 2026-06-08 08:47:42 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr8:22,614,211
INFO 2026-06-08 08:47:42 MarkDuplicates Tracking 782278 as yet unmatched pairs. 40442 records in RAM.
INFO 2026-06-08 08:47:43 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr8:26,291,708
INFO 2026-06-08 08:47:43 MarkDuplicates Tracking 779055 as yet unmatched pairs. 37204 records in RAM.
INFO 2026-06-08 08:47:45 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr8:30,799,616
INFO 2026-06-08 08:47:45 MarkDuplicates Tracking 776285 as yet unmatched pairs. 34423 records in RAM.
INFO 2026-06-08 08:47:47 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr8:38,820,284
INFO 2026-06-08 08:47:47 MarkDuplicates Tracking 773562 as yet unmatched pairs. 31699 records in RAM.
INFO 2026-06-08 08:47:48 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr8:47,817,541
INFO 2026-06-08 08:47:48 MarkDuplicates Tracking 770592 as yet unmatched pairs. 28728 records in RAM.
INFO 2026-06-08 08:47:50 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr8:66,429,974
INFO 2026-06-08 08:47:50 MarkDuplicates Tracking 767869 as yet unmatched pairs. 25998 records in RAM.
INFO 2026-06-08 08:47:51 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr8:81,693,904
INFO 2026-06-08 08:47:51 MarkDuplicates Tracking 765540 as yet unmatched pairs. 23663 records in RAM.
INFO 2026-06-08 08:47:53 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr8:100,259,064
INFO 2026-06-08 08:47:53 MarkDuplicates Tracking 763236 as yet unmatched pairs. 21349 records in RAM.
INFO 2026-06-08 08:47:55 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr8:116,646,548
INFO 2026-06-08 08:47:55 MarkDuplicates Tracking 760537 as yet unmatched pairs. 18646 records in RAM.
INFO 2026-06-08 08:47:56 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr8:133,246,643
INFO 2026-06-08 08:47:56 MarkDuplicates Tracking 758635 as yet unmatched pairs. 16720 records in RAM.
INFO 2026-06-08 08:47:57 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr8:143,693,704
INFO 2026-06-08 08:47:57 MarkDuplicates Tracking 754683 as yet unmatched pairs. 12757 records in RAM.
INFO 2026-06-08 08:47:59 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,812
INFO 2026-06-08 08:47:59 MarkDuplicates Tracking 752910 as yet unmatched pairs. 10980 records in RAM.
INFO 2026-06-08 08:48:00 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,990
INFO 2026-06-08 08:48:00 MarkDuplicates Tracking 753832 as yet unmatched pairs. 11902 records in RAM.
INFO 2026-06-08 08:48:01 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,232
INFO 2026-06-08 08:48:01 MarkDuplicates Tracking 750645 as yet unmatched pairs. 8714 records in RAM.
INFO 2026-06-08 08:48:03 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr8:143,922,728
INFO 2026-06-08 08:48:03 MarkDuplicates Tracking 748237 as yet unmatched pairs. 6304 records in RAM.
INFO 2026-06-08 08:48:04 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr8:144,321,397
INFO 2026-06-08 08:48:04 MarkDuplicates Tracking 743927 as yet unmatched pairs. 1991 records in RAM.
INFO 2026-06-08 08:48:06 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chr9:6,413,528
INFO 2026-06-08 08:48:06 MarkDuplicates Tracking 741046 as yet unmatched pairs. 42756 records in RAM.
INFO 2026-06-08 08:48:09 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 2s. Last read position: chr9:33,264,235
INFO 2026-06-08 08:48:09 MarkDuplicates Tracking 739318 as yet unmatched pairs. 41012 records in RAM.
INFO 2026-06-08 08:48:11 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr9:35,703,889
INFO 2026-06-08 08:48:11 MarkDuplicates Tracking 736198 as yet unmatched pairs. 37873 records in RAM.
INFO 2026-06-08 08:48:12 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr9:71,866,997
INFO 2026-06-08 08:48:12 MarkDuplicates Tracking 733219 as yet unmatched pairs. 34883 records in RAM.
INFO 2026-06-08 08:48:14 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr9:87,706,418
INFO 2026-06-08 08:48:14 MarkDuplicates Tracking 730743 as yet unmatched pairs. 32406 records in RAM.
INFO 2026-06-08 08:48:16 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr9:94,800,781
INFO 2026-06-08 08:48:16 MarkDuplicates Tracking 727991 as yet unmatched pairs. 29645 records in RAM.
INFO 2026-06-08 08:48:17 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr9:106,926,040
INFO 2026-06-08 08:48:17 MarkDuplicates Tracking 725137 as yet unmatched pairs. 26783 records in RAM.
INFO 2026-06-08 08:48:19 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr9:114,359,555
INFO 2026-06-08 08:48:19 MarkDuplicates Tracking 722428 as yet unmatched pairs. 24061 records in RAM.
INFO 2026-06-08 08:48:20 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr9:122,285,210
INFO 2026-06-08 08:48:20 MarkDuplicates Tracking 719564 as yet unmatched pairs. 21197 records in RAM.
INFO 2026-06-08 08:48:22 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr9:127,506,846
INFO 2026-06-08 08:48:22 MarkDuplicates Tracking 717261 as yet unmatched pairs. 18888 records in RAM.
INFO 2026-06-08 08:48:24 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr9:128,577,203
INFO 2026-06-08 08:48:24 MarkDuplicates Tracking 714269 as yet unmatched pairs. 15895 records in RAM.
INFO 2026-06-08 08:48:25 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr9:130,854,921
INFO 2026-06-08 08:48:25 MarkDuplicates Tracking 711563 as yet unmatched pairs. 13187 records in RAM.
INFO 2026-06-08 08:48:27 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr9:132,330,333
INFO 2026-06-08 08:48:27 MarkDuplicates Tracking 708127 as yet unmatched pairs. 9748 records in RAM.
INFO 2026-06-08 08:48:28 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr9:135,815,890
INFO 2026-06-08 08:48:28 MarkDuplicates Tracking 705292 as yet unmatched pairs. 6912 records in RAM.
INFO 2026-06-08 08:48:30 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr9:136,859,124
INFO 2026-06-08 08:48:30 MarkDuplicates Tracking 702138 as yet unmatched pairs. 3757 records in RAM.
INFO 2026-06-08 08:48:31 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr9:137,777,948
INFO 2026-06-08 08:48:31 MarkDuplicates Tracking 698660 as yet unmatched pairs. 274 records in RAM.
INFO 2026-06-08 08:48:33 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 2s. Last read position: chr10:11,321,215
INFO 2026-06-08 08:48:33 MarkDuplicates Tracking 696262 as yet unmatched pairs. 38454 records in RAM.
INFO 2026-06-08 08:48:35 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr10:26,533,500
INFO 2026-06-08 08:48:35 MarkDuplicates Tracking 693440 as yet unmatched pairs. 35628 records in RAM.
INFO 2026-06-08 08:48:37 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr10:32,055,872
INFO 2026-06-08 08:48:37 MarkDuplicates Tracking 691694 as yet unmatched pairs. 33875 records in RAM.
INFO 2026-06-08 08:48:39 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr10:45,424,075
INFO 2026-06-08 08:48:39 MarkDuplicates Tracking 688610 as yet unmatched pairs. 30765 records in RAM.
INFO 2026-06-08 08:48:41 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr10:48,873,606
INFO 2026-06-08 08:48:41 MarkDuplicates Tracking 686586 as yet unmatched pairs. 28740 records in RAM.
INFO 2026-06-08 08:48:42 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr10:67,823,322
INFO 2026-06-08 08:48:42 MarkDuplicates Tracking 684141 as yet unmatched pairs. 26288 records in RAM.
INFO 2026-06-08 08:48:44 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr10:73,396,573
INFO 2026-06-08 08:48:44 MarkDuplicates Tracking 681696 as yet unmatched pairs. 23839 records in RAM.
INFO 2026-06-08 08:48:45 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr10:78,037,200
INFO 2026-06-08 08:48:45 MarkDuplicates Tracking 680656 as yet unmatched pairs. 22791 records in RAM.
INFO 2026-06-08 08:48:47 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr10:87,864,382
INFO 2026-06-08 08:48:47 MarkDuplicates Tracking 677046 as yet unmatched pairs. 19172 records in RAM.
INFO 2026-06-08 08:48:49 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr10:95,839,728
INFO 2026-06-08 08:48:49 MarkDuplicates Tracking 674191 as yet unmatched pairs. 16316 records in RAM.
INFO 2026-06-08 08:48:50 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr10:100,945,418
INFO 2026-06-08 08:48:50 MarkDuplicates Tracking 671285 as yet unmatched pairs. 13408 records in RAM.
INFO 2026-06-08 08:48:51 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr10:102,809,990
INFO 2026-06-08 08:48:51 MarkDuplicates Tracking 668203 as yet unmatched pairs. 10323 records in RAM.
INFO 2026-06-08 08:48:53 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr10:114,833,274
INFO 2026-06-08 08:48:53 MarkDuplicates Tracking 665803 as yet unmatched pairs. 7914 records in RAM.
INFO 2026-06-08 08:48:55 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr10:122,050,487
INFO 2026-06-08 08:48:55 MarkDuplicates Tracking 663313 as yet unmatched pairs. 5411 records in RAM.
INFO 2026-06-08 08:48:56 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr10:124,834,681
INFO 2026-06-08 08:48:56 MarkDuplicates Tracking 661019 as yet unmatched pairs. 3113 records in RAM.
INFO 2026-06-08 08:48:58 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr10:133,537,146
INFO 2026-06-08 08:48:58 MarkDuplicates Tracking 657958 as yet unmatched pairs. 46 records in RAM.
INFO 2026-06-08 08:49:00 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 2s. Last read position: chr11:320,577
INFO 2026-06-08 08:49:00 MarkDuplicates Tracking 658208 as yet unmatched pairs. 116145 records in RAM.
INFO 2026-06-08 08:49:02 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr11:726,122
INFO 2026-06-08 08:49:02 MarkDuplicates Tracking 652532 as yet unmatched pairs. 110468 records in RAM.
INFO 2026-06-08 08:49:04 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr11:1,178,615
INFO 2026-06-08 08:49:04 MarkDuplicates Tracking 649606 as yet unmatched pairs. 107540 records in RAM.
INFO 2026-06-08 08:49:05 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr11:1,184,900
INFO 2026-06-08 08:49:05 MarkDuplicates Tracking 647335 as yet unmatched pairs. 105267 records in RAM.
INFO 2026-06-08 08:49:07 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr11:1,188,831
INFO 2026-06-08 08:49:07 MarkDuplicates Tracking 647530 as yet unmatched pairs. 105453 records in RAM.
INFO 2026-06-08 08:49:08 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr11:1,191,736
INFO 2026-06-08 08:49:08 MarkDuplicates Tracking 645023 as yet unmatched pairs. 102940 records in RAM.
INFO 2026-06-08 08:49:11 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 2s. Last read position: chr11:1,231,503
INFO 2026-06-08 08:49:11 MarkDuplicates Tracking 641877 as yet unmatched pairs. 99782 records in RAM.
INFO 2026-06-08 08:49:13 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr11:1,242,162
INFO 2026-06-08 08:49:13 MarkDuplicates Tracking 639418 as yet unmatched pairs. 97317 records in RAM.
INFO 2026-06-08 08:50:11 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 58s. Last read position: chr11:1,243,078
INFO 2026-06-08 08:50:11 MarkDuplicates Tracking 636781 as yet unmatched pairs. 94680 records in RAM.
INFO 2026-06-08 08:50:13 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr11:1,243,491
INFO 2026-06-08 08:50:13 MarkDuplicates Tracking 637841 as yet unmatched pairs. 95740 records in RAM.
INFO 2026-06-08 08:50:14 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr11:1,244,028
INFO 2026-06-08 08:50:14 MarkDuplicates Tracking 638989 as yet unmatched pairs. 96887 records in RAM.
INFO 2026-06-08 08:50:15 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr11:1,244,469
INFO 2026-06-08 08:50:15 MarkDuplicates Tracking 636055 as yet unmatched pairs. 93953 records in RAM.
INFO 2026-06-08 08:50:17 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr11:1,245,000
INFO 2026-06-08 08:50:17 MarkDuplicates Tracking 634469 as yet unmatched pairs. 92367 records in RAM.
INFO 2026-06-08 08:50:18 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr11:1,245,286
INFO 2026-06-08 08:50:18 MarkDuplicates Tracking 635965 as yet unmatched pairs. 93863 records in RAM.
INFO 2026-06-08 08:50:19 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr11:1,246,184
INFO 2026-06-08 08:50:19 MarkDuplicates Tracking 634922 as yet unmatched pairs. 92820 records in RAM.
INFO 2026-06-08 08:50:20 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr11:1,246,917
INFO 2026-06-08 08:50:20 MarkDuplicates Tracking 633704 as yet unmatched pairs. 91602 records in RAM.
INFO 2026-06-08 08:50:22 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr11:1,247,321
INFO 2026-06-08 08:50:22 MarkDuplicates Tracking 634397 as yet unmatched pairs. 92295 records in RAM.
INFO 2026-06-08 08:50:24 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr11:1,248,004
INFO 2026-06-08 08:50:24 MarkDuplicates Tracking 630520 as yet unmatched pairs. 88418 records in RAM.
INFO 2026-06-08 08:50:25 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr11:1,248,348
INFO 2026-06-08 08:50:25 MarkDuplicates Tracking 629918 as yet unmatched pairs. 87816 records in RAM.
INFO 2026-06-08 08:50:26 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr11:1,248,878
INFO 2026-06-08 08:50:26 MarkDuplicates Tracking 632417 as yet unmatched pairs. 90313 records in RAM.
INFO 2026-06-08 08:50:27 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr11:1,249,442
INFO 2026-06-08 08:50:27 MarkDuplicates Tracking 626762 as yet unmatched pairs. 84654 records in RAM.
INFO 2026-06-08 08:50:29 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr11:1,250,249
INFO 2026-06-08 08:50:29 MarkDuplicates Tracking 623865 as yet unmatched pairs. 81757 records in RAM.
INFO 2026-06-08 08:50:31 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr11:1,250,831
INFO 2026-06-08 08:50:31 MarkDuplicates Tracking 620583 as yet unmatched pairs. 78475 records in RAM.
INFO 2026-06-08 08:50:33 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr11:1,254,760
INFO 2026-06-08 08:50:33 MarkDuplicates Tracking 617444 as yet unmatched pairs. 75330 records in RAM.
INFO 2026-06-08 08:50:36 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 3s. Last read position: chr11:1,757,458
INFO 2026-06-08 08:50:36 MarkDuplicates Tracking 616627 as yet unmatched pairs. 74507 records in RAM.
INFO 2026-06-08 08:50:38 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr11:3,773,680
INFO 2026-06-08 08:50:38 MarkDuplicates Tracking 610544 as yet unmatched pairs. 68421 records in RAM.
INFO 2026-06-08 08:50:39 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr11:9,434,944
INFO 2026-06-08 08:50:39 MarkDuplicates Tracking 607992 as yet unmatched pairs. 65864 records in RAM.
INFO 2026-06-08 08:50:41 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr11:16,754,875
INFO 2026-06-08 08:50:41 MarkDuplicates Tracking 605790 as yet unmatched pairs. 63658 records in RAM.
INFO 2026-06-08 08:50:42 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr11:33,057,949
INFO 2026-06-08 08:50:42 MarkDuplicates Tracking 602503 as yet unmatched pairs. 60367 records in RAM.
INFO 2026-06-08 08:50:44 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr11:46,299,949
INFO 2026-06-08 08:50:44 MarkDuplicates Tracking 602306 as yet unmatched pairs. 60165 records in RAM.
INFO 2026-06-08 08:50:46 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr11:46,809,399
INFO 2026-06-08 08:50:46 MarkDuplicates Tracking 597269 as yet unmatched pairs. 55126 records in RAM.
INFO 2026-06-08 08:50:47 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr11:57,682,505
INFO 2026-06-08 08:50:47 MarkDuplicates Tracking 594551 as yet unmatched pairs. 52389 records in RAM.
INFO 2026-06-08 08:50:49 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr11:61,313,952
INFO 2026-06-08 08:50:49 MarkDuplicates Tracking 591686 as yet unmatched pairs. 49524 records in RAM.
INFO 2026-06-08 08:50:50 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr11:62,528,749
INFO 2026-06-08 08:50:50 MarkDuplicates Tracking 589476 as yet unmatched pairs. 47297 records in RAM.
INFO 2026-06-08 08:50:52 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr11:63,539,544
INFO 2026-06-08 08:50:52 MarkDuplicates Tracking 587145 as yet unmatched pairs. 44957 records in RAM.
INFO 2026-06-08 08:50:53 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr11:64,768,108
INFO 2026-06-08 08:50:53 MarkDuplicates Tracking 584169 as yet unmatched pairs. 41980 records in RAM.
INFO 2026-06-08 08:50:55 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr11:65,539,724
INFO 2026-06-08 08:50:55 MarkDuplicates Tracking 580591 as yet unmatched pairs. 38375 records in RAM.
INFO 2026-06-08 08:50:57 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr11:65,718,542
INFO 2026-06-08 08:50:57 MarkDuplicates Tracking 577050 as yet unmatched pairs. 34827 records in RAM.
INFO 2026-06-08 08:50:58 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr11:66,721,166
INFO 2026-06-08 08:50:58 MarkDuplicates Tracking 573797 as yet unmatched pairs. 31566 records in RAM.
INFO 2026-06-08 08:51:00 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr11:67,585,228
INFO 2026-06-08 08:51:00 MarkDuplicates Tracking 572901 as yet unmatched pairs. 30668 records in RAM.
INFO 2026-06-08 08:51:01 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr11:68,609,913
INFO 2026-06-08 08:51:01 MarkDuplicates Tracking 567511 as yet unmatched pairs. 25273 records in RAM.
INFO 2026-06-08 08:51:03 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr11:72,009,283
INFO 2026-06-08 08:51:03 MarkDuplicates Tracking 565143 as yet unmatched pairs. 22905 records in RAM.
INFO 2026-06-08 08:51:04 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr11:72,770,318
INFO 2026-06-08 08:51:04 MarkDuplicates Tracking 561683 as yet unmatched pairs. 19434 records in RAM.
INFO 2026-06-08 08:51:06 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr11:76,546,024
INFO 2026-06-08 08:51:06 MarkDuplicates Tracking 558869 as yet unmatched pairs. 16619 records in RAM.
INFO 2026-06-08 08:51:08 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr11:93,698,994
INFO 2026-06-08 08:51:08 MarkDuplicates Tracking 556131 as yet unmatched pairs. 13875 records in RAM.
INFO 2026-06-08 08:51:10 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr11:104,942,913
INFO 2026-06-08 08:51:10 MarkDuplicates Tracking 553520 as yet unmatched pairs. 11262 records in RAM.
INFO 2026-06-08 08:51:12 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr11:117,195,811
INFO 2026-06-08 08:51:12 MarkDuplicates Tracking 551063 as yet unmatched pairs. 8802 records in RAM.
INFO 2026-06-08 08:51:14 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 2s. Last read position: chr11:118,900,140
INFO 2026-06-08 08:51:14 MarkDuplicates Tracking 548790 as yet unmatched pairs. 6528 records in RAM.
INFO 2026-06-08 08:51:15 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr11:123,059,774
INFO 2026-06-08 08:51:15 MarkDuplicates Tracking 547307 as yet unmatched pairs. 5038 records in RAM.
INFO 2026-06-08 08:51:17 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr11:130,194,068
INFO 2026-06-08 08:51:17 MarkDuplicates Tracking 543169 as yet unmatched pairs. 893 records in RAM.
INFO 2026-06-08 08:51:19 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: chr12:2,803,174
INFO 2026-06-08 08:51:19 MarkDuplicates Tracking 540515 as yet unmatched pairs. 72291 records in RAM.
INFO 2026-06-08 08:51:21 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr12:6,374,630
INFO 2026-06-08 08:51:21 MarkDuplicates Tracking 543626 as yet unmatched pairs. 75399 records in RAM.
INFO 2026-06-08 08:51:22 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr12:6,936,516
INFO 2026-06-08 08:51:22 MarkDuplicates Tracking 535234 as yet unmatched pairs. 67004 records in RAM.
INFO 2026-06-08 08:51:24 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr12:8,932,893
INFO 2026-06-08 08:51:24 MarkDuplicates Tracking 532189 as yet unmatched pairs. 63950 records in RAM.
INFO 2026-06-08 08:51:25 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr12:11,267,729
INFO 2026-06-08 08:51:25 MarkDuplicates Tracking 530852 as yet unmatched pairs. 62606 records in RAM.
INFO 2026-06-08 08:51:27 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr12:13,213,735
INFO 2026-06-08 08:51:27 MarkDuplicates Tracking 528562 as yet unmatched pairs. 60314 records in RAM.
INFO 2026-06-08 08:51:28 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr12:25,221,066
INFO 2026-06-08 08:51:28 MarkDuplicates Tracking 525687 as yet unmatched pairs. 57438 records in RAM.
INFO 2026-06-08 08:51:30 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr12:45,926,505
INFO 2026-06-08 08:51:30 MarkDuplicates Tracking 523437 as yet unmatched pairs. 55186 records in RAM.
INFO 2026-06-08 08:51:31 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr12:49,039,864
INFO 2026-06-08 08:51:31 MarkDuplicates Tracking 520523 as yet unmatched pairs. 52271 records in RAM.
INFO 2026-06-08 08:51:33 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr12:49,762,900
INFO 2026-06-08 08:51:33 MarkDuplicates Tracking 518926 as yet unmatched pairs. 50668 records in RAM.
INFO 2026-06-08 08:51:35 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr12:52,235,223
INFO 2026-06-08 08:51:35 MarkDuplicates Tracking 516083 as yet unmatched pairs. 47825 records in RAM.
INFO 2026-06-08 08:51:36 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr12:53,383,004
INFO 2026-06-08 08:51:36 MarkDuplicates Tracking 512055 as yet unmatched pairs. 43789 records in RAM.
INFO 2026-06-08 08:51:38 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr12:55,716,130
INFO 2026-06-08 08:51:38 MarkDuplicates Tracking 509844 as yet unmatched pairs. 41568 records in RAM.
INFO 2026-06-08 08:51:41 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 2s. Last read position: chr12:56,178,454
INFO 2026-06-08 08:51:41 MarkDuplicates Tracking 507322 as yet unmatched pairs. 39046 records in RAM.
INFO 2026-06-08 08:51:42 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr12:56,774,037
INFO 2026-06-08 08:51:42 MarkDuplicates Tracking 504516 as yet unmatched pairs. 36237 records in RAM.
INFO 2026-06-08 08:51:44 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr12:57,106,205
INFO 2026-06-08 08:51:44 MarkDuplicates Tracking 502573 as yet unmatched pairs. 34289 records in RAM.
INFO 2026-06-08 08:51:45 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr12:57,716,165
INFO 2026-06-08 08:51:45 MarkDuplicates Tracking 499366 as yet unmatched pairs. 31062 records in RAM.
INFO 2026-06-08 08:51:47 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr12:68,689,533
INFO 2026-06-08 08:51:47 MarkDuplicates Tracking 496482 as yet unmatched pairs. 28171 records in RAM.
INFO 2026-06-08 08:51:49 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr12:89,525,162
INFO 2026-06-08 08:51:49 MarkDuplicates Tracking 493956 as yet unmatched pairs. 25642 records in RAM.
INFO 2026-06-08 08:51:50 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr12:101,796,676
INFO 2026-06-08 08:51:50 MarkDuplicates Tracking 491940 as yet unmatched pairs. 23623 records in RAM.
INFO 2026-06-08 08:51:52 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr12:109,489,974
INFO 2026-06-08 08:51:52 MarkDuplicates Tracking 489085 as yet unmatched pairs. 20766 records in RAM.
INFO 2026-06-08 08:51:53 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr12:112,141,040
INFO 2026-06-08 08:51:53 MarkDuplicates Tracking 486291 as yet unmatched pairs. 17970 records in RAM.
INFO 2026-06-08 08:51:55 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr12:116,015,230
INFO 2026-06-08 08:51:55 MarkDuplicates Tracking 484116 as yet unmatched pairs. 15785 records in RAM.
INFO 2026-06-08 08:51:56 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr12:120,534,702
INFO 2026-06-08 08:51:56 MarkDuplicates Tracking 480887 as yet unmatched pairs. 12553 records in RAM.
INFO 2026-06-08 08:51:58 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr12:122,860,767
INFO 2026-06-08 08:51:58 MarkDuplicates Tracking 477847 as yet unmatched pairs. 9513 records in RAM.
INFO 2026-06-08 08:51:59 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr12:124,346,612
INFO 2026-06-08 08:51:59 MarkDuplicates Tracking 476637 as yet unmatched pairs. 8296 records in RAM.
INFO 2026-06-08 08:52:01 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr12:131,131,748
INFO 2026-06-08 08:52:01 MarkDuplicates Tracking 473310 as yet unmatched pairs. 4966 records in RAM.
INFO 2026-06-08 08:52:03 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr12:132,782,354
INFO 2026-06-08 08:52:03 MarkDuplicates Tracking 469660 as yet unmatched pairs. 1306 records in RAM.
INFO 2026-06-08 08:52:04 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr13:20,989,090
INFO 2026-06-08 08:52:04 MarkDuplicates Tracking 466653 as yet unmatched pairs. 18094 records in RAM.
INFO 2026-06-08 08:52:06 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr13:33,126,107
INFO 2026-06-08 08:52:06 MarkDuplicates Tracking 464231 as yet unmatched pairs. 15665 records in RAM.
INFO 2026-06-08 08:52:08 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr13:45,340,154
INFO 2026-06-08 08:52:08 MarkDuplicates Tracking 463476 as yet unmatched pairs. 14907 records in RAM.
INFO 2026-06-08 08:52:10 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr13:73,075,737
INFO 2026-06-08 08:52:10 MarkDuplicates Tracking 459631 as yet unmatched pairs. 11058 records in RAM.
INFO 2026-06-08 08:52:12 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 2s. Last read position: chr13:95,186,812
INFO 2026-06-08 08:52:12 MarkDuplicates Tracking 457192 as yet unmatched pairs. 8619 records in RAM.
INFO 2026-06-08 08:52:14 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr13:109,782,700
INFO 2026-06-08 08:52:14 MarkDuplicates Tracking 454015 as yet unmatched pairs. 5436 records in RAM.
INFO 2026-06-08 08:52:15 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr13:112,858,217
INFO 2026-06-08 08:52:15 MarkDuplicates Tracking 453566 as yet unmatched pairs. 4987 records in RAM.
INFO 2026-06-08 08:52:17 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr14:20,993,121
INFO 2026-06-08 08:52:17 MarkDuplicates Tracking 447825 as yet unmatched pairs. 36419 records in RAM.
INFO 2026-06-08 08:52:19 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr14:23,061,513
INFO 2026-06-08 08:52:19 MarkDuplicates Tracking 445035 as yet unmatched pairs. 33629 records in RAM.
INFO 2026-06-08 08:52:20 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr14:24,190,469
INFO 2026-06-08 08:52:20 MarkDuplicates Tracking 442697 as yet unmatched pairs. 31291 records in RAM.
INFO 2026-06-08 08:52:22 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr14:33,950,549
INFO 2026-06-08 08:52:22 MarkDuplicates Tracking 439552 as yet unmatched pairs. 28145 records in RAM.
INFO 2026-06-08 08:52:23 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr14:49,828,326
INFO 2026-06-08 08:52:23 MarkDuplicates Tracking 436750 as yet unmatched pairs. 25335 records in RAM.
INFO 2026-06-08 08:52:25 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr14:64,049,673
INFO 2026-06-08 08:52:25 MarkDuplicates Tracking 434231 as yet unmatched pairs. 22802 records in RAM.
INFO 2026-06-08 08:52:27 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr14:73,170,958
INFO 2026-06-08 08:52:27 MarkDuplicates Tracking 431450 as yet unmatched pairs. 20016 records in RAM.
INFO 2026-06-08 08:52:28 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr14:77,737,028
INFO 2026-06-08 08:52:28 MarkDuplicates Tracking 428948 as yet unmatched pairs. 17511 records in RAM.
INFO 2026-06-08 08:52:30 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr14:93,242,951
INFO 2026-06-08 08:52:30 MarkDuplicates Tracking 426267 as yet unmatched pairs. 14830 records in RAM.
INFO 2026-06-08 08:52:31 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr14:101,997,080
INFO 2026-06-08 08:52:31 MarkDuplicates Tracking 423830 as yet unmatched pairs. 12385 records in RAM.
INFO 2026-06-08 08:52:33 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 2s. Last read position: chr14:103,662,754
INFO 2026-06-08 08:52:33 MarkDuplicates Tracking 420681 as yet unmatched pairs. 9232 records in RAM.
INFO 2026-06-08 08:52:35 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr14:104,944,898
INFO 2026-06-08 08:52:35 MarkDuplicates Tracking 418331 as yet unmatched pairs. 6879 records in RAM.
INFO 2026-06-08 08:52:37 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr14:105,643,240
INFO 2026-06-08 08:52:37 MarkDuplicates Tracking 415069 as yet unmatched pairs. 3615 records in RAM.
INFO 2026-06-08 08:52:38 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr14:105,844,848
INFO 2026-06-08 08:52:38 MarkDuplicates Tracking 412634 as yet unmatched pairs. 1177 records in RAM.
INFO 2026-06-08 08:52:40 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr15:29,719,077
INFO 2026-06-08 08:52:40 MarkDuplicates Tracking 410365 as yet unmatched pairs. 21834 records in RAM.
INFO 2026-06-08 08:52:41 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr15:40,411,670
INFO 2026-06-08 08:52:41 MarkDuplicates Tracking 408187 as yet unmatched pairs. 19649 records in RAM.
INFO 2026-06-08 08:52:43 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr15:43,581,377
INFO 2026-06-08 08:52:43 MarkDuplicates Tracking 405575 as yet unmatched pairs. 17031 records in RAM.
INFO 2026-06-08 08:52:44 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr15:52,205,827
INFO 2026-06-08 08:52:44 MarkDuplicates Tracking 403197 as yet unmatched pairs. 14645 records in RAM.
INFO 2026-06-08 08:52:46 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr15:63,633,848
INFO 2026-06-08 08:52:46 MarkDuplicates Tracking 400648 as yet unmatched pairs. 12087 records in RAM.
INFO 2026-06-08 08:52:48 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr15:71,898,846
INFO 2026-06-08 08:52:48 MarkDuplicates Tracking 397974 as yet unmatched pairs. 9410 records in RAM.
INFO 2026-06-08 08:52:49 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr15:75,639,614
INFO 2026-06-08 08:52:49 MarkDuplicates Tracking 395063 as yet unmatched pairs. 6499 records in RAM.
INFO 2026-06-08 08:52:51 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr15:84,473,756
INFO 2026-06-08 08:52:51 MarkDuplicates Tracking 392877 as yet unmatched pairs. 4312 records in RAM.
INFO 2026-06-08 08:52:52 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr15:90,476,782
INFO 2026-06-08 08:52:52 MarkDuplicates Tracking 390501 as yet unmatched pairs. 1936 records in RAM.
INFO 2026-06-08 08:52:54 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr16:304,392
INFO 2026-06-08 08:52:54 MarkDuplicates Tracking 387842 as yet unmatched pairs. 71836 records in RAM.
INFO 2026-06-08 08:52:56 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr16:765,595
INFO 2026-06-08 08:52:56 MarkDuplicates Tracking 386940 as yet unmatched pairs. 70934 records in RAM.
INFO 2026-06-08 08:52:58 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 2s. Last read position: chr16:1,659,924
INFO 2026-06-08 08:52:58 MarkDuplicates Tracking 381323 as yet unmatched pairs. 65317 records in RAM.
INFO 2026-06-08 08:52:59 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr16:2,118,183
INFO 2026-06-08 08:52:59 MarkDuplicates Tracking 377851 as yet unmatched pairs. 61845 records in RAM.
INFO 2026-06-08 08:53:00 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr16:2,765,332
INFO 2026-06-08 08:53:00 MarkDuplicates Tracking 376721 as yet unmatched pairs. 60713 records in RAM.
INFO 2026-06-08 08:53:02 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr16:3,311,679
INFO 2026-06-08 08:53:02 MarkDuplicates Tracking 371932 as yet unmatched pairs. 55924 records in RAM.
INFO 2026-06-08 08:53:04 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 2s. Last read position: chr16:4,876,802
INFO 2026-06-08 08:53:04 MarkDuplicates Tracking 369015 as yet unmatched pairs. 53005 records in RAM.
INFO 2026-06-08 08:53:06 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr16:11,929,157
INFO 2026-06-08 08:53:06 MarkDuplicates Tracking 366309 as yet unmatched pairs. 50298 records in RAM.
INFO 2026-06-08 08:53:08 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr16:14,930,664
INFO 2026-06-08 08:53:08 MarkDuplicates Tracking 364483 as yet unmatched pairs. 48465 records in RAM.
INFO 2026-06-08 08:53:10 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr16:16,317,548
INFO 2026-06-08 08:53:10 MarkDuplicates Tracking 362742 as yet unmatched pairs. 46724 records in RAM.
INFO 2026-06-08 08:53:11 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr16:18,380,449
INFO 2026-06-08 08:53:11 MarkDuplicates Tracking 362076 as yet unmatched pairs. 46058 records in RAM.
INFO 2026-06-08 08:53:12 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr16:19,610,327
INFO 2026-06-08 08:53:12 MarkDuplicates Tracking 359584 as yet unmatched pairs. 43566 records in RAM.
INFO 2026-06-08 08:53:13 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 1s. Last read position: chr16:21,424,903
INFO 2026-06-08 08:53:13 MarkDuplicates Tracking 358983 as yet unmatched pairs. 42965 records in RAM.
INFO 2026-06-08 08:53:15 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr16:21,887,651
INFO 2026-06-08 08:53:15 MarkDuplicates Tracking 357943 as yet unmatched pairs. 41924 records in RAM.
INFO 2026-06-08 08:53:16 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,537
INFO 2026-06-08 08:53:16 MarkDuplicates Tracking 357401 as yet unmatched pairs. 41382 records in RAM.
INFO 2026-06-08 08:53:17 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr16:25,132,514
INFO 2026-06-08 08:53:17 MarkDuplicates Tracking 354789 as yet unmatched pairs. 38768 records in RAM.
INFO 2026-06-08 08:53:18 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr16:28,834,200
INFO 2026-06-08 08:53:18 MarkDuplicates Tracking 353043 as yet unmatched pairs. 37022 records in RAM.
INFO 2026-06-08 08:53:20 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr16:29,483,910
INFO 2026-06-08 08:53:20 MarkDuplicates Tracking 352594 as yet unmatched pairs. 36573 records in RAM.
INFO 2026-06-08 08:53:21 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr16:29,983,159
INFO 2026-06-08 08:53:21 MarkDuplicates Tracking 349614 as yet unmatched pairs. 33593 records in RAM.
INFO 2026-06-08 08:53:23 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr16:30,231,505
INFO 2026-06-08 08:53:23 MarkDuplicates Tracking 348031 as yet unmatched pairs. 32009 records in RAM.
INFO 2026-06-08 08:53:24 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr16:30,739,475
INFO 2026-06-08 08:53:24 MarkDuplicates Tracking 345466 as yet unmatched pairs. 29436 records in RAM.
INFO 2026-06-08 08:53:26 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr16:31,191,393
INFO 2026-06-08 08:53:26 MarkDuplicates Tracking 343605 as yet unmatched pairs. 27570 records in RAM.
INFO 2026-06-08 08:53:28 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr16:53,645,692
INFO 2026-06-08 08:53:28 MarkDuplicates Tracking 339844 as yet unmatched pairs. 23808 records in RAM.
INFO 2026-06-08 08:53:29 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 1s. Last read position: chr16:58,009,950
INFO 2026-06-08 08:53:29 MarkDuplicates Tracking 337444 as yet unmatched pairs. 21404 records in RAM.
INFO 2026-06-08 08:53:31 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr16:67,637,694
INFO 2026-06-08 08:53:31 MarkDuplicates Tracking 333895 as yet unmatched pairs. 17855 records in RAM.
INFO 2026-06-08 08:53:33 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 1s. Last read position: chr16:69,693,607
INFO 2026-06-08 08:53:33 MarkDuplicates Tracking 331114 as yet unmatched pairs. 15073 records in RAM.
INFO 2026-06-08 08:53:34 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr16:72,793,363
INFO 2026-06-08 08:53:34 MarkDuplicates Tracking 328510 as yet unmatched pairs. 12466 records in RAM.
INFO 2026-06-08 08:53:36 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr16:83,808,110
INFO 2026-06-08 08:53:36 MarkDuplicates Tracking 326024 as yet unmatched pairs. 9974 records in RAM.
INFO 2026-06-08 08:53:38 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr16:88,436,336
INFO 2026-06-08 08:53:38 MarkDuplicates Tracking 322472 as yet unmatched pairs. 6417 records in RAM.
INFO 2026-06-08 08:53:39 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr16:89,282,606
INFO 2026-06-08 08:53:39 MarkDuplicates Tracking 319176 as yet unmatched pairs. 3121 records in RAM.
INFO 2026-06-08 08:53:41 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 2s. Last read position: chr17:532,797
INFO 2026-06-08 08:53:41 MarkDuplicates Tracking 315961 as yet unmatched pairs. 101519 records in RAM.
INFO 2026-06-08 08:53:43 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr17:1,676,025
INFO 2026-06-08 08:53:43 MarkDuplicates Tracking 313121 as yet unmatched pairs. 98671 records in RAM.
INFO 2026-06-08 08:53:45 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr17:3,818,557
INFO 2026-06-08 08:53:45 MarkDuplicates Tracking 310103 as yet unmatched pairs. 95652 records in RAM.
INFO 2026-06-08 08:53:46 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr17:4,968,741
INFO 2026-06-08 08:53:46 MarkDuplicates Tracking 307202 as yet unmatched pairs. 92751 records in RAM.
INFO 2026-06-08 08:53:48 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr17:7,261,962
INFO 2026-06-08 08:53:48 MarkDuplicates Tracking 304458 as yet unmatched pairs. 90006 records in RAM.
INFO 2026-06-08 08:53:50 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr17:7,564,750
INFO 2026-06-08 08:53:50 MarkDuplicates Tracking 301734 as yet unmatched pairs. 87278 records in RAM.
INFO 2026-06-08 08:53:51 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr17:8,143,780
INFO 2026-06-08 08:53:51 MarkDuplicates Tracking 299549 as yet unmatched pairs. 85093 records in RAM.
INFO 2026-06-08 08:53:53 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr17:16,121,069
INFO 2026-06-08 08:53:53 MarkDuplicates Tracking 296476 as yet unmatched pairs. 82019 records in RAM.
INFO 2026-06-08 08:53:55 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 2s. Last read position: chr17:18,018,535
INFO 2026-06-08 08:53:55 MarkDuplicates Tracking 293440 as yet unmatched pairs. 78983 records in RAM.
INFO 2026-06-08 08:53:57 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr17:21,004,281
INFO 2026-06-08 08:53:57 MarkDuplicates Tracking 290863 as yet unmatched pairs. 76406 records in RAM.
INFO 2026-06-08 08:53:58 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr17:28,693,716
INFO 2026-06-08 08:53:58 MarkDuplicates Tracking 288031 as yet unmatched pairs. 73569 records in RAM.
INFO 2026-06-08 08:54:00 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr17:30,900,448
INFO 2026-06-08 08:54:00 MarkDuplicates Tracking 285177 as yet unmatched pairs. 70715 records in RAM.
INFO 2026-06-08 08:54:01 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr17:35,820,036
INFO 2026-06-08 08:54:01 MarkDuplicates Tracking 284761 as yet unmatched pairs. 70296 records in RAM.
INFO 2026-06-08 08:54:03 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr17:38,014,204
INFO 2026-06-08 08:54:03 MarkDuplicates Tracking 280689 as yet unmatched pairs. 66224 records in RAM.
INFO 2026-06-08 08:54:04 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr17:39,184,084
INFO 2026-06-08 08:54:04 MarkDuplicates Tracking 278231 as yet unmatched pairs. 63765 records in RAM.
INFO 2026-06-08 08:54:06 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr17:39,716,402
INFO 2026-06-08 08:54:06 MarkDuplicates Tracking 280098 as yet unmatched pairs. 65632 records in RAM.
INFO 2026-06-08 08:54:07 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr17:40,291,133
INFO 2026-06-08 08:54:07 MarkDuplicates Tracking 272343 as yet unmatched pairs. 57877 records in RAM.
INFO 2026-06-08 08:54:09 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr17:42,020,187
INFO 2026-06-08 08:54:09 MarkDuplicates Tracking 269500 as yet unmatched pairs. 55033 records in RAM.
INFO 2026-06-08 08:54:10 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr17:43,197,000
INFO 2026-06-08 08:54:10 MarkDuplicates Tracking 266805 as yet unmatched pairs. 52338 records in RAM.
INFO 2026-06-08 08:54:12 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr17:44,928,460
INFO 2026-06-08 08:54:12 MarkDuplicates Tracking 263783 as yet unmatched pairs. 49316 records in RAM.
INFO 2026-06-08 08:54:13 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 1s. Last read position: chr17:47,017,356
INFO 2026-06-08 08:54:13 MarkDuplicates Tracking 261790 as yet unmatched pairs. 47323 records in RAM.
INFO 2026-06-08 08:54:15 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chr17:50,071,354
INFO 2026-06-08 08:54:15 MarkDuplicates Tracking 259312 as yet unmatched pairs. 44844 records in RAM.
INFO 2026-06-08 08:54:17 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,863
INFO 2026-06-08 08:54:17 MarkDuplicates Tracking 260554 as yet unmatched pairs. 46085 records in RAM.
INFO 2026-06-08 08:54:19 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,516
INFO 2026-06-08 08:54:19 MarkDuplicates Tracking 256876 as yet unmatched pairs. 42407 records in RAM.
INFO 2026-06-08 08:54:21 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 2s. Last read position: chr17:50,699,450
INFO 2026-06-08 08:54:21 MarkDuplicates Tracking 249717 as yet unmatched pairs. 35248 records in RAM.
INFO 2026-06-08 08:54:22 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr17:59,647,547
INFO 2026-06-08 08:54:22 MarkDuplicates Tracking 248914 as yet unmatched pairs. 34443 records in RAM.
INFO 2026-06-08 08:54:24 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr17:60,017,295
INFO 2026-06-08 08:54:24 MarkDuplicates Tracking 244428 as yet unmatched pairs. 29957 records in RAM.
INFO 2026-06-08 08:54:26 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr17:64,213,601
INFO 2026-06-08 08:54:26 MarkDuplicates Tracking 241726 as yet unmatched pairs. 27242 records in RAM.
INFO 2026-06-08 08:54:27 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr17:67,959,595
INFO 2026-06-08 08:54:27 MarkDuplicates Tracking 239470 as yet unmatched pairs. 24986 records in RAM.
INFO 2026-06-08 08:54:28 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr17:74,209,254
INFO 2026-06-08 08:54:28 MarkDuplicates Tracking 236704 as yet unmatched pairs. 22220 records in RAM.
INFO 2026-06-08 08:54:30 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr17:75,706,337
INFO 2026-06-08 08:54:30 MarkDuplicates Tracking 233880 as yet unmatched pairs. 19393 records in RAM.
INFO 2026-06-08 08:54:32 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 1s. Last read position: chr17:76,270,252
INFO 2026-06-08 08:54:32 MarkDuplicates Tracking 231014 as yet unmatched pairs. 16524 records in RAM.
INFO 2026-06-08 08:54:33 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr17:78,803,451
INFO 2026-06-08 08:54:33 MarkDuplicates Tracking 227503 as yet unmatched pairs. 13009 records in RAM.
INFO 2026-06-08 08:54:35 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr17:80,332,444
INFO 2026-06-08 08:54:35 MarkDuplicates Tracking 225071 as yet unmatched pairs. 10575 records in RAM.
INFO 2026-06-08 08:54:36 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr17:81,511,307
INFO 2026-06-08 08:54:36 MarkDuplicates Tracking 222977 as yet unmatched pairs. 8477 records in RAM.
INFO 2026-06-08 08:54:38 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr17:82,017,078
INFO 2026-06-08 08:54:38 MarkDuplicates Tracking 218375 as yet unmatched pairs. 3875 records in RAM.
INFO 2026-06-08 08:54:40 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr17:82,727,115
INFO 2026-06-08 08:54:40 MarkDuplicates Tracking 215096 as yet unmatched pairs. 596 records in RAM.
INFO 2026-06-08 08:54:42 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr18:3,457,812
INFO 2026-06-08 08:54:42 MarkDuplicates Tracking 212451 as yet unmatched pairs. 17931 records in RAM.
INFO 2026-06-08 08:54:43 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr18:12,952,048
INFO 2026-06-08 08:54:43 MarkDuplicates Tracking 209764 as yet unmatched pairs. 15241 records in RAM.
INFO 2026-06-08 08:54:45 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr18:23,921,022
INFO 2026-06-08 08:54:45 MarkDuplicates Tracking 207590 as yet unmatched pairs. 13063 records in RAM.
INFO 2026-06-08 08:54:47 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 1s. Last read position: chr18:36,126,690
INFO 2026-06-08 08:54:47 MarkDuplicates Tracking 204659 as yet unmatched pairs. 10127 records in RAM.
INFO 2026-06-08 08:54:49 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr18:50,279,894
INFO 2026-06-08 08:54:49 MarkDuplicates Tracking 202321 as yet unmatched pairs. 7786 records in RAM.
INFO 2026-06-08 08:54:50 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr18:58,984,310
INFO 2026-06-08 08:54:50 MarkDuplicates Tracking 199346 as yet unmatched pairs. 4811 records in RAM.
INFO 2026-06-08 08:54:52 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr18:75,285,606
INFO 2026-06-08 08:54:52 MarkDuplicates Tracking 196545 as yet unmatched pairs. 2008 records in RAM.
INFO 2026-06-08 08:54:55 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 2s. Last read position: chr19:890,988
INFO 2026-06-08 08:54:55 MarkDuplicates Tracking 193590 as yet unmatched pairs. 86351 records in RAM.
INFO 2026-06-08 08:54:56 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr19:1,555,817
INFO 2026-06-08 08:54:56 MarkDuplicates Tracking 189989 as yet unmatched pairs. 82750 records in RAM.
INFO 2026-06-08 08:54:58 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr19:3,633,058
INFO 2026-06-08 08:54:58 MarkDuplicates Tracking 186507 as yet unmatched pairs. 79268 records in RAM.
INFO 2026-06-08 08:55:00 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 1s. Last read position: chr19:6,418,047
INFO 2026-06-08 08:55:00 MarkDuplicates Tracking 183559 as yet unmatched pairs. 76316 records in RAM.
INFO 2026-06-08 08:55:01 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr19:7,615,488
INFO 2026-06-08 08:55:01 MarkDuplicates Tracking 180643 as yet unmatched pairs. 73399 records in RAM.
INFO 2026-06-08 08:55:03 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr19:10,357,854
INFO 2026-06-08 08:55:03 MarkDuplicates Tracking 177837 as yet unmatched pairs. 70579 records in RAM.
INFO 2026-06-08 08:55:05 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 1s. Last read position: chr19:12,016,023
INFO 2026-06-08 08:55:05 MarkDuplicates Tracking 174821 as yet unmatched pairs. 67559 records in RAM.
INFO 2026-06-08 08:55:06 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr19:14,433,492
INFO 2026-06-08 08:55:06 MarkDuplicates Tracking 171814 as yet unmatched pairs. 64551 records in RAM.
INFO 2026-06-08 08:55:08 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr19:16,086,457
INFO 2026-06-08 08:55:08 MarkDuplicates Tracking 168939 as yet unmatched pairs. 61676 records in RAM.
INFO 2026-06-08 08:55:09 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr19:18,166,179
INFO 2026-06-08 08:55:09 MarkDuplicates Tracking 165591 as yet unmatched pairs. 58327 records in RAM.
INFO 2026-06-08 08:55:11 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 1s. Last read position: chr19:18,747,095
INFO 2026-06-08 08:55:11 MarkDuplicates Tracking 163227 as yet unmatched pairs. 55962 records in RAM.
INFO 2026-06-08 08:55:12 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chr19:23,827,544
INFO 2026-06-08 08:55:12 MarkDuplicates Tracking 159308 as yet unmatched pairs. 52043 records in RAM.
INFO 2026-06-08 08:55:14 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr19:35,267,238
INFO 2026-06-08 08:55:14 MarkDuplicates Tracking 157273 as yet unmatched pairs. 50008 records in RAM.
INFO 2026-06-08 08:55:16 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr19:38,119,392
INFO 2026-06-08 08:55:16 MarkDuplicates Tracking 153360 as yet unmatched pairs. 46088 records in RAM.
INFO 2026-06-08 08:55:18 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr19:39,397,654
INFO 2026-06-08 08:55:18 MarkDuplicates Tracking 150228 as yet unmatched pairs. 42956 records in RAM.
INFO 2026-06-08 08:55:19 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr19:40,377,985
INFO 2026-06-08 08:55:19 MarkDuplicates Tracking 147605 as yet unmatched pairs. 40333 records in RAM.
INFO 2026-06-08 08:55:21 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr19:41,717,614
INFO 2026-06-08 08:55:21 MarkDuplicates Tracking 146975 as yet unmatched pairs. 39703 records in RAM.
INFO 2026-06-08 08:55:22 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr19:41,762,057
INFO 2026-06-08 08:55:22 MarkDuplicates Tracking 143003 as yet unmatched pairs. 35731 records in RAM.
INFO 2026-06-08 08:55:24 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr19:42,287,708
INFO 2026-06-08 08:55:24 MarkDuplicates Tracking 139528 as yet unmatched pairs. 32256 records in RAM.
INFO 2026-06-08 08:55:25 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr19:44,777,976
INFO 2026-06-08 08:55:25 MarkDuplicates Tracking 136115 as yet unmatched pairs. 28840 records in RAM.
INFO 2026-06-08 08:55:27 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr19:45,064,300
INFO 2026-06-08 08:55:27 MarkDuplicates Tracking 132645 as yet unmatched pairs. 25368 records in RAM.
INFO 2026-06-08 08:55:29 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 2s. Last read position: chr19:46,782,525
INFO 2026-06-08 08:55:29 MarkDuplicates Tracking 129309 as yet unmatched pairs. 22031 records in RAM.
INFO 2026-06-08 08:55:31 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: chr19:48,615,888
INFO 2026-06-08 08:55:31 MarkDuplicates Tracking 127189 as yet unmatched pairs. 19911 records in RAM.
INFO 2026-06-08 08:55:32 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 1s. Last read position: chr19:49,497,240
INFO 2026-06-08 08:55:32 MarkDuplicates Tracking 124427 as yet unmatched pairs. 17149 records in RAM.
INFO 2026-06-08 08:55:34 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 1s. Last read position: chr19:49,880,239
INFO 2026-06-08 08:55:34 MarkDuplicates Tracking 120148 as yet unmatched pairs. 12867 records in RAM.
INFO 2026-06-08 08:55:36 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr19:50,482,618
INFO 2026-06-08 08:55:36 MarkDuplicates Tracking 117141 as yet unmatched pairs. 9860 records in RAM.
INFO 2026-06-08 08:55:37 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chr19:54,169,587
INFO 2026-06-08 08:55:37 MarkDuplicates Tracking 114639 as yet unmatched pairs. 7358 records in RAM.
INFO 2026-06-08 08:55:39 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 1s. Last read position: chr19:55,386,424
INFO 2026-06-08 08:55:39 MarkDuplicates Tracking 112258 as yet unmatched pairs. 4977 records in RAM.
INFO 2026-06-08 08:55:40 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr19:57,875,160
INFO 2026-06-08 08:55:40 MarkDuplicates Tracking 108808 as yet unmatched pairs. 1523 records in RAM.
INFO 2026-06-08 08:55:42 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chr20:2,838,611
INFO 2026-06-08 08:55:42 MarkDuplicates Tracking 105912 as yet unmatched pairs. 32766 records in RAM.
INFO 2026-06-08 08:55:44 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr20:9,338,960
INFO 2026-06-08 08:55:44 MarkDuplicates Tracking 103066 as yet unmatched pairs. 29918 records in RAM.
INFO 2026-06-08 08:55:45 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 1s. Last read position: chr20:20,601,750
INFO 2026-06-08 08:55:45 MarkDuplicates Tracking 100334 as yet unmatched pairs. 27186 records in RAM.
INFO 2026-06-08 08:55:47 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chr20:32,367,679
INFO 2026-06-08 08:55:47 MarkDuplicates Tracking 97317 as yet unmatched pairs. 24169 records in RAM.
INFO 2026-06-08 08:55:48 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 1s. Last read position: chr20:34,854,612
INFO 2026-06-08 08:55:48 MarkDuplicates Tracking 94482 as yet unmatched pairs. 21334 records in RAM.
INFO 2026-06-08 08:55:50 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 1s. Last read position: chr20:37,184,237
INFO 2026-06-08 08:55:50 MarkDuplicates Tracking 91807 as yet unmatched pairs. 18655 records in RAM.
INFO 2026-06-08 08:55:51 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 1s. Last read position: chr20:43,570,615
INFO 2026-06-08 08:55:51 MarkDuplicates Tracking 88694 as yet unmatched pairs. 15540 records in RAM.
INFO 2026-06-08 08:55:53 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chr20:45,894,042
INFO 2026-06-08 08:55:53 MarkDuplicates Tracking 86429 as yet unmatched pairs. 13273 records in RAM.
INFO 2026-06-08 08:55:55 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 1s. Last read position: chr20:50,737,962
INFO 2026-06-08 08:55:55 MarkDuplicates Tracking 83167 as yet unmatched pairs. 10011 records in RAM.
INFO 2026-06-08 08:55:56 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr20:58,910,358
INFO 2026-06-08 08:55:56 MarkDuplicates Tracking 81218 as yet unmatched pairs. 8062 records in RAM.
INFO 2026-06-08 08:55:58 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 1s. Last read position: chr20:62,352,259
INFO 2026-06-08 08:55:58 MarkDuplicates Tracking 77445 as yet unmatched pairs. 4285 records in RAM.
INFO 2026-06-08 08:55:59 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr20:63,951,245
INFO 2026-06-08 08:55:59 MarkDuplicates Tracking 73654 as yet unmatched pairs. 494 records in RAM.
INFO 2026-06-08 08:56:00 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:13:59s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,931
INFO 2026-06-08 08:56:00 MarkDuplicates Tracking 71869 as yet unmatched pairs. 10246 records in RAM.
INFO 2026-06-08 08:56:01 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 0s. Last read position: chr21:8,444,598
INFO 2026-06-08 08:56:01 MarkDuplicates Tracking 70188 as yet unmatched pairs. 8560 records in RAM.
INFO 2026-06-08 08:56:03 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: chr21:34,670,716
INFO 2026-06-08 08:56:03 MarkDuplicates Tracking 68020 as yet unmatched pairs. 6390 records in RAM.
INFO 2026-06-08 08:56:05 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 1s. Last read position: chr21:43,418,526
INFO 2026-06-08 08:56:05 MarkDuplicates Tracking 64919 as yet unmatched pairs. 3288 records in RAM.
INFO 2026-06-08 08:56:07 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 2s. Last read position: chr21:46,649,627
INFO 2026-06-08 08:56:07 MarkDuplicates Tracking 61766 as yet unmatched pairs. 134 records in RAM.
INFO 2026-06-08 08:56:09 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 1s. Last read position: chr22:22,901,059
INFO 2026-06-08 08:56:09 MarkDuplicates Tracking 58911 as yet unmatched pairs. 21243 records in RAM.
INFO 2026-06-08 08:56:10 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 1s. Last read position: chr22:26,536,436
INFO 2026-06-08 08:56:10 MarkDuplicates Tracking 55734 as yet unmatched pairs. 18066 records in RAM.
INFO 2026-06-08 08:56:12 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:14:11s. Time for last 1,000,000: 1s. Last read position: chr22:30,334,641
INFO 2026-06-08 08:56:12 MarkDuplicates Tracking 52956 as yet unmatched pairs. 15288 records in RAM.
INFO 2026-06-08 08:56:14 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 1s. Last read position: chr22:36,349,066
INFO 2026-06-08 08:56:14 MarkDuplicates Tracking 50162 as yet unmatched pairs. 12493 records in RAM.
INFO 2026-06-08 08:56:16 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 1s. Last read position: chr22:39,521,665
INFO 2026-06-08 08:56:16 MarkDuplicates Tracking 48932 as yet unmatched pairs. 11263 records in RAM.
INFO 2026-06-08 08:56:17 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 1s. Last read position: chr22:42,623,844
INFO 2026-06-08 08:56:17 MarkDuplicates Tracking 44310 as yet unmatched pairs. 6641 records in RAM.
INFO 2026-06-08 08:56:19 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 1s. Last read position: chr22:50,255,837
INFO 2026-06-08 08:56:19 MarkDuplicates Tracking 40533 as yet unmatched pairs. 2864 records in RAM.
INFO 2026-06-08 08:56:20 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 1s. Last read position: chrX:2,291,525
INFO 2026-06-08 08:56:20 MarkDuplicates Tracking 37164 as yet unmatched pairs. 29358 records in RAM.
INFO 2026-06-08 08:56:22 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 1s. Last read position: chrX:19,355,429
INFO 2026-06-08 08:56:22 MarkDuplicates Tracking 34545 as yet unmatched pairs. 26736 records in RAM.
INFO 2026-06-08 08:56:24 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 1s. Last read position: chrX:41,152,947
INFO 2026-06-08 08:56:24 MarkDuplicates Tracking 32124 as yet unmatched pairs. 24315 records in RAM.
INFO 2026-06-08 08:56:25 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 1s. Last read position: chrX:48,462,968
INFO 2026-06-08 08:56:25 MarkDuplicates Tracking 29311 as yet unmatched pairs. 21501 records in RAM.
INFO 2026-06-08 08:56:27 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 1s. Last read position: chrX:53,194,634
INFO 2026-06-08 08:56:27 MarkDuplicates Tracking 26649 as yet unmatched pairs. 18838 records in RAM.
INFO 2026-06-08 08:56:28 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chrX:57,908,097
INFO 2026-06-08 08:56:28 MarkDuplicates Tracking 23728 as yet unmatched pairs. 15917 records in RAM.
INFO 2026-06-08 08:56:30 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:14:28s. Time for last 1,000,000: 1s. Last read position: chrX:72,273,833
INFO 2026-06-08 08:56:30 MarkDuplicates Tracking 21383 as yet unmatched pairs. 13572 records in RAM.
INFO 2026-06-08 08:56:31 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:14:30s. Time for last 1,000,000: 1s. Last read position: chrX:101,656,782
INFO 2026-06-08 08:56:31 MarkDuplicates Tracking 18730 as yet unmatched pairs. 10919 records in RAM.
INFO 2026-06-08 08:56:33 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 1s. Last read position: chrX:124,090,652
INFO 2026-06-08 08:56:33 MarkDuplicates Tracking 16521 as yet unmatched pairs. 8710 records in RAM.
INFO 2026-06-08 08:56:34 MarkDuplicates Read 491,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 1s. Last read position: chrX:136,874,422
INFO 2026-06-08 08:56:34 MarkDuplicates Tracking 14494 as yet unmatched pairs. 6683 records in RAM.
INFO 2026-06-08 08:56:36 MarkDuplicates Read 492,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 1s. Last read position: chrX:154,348,896
INFO 2026-06-08 08:56:36 MarkDuplicates Tracking 11677 as yet unmatched pairs. 3866 records in RAM.
INFO 2026-06-08 08:56:38 MarkDuplicates Read 493,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 1s. Last read position: chrX:155,381,087
INFO 2026-06-08 08:56:38 MarkDuplicates Tracking 7890 as yet unmatched pairs. 79 records in RAM.
INFO 2026-06-08 08:56:39 MarkDuplicates Read 494,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,128
INFO 2026-06-08 08:56:39 MarkDuplicates Tracking 5999 as yet unmatched pairs. 71 records in RAM.
INFO 2026-06-08 08:56:41 MarkDuplicates Read 495,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 2s. Last read position: KI270733.1:169,520
INFO 2026-06-08 08:56:41 MarkDuplicates Tracking 307 as yet unmatched pairs. 210 records in RAM.
INFO 2026-06-08 08:56:42 MarkDuplicates Read 495570590 records. 0 pairs never matched.
INFO 2026-06-08 08:57:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 42079431880; totalMemory: 60062433280; maxMemory: 63585648640
INFO 2026-06-08 08:57:42 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:57:58 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:58:14 OpticalDuplicateFinder Large duplicate set. size = 1261
INFO 2026-06-08 08:58:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,797
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1083
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,877
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1215
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,145
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1272
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,702
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 3007
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,584
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,612
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,085
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1475
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,187
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1777
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,440
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1607
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,735
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1105
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,336
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1149
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,134
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1721
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,034
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1207
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,652
INFO 2026-06-08 08:58:16 OpticalDuplicateFinder Large duplicate set. size = 1021
INFO 2026-06-08 08:58:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,680
INFO 2026-06-08 08:58:17 OpticalDuplicateFinder Large duplicate set. size = 1082
INFO 2026-06-08 08:58:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,612
INFO 2026-06-08 08:58:17 OpticalDuplicateFinder Large duplicate set. size = 1258
INFO 2026-06-08 08:58:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,572
INFO 2026-06-08 08:58:17 OpticalDuplicateFinder Large duplicate set. size = 1050
INFO 2026-06-08 08:58:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,569
INFO 2026-06-08 08:58:20 OpticalDuplicateFinder Large duplicate set. size = 1135
INFO 2026-06-08 08:58:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,816
INFO 2026-06-08 08:58:20 OpticalDuplicateFinder Large duplicate set. size = 1317
INFO 2026-06-08 08:58:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,797
INFO 2026-06-08 08:58:20 OpticalDuplicateFinder Large duplicate set. size = 1841
INFO 2026-06-08 08:58:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,324
INFO 2026-06-08 08:58:21 OpticalDuplicateFinder Large duplicate set. size = 1080
INFO 2026-06-08 08:58:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,194
INFO 2026-06-08 08:58:21 OpticalDuplicateFinder Large duplicate set. size = 1905
INFO 2026-06-08 08:58:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,027
INFO 2026-06-08 08:58:28 OpticalDuplicateFinder Large duplicate set. size = 1109
INFO 2026-06-08 08:58:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,521
INFO 2026-06-08 08:58:29 OpticalDuplicateFinder Large duplicate set. size = 1241
INFO 2026-06-08 08:58:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,589
INFO 2026-06-08 08:58:29 OpticalDuplicateFinder Large duplicate set. size = 1468
INFO 2026-06-08 08:58:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,966
INFO 2026-06-08 08:58:29 OpticalDuplicateFinder Large duplicate set. size = 1168
INFO 2026-06-08 08:58:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,806
INFO 2026-06-08 08:58:29 OpticalDuplicateFinder Large duplicate set. size = 1582
INFO 2026-06-08 08:58:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,671
INFO 2026-06-08 08:58:43 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:58:43 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:59:34 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:59:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 37301337152; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:59:44 MarkDuplicates Marking 246572283 records as duplicates.
INFO 2026-06-08 08:59:44 MarkDuplicates Found 14398902 optical duplicate clusters.
INFO 2026-06-08 08:59:44 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 09:00:00 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:25,246,702
INFO 2026-06-08 09:00:16 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 16s. Last read position: chr1:67,420,100
INFO 2026-06-08 09:00:32 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:48s. Time for last 10,000,000: 15s. Last read position: chr1:150,968,502
INFO 2026-06-08 09:00:48 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:03s. Time for last 10,000,000: 15s. Last read position: chr1:169,106,754
INFO 2026-06-08 09:01:04 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:19s. Time for last 10,000,000: 15s. Last read position: chr1:214,384,336
INFO 2026-06-08 09:01:20 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:35s. Time for last 10,000,000: 16s. Last read position: chr2:32,916,255
INFO 2026-06-08 09:01:36 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:51s. Time for last 10,000,000: 15s. Last read position: chr2:85,659,671
INFO 2026-06-08 09:01:52 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 15s. Last read position: chr2:138,005,103
INFO 2026-06-08 09:02:08 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:23s. Time for last 10,000,000: 15s. Last read position: chr2:227,472,454
INFO 2026-06-08 09:02:24 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:39s. Time for last 10,000,000: 16s. Last read position: chr3:57,584,402
INFO 2026-06-08 09:02:40 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:55s. Time for last 10,000,000: 15s. Last read position: chr3:195,781,099
INFO 2026-06-08 09:02:55 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:11s. Time for last 10,000,000: 15s. Last read position: chr4:25,669,672
INFO 2026-06-08 09:03:11 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:27s. Time for last 10,000,000: 16s. Last read position: chr4:151,175,156
INFO 2026-06-08 09:03:27 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:43s. Time for last 10,000,000: 16s. Last read position: chr5:115,831,767
INFO 2026-06-08 09:03:43 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:59s. Time for last 10,000,000: 16s. Last read position: chr5:173,953,178
INFO 2026-06-08 09:03:59 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:15s. Time for last 10,000,000: 15s. Last read position: chr6:31,829,102
INFO 2026-06-08 09:04:15 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:31s. Time for last 10,000,000: 16s. Last read position: chr6:136,372,512
INFO 2026-06-08 09:04:31 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:47s. Time for last 10,000,000: 16s. Last read position: chr7:55,912,681
INFO 2026-06-08 09:04:48 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:03s. Time for last 10,000,000: 16s. Last read position: chr7:116,755,397
INFO 2026-06-08 09:05:04 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:19s. Time for last 10,000,000: 16s. Last read position: chr8:26,291,708
INFO 2026-06-08 09:05:20 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:36s. Time for last 10,000,000: 16s. Last read position: chr8:143,859,812
INFO 2026-06-08 09:05:36 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:52s. Time for last 10,000,000: 16s. Last read position: chr9:94,800,781
INFO 2026-06-08 09:05:53 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:08s. Time for last 10,000,000: 16s. Last read position: chr9:137,777,948
INFO 2026-06-08 09:06:09 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:25s. Time for last 10,000,000: 16s. Last read position: chr10:95,839,728
INFO 2026-06-08 09:06:25 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:41s. Time for last 10,000,000: 16s. Last read position: chr11:1,184,900
INFO 2026-06-08 09:06:41 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:56s. Time for last 10,000,000: 15s. Last read position: chr11:1,245,286
INFO 2026-06-08 09:06:56 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:11s. Time for last 10,000,000: 15s. Last read position: chr11:1,254,760
INFO 2026-06-08 09:07:12 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:28s. Time for last 10,000,000: 16s. Last read position: chr11:62,528,749
INFO 2026-06-08 09:07:28 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:44s. Time for last 10,000,000: 16s. Last read position: chr11:76,546,024
INFO 2026-06-08 09:07:45 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:00s. Time for last 10,000,000: 16s. Last read position: chr12:8,932,893
INFO 2026-06-08 09:08:01 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:16s. Time for last 10,000,000: 16s. Last read position: chr12:56,178,454
INFO 2026-06-08 09:08:17 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:33s. Time for last 10,000,000: 16s. Last read position: chr12:120,534,702
INFO 2026-06-08 09:08:34 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:49s. Time for last 10,000,000: 16s. Last read position: chr13:109,782,700
INFO 2026-06-08 09:08:50 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:06s. Time for last 10,000,000: 16s. Last read position: chr14:93,242,951
INFO 2026-06-08 09:09:06 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:22s. Time for last 10,000,000: 16s. Last read position: chr15:63,633,848
INFO 2026-06-08 09:09:22 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:38s. Time for last 10,000,000: 16s. Last read position: chr16:3,311,679
INFO 2026-06-08 09:09:38 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:54s. Time for last 10,000,000: 16s. Last read position: chr16:25,132,514
INFO 2026-06-08 09:09:55 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:10s. Time for last 10,000,000: 16s. Last read position: chr16:69,693,607
INFO 2026-06-08 09:10:11 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:26s. Time for last 10,000,000: 16s. Last read position: chr17:7,564,750
INFO 2026-06-08 09:10:27 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:42s. Time for last 10,000,000: 16s. Last read position: chr17:39,716,402
INFO 2026-06-08 09:10:43 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:10:58s. Time for last 10,000,000: 15s. Last read position: chr17:59,647,547
INFO 2026-06-08 09:10:59 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:11:15s. Time for last 10,000,000: 16s. Last read position: chr17:82,017,078
INFO 2026-06-08 09:11:16 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:11:31s. Time for last 10,000,000: 16s. Last read position: chr19:1,555,817
INFO 2026-06-08 09:11:32 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:11:48s. Time for last 10,000,000: 16s. Last read position: chr19:23,827,544
INFO 2026-06-08 09:11:48 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:12:04s. Time for last 10,000,000: 16s. Last read position: chr19:46,782,525
INFO 2026-06-08 09:12:04 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:12:20s. Time for last 10,000,000: 15s. Last read position: chr20:20,601,750
INFO 2026-06-08 09:12:21 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:12:36s. Time for last 10,000,000: 16s. Last read position: chr21:8,258,931
INFO 2026-06-08 09:12:37 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:12:52s. Time for last 10,000,000: 16s. Last read position: chr22:42,623,844
INFO 2026-06-08 09:12:53 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:13:08s. Time for last 10,000,000: 16s. Last read position: chrX:124,090,652
INFO 2026-06-08 09:13:11 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 09:13:11 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 09:13:11 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 09:13:11 MarkDuplicates Before output close freeMemory: 202130984; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 09:13:11 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 09:13:11 MarkDuplicates After output close freeMemory: 104804504; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 09:13:11 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 31.19 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory