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-13a2f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:56:39.111 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 07:56:39 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-13a2f6-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 07:56:39 GMT 2026] Executing as ?@nf-0a553a95f294a4ad20d16e4260f2a3a4-07dae-2p9vz 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 07:56:39 MarkDuplicates Start of doWork freeMemory: 105828656; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:56:39 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:56:39 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:56:46 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:8,868,006
INFO 2026-06-08 07:56:46 MarkDuplicates Tracking 3048 as yet unmatched pairs. 142 records in RAM.
INFO 2026-06-08 07:56:49 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:19,655,087
INFO 2026-06-08 07:56:49 MarkDuplicates Tracking 5552 as yet unmatched pairs. 228 records in RAM.
INFO 2026-06-08 07:56:52 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:25,245,128
INFO 2026-06-08 07:56:52 MarkDuplicates Tracking 8123 as yet unmatched pairs. 88 records in RAM.
INFO 2026-06-08 07:56:55 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:32,184,584
INFO 2026-06-08 07:56:55 MarkDuplicates Tracking 10687 as yet unmatched pairs. 17 records in RAM.
INFO 2026-06-08 07:56:57 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:39,361,557
INFO 2026-06-08 07:56:57 MarkDuplicates Tracking 13251 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 07:57:00 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:44,800,484
INFO 2026-06-08 07:57:00 MarkDuplicates Tracking 15729 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:57:04 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: chr1:66,984,689
INFO 2026-06-08 07:57:04 MarkDuplicates Tracking 18133 as yet unmatched pairs. 28 records in RAM.
INFO 2026-06-08 07:57:07 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:102,962,733
INFO 2026-06-08 07:57:07 MarkDuplicates Tracking 20381 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 07:57:10 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: chr1:114,734,096
INFO 2026-06-08 07:57:10 MarkDuplicates Tracking 22755 as yet unmatched pairs. 104 records in RAM.
INFO 2026-06-08 07:57:13 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr1:145,957,637
INFO 2026-06-08 07:57:13 MarkDuplicates Tracking 24591 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:57:16 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr1:149,944,628
INFO 2026-06-08 07:57:16 MarkDuplicates Tracking 25719 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:57:19 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 3s. Last read position: chr1:152,307,782
INFO 2026-06-08 07:57:19 MarkDuplicates Tracking 27985 as yet unmatched pairs. 230 records in RAM.
INFO 2026-06-08 07:57:22 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:154,869,683
INFO 2026-06-08 07:57:22 MarkDuplicates Tracking 30136 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:57:24 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr1:156,137,197
INFO 2026-06-08 07:57:24 MarkDuplicates Tracking 33052 as yet unmatched pairs. 178 records in RAM.
INFO 2026-06-08 07:57:27 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:161,998,038
INFO 2026-06-08 07:57:27 MarkDuplicates Tracking 35485 as yet unmatched pairs. 110 records in RAM.
INFO 2026-06-08 07:57:30 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr1:183,023,898
INFO 2026-06-08 07:57:30 MarkDuplicates Tracking 37922 as yet unmatched pairs. 81 records in RAM.
INFO 2026-06-08 07:57:33 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: chr1:201,817,134
INFO 2026-06-08 07:57:33 MarkDuplicates Tracking 40177 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-08 07:57:36 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:211,372,457
INFO 2026-06-08 07:57:36 MarkDuplicates Tracking 42526 as yet unmatched pairs. 11 records in RAM.
INFO 2026-06-08 07:57:38 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr1:229,527,270
INFO 2026-06-08 07:57:38 MarkDuplicates Tracking 45020 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 07:57:42 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr2:6,897,017
INFO 2026-06-08 07:57:42 MarkDuplicates Tracking 47609 as yet unmatched pairs. 47557 records in RAM.
INFO 2026-06-08 07:57:44 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr2:27,202,836
INFO 2026-06-08 07:57:44 MarkDuplicates Tracking 50127 as yet unmatched pairs. 50073 records in RAM.
INFO 2026-06-08 07:57:47 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,263
INFO 2026-06-08 07:57:47 MarkDuplicates Tracking 79011 as yet unmatched pairs. 51859 records in RAM.
INFO 2026-06-08 07:57:52 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,406
INFO 2026-06-08 07:57:52 MarkDuplicates Tracking 471017 as yet unmatched pairs. 51720 records in RAM.
INFO 2026-06-08 07:57:54 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr2:43,948,454
INFO 2026-06-08 07:57:54 MarkDuplicates Tracking 502250 as yet unmatched pairs. 50199 records in RAM.
INFO 2026-06-08 07:57:57 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr2:64,636,474
INFO 2026-06-08 07:57:57 MarkDuplicates Tracking 499898 as yet unmatched pairs. 47840 records in RAM.
INFO 2026-06-08 07:58:00 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: chr2:74,877,205
INFO 2026-06-08 07:58:00 MarkDuplicates Tracking 497351 as yet unmatched pairs. 45293 records in RAM.
INFO 2026-06-08 07:58:03 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr2:97,656,874
INFO 2026-06-08 07:58:03 MarkDuplicates Tracking 495280 as yet unmatched pairs. 43219 records in RAM.
INFO 2026-06-08 07:58:05 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr2:108,767,131
INFO 2026-06-08 07:58:05 MarkDuplicates Tracking 493050 as yet unmatched pairs. 40985 records in RAM.
INFO 2026-06-08 07:58:07 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr2:113,217,904
INFO 2026-06-08 07:58:07 MarkDuplicates Tracking 492065 as yet unmatched pairs. 40000 records in RAM.
INFO 2026-06-08 07:58:10 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr2:130,152,656
INFO 2026-06-08 07:58:10 MarkDuplicates Tracking 488951 as yet unmatched pairs. 36886 records in RAM.
INFO 2026-06-08 07:58:12 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr2:162,173,755
INFO 2026-06-08 07:58:12 MarkDuplicates Tracking 486463 as yet unmatched pairs. 34394 records in RAM.
INFO 2026-06-08 07:58:16 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: chr2:186,637,064
INFO 2026-06-08 07:58:16 MarkDuplicates Tracking 484175 as yet unmatched pairs. 32100 records in RAM.
INFO 2026-06-08 07:58:19 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 3s. Last read position: chr2:189,755,465
INFO 2026-06-08 07:58:19 MarkDuplicates Tracking 481412 as yet unmatched pairs. 29337 records in RAM.
INFO 2026-06-08 07:58:22 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr2:215,361,505
INFO 2026-06-08 07:58:22 MarkDuplicates Tracking 484618 as yet unmatched pairs. 32534 records in RAM.
INFO 2026-06-08 07:58:25 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr2:215,370,394
INFO 2026-06-08 07:58:25 MarkDuplicates Tracking 481021 as yet unmatched pairs. 28935 records in RAM.
INFO 2026-06-08 07:58:27 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr2:215,375,246
INFO 2026-06-08 07:58:27 MarkDuplicates Tracking 477222 as yet unmatched pairs. 25136 records in RAM.
INFO 2026-06-08 07:58:30 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr2:215,379,191
INFO 2026-06-08 07:58:30 MarkDuplicates Tracking 474819 as yet unmatched pairs. 22733 records in RAM.
INFO 2026-06-08 07:58:32 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr2:215,386,854
INFO 2026-06-08 07:58:32 MarkDuplicates Tracking 472838 as yet unmatched pairs. 20751 records in RAM.
INFO 2026-06-08 07:58:35 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr2:215,404,391
INFO 2026-06-08 07:58:35 MarkDuplicates Tracking 468883 as yet unmatched pairs. 16796 records in RAM.
INFO 2026-06-08 07:58:39 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: chr2:215,409,680
INFO 2026-06-08 07:58:39 MarkDuplicates Tracking 465697 as yet unmatched pairs. 13609 records in RAM.
INFO 2026-06-08 07:58:43 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 4s. Last read position: chr2:215,423,423
INFO 2026-06-08 07:58:43 MarkDuplicates Tracking 464031 as yet unmatched pairs. 11942 records in RAM.
INFO 2026-06-08 07:58:46 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 3s. Last read position: chr2:215,431,927
INFO 2026-06-08 07:58:46 MarkDuplicates Tracking 463096 as yet unmatched pairs. 11006 records in RAM.
INFO 2026-06-08 07:58:49 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr2:219,539,309
INFO 2026-06-08 07:58:49 MarkDuplicates Tracking 456981 as yet unmatched pairs. 4890 records in RAM.
INFO 2026-06-08 07:58:52 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr2:237,353,340
INFO 2026-06-08 07:58:52 MarkDuplicates Tracking 454581 as yet unmatched pairs. 2478 records in RAM.
INFO 2026-06-08 07:58:55 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr3:4,983,479
INFO 2026-06-08 07:58:55 MarkDuplicates Tracking 451959 as yet unmatched pairs. 31304 records in RAM.
INFO 2026-06-08 07:58:58 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 3s. Last read position: chr3:25,733,889
INFO 2026-06-08 07:58:58 MarkDuplicates Tracking 449410 as yet unmatched pairs. 28752 records in RAM.
INFO 2026-06-08 07:59:01 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 2s. Last read position: chr3:46,687,045
INFO 2026-06-08 07:59:01 MarkDuplicates Tracking 446901 as yet unmatched pairs. 26238 records in RAM.
INFO 2026-06-08 07:59:03 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 2s. Last read position: chr3:49,362,605
INFO 2026-06-08 07:59:03 MarkDuplicates Tracking 444290 as yet unmatched pairs. 23625 records in RAM.
INFO 2026-06-08 07:59:06 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr3:57,257,253
INFO 2026-06-08 07:59:06 MarkDuplicates Tracking 441563 as yet unmatched pairs. 20898 records in RAM.
INFO 2026-06-08 07:59:09 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr3:99,849,278
INFO 2026-06-08 07:59:09 MarkDuplicates Tracking 439218 as yet unmatched pairs. 18549 records in RAM.
INFO 2026-06-08 07:59:11 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr3:121,696,011
INFO 2026-06-08 07:59:11 MarkDuplicates Tracking 436602 as yet unmatched pairs. 15930 records in RAM.
INFO 2026-06-08 07:59:14 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr3:129,130,112
INFO 2026-06-08 07:59:14 MarkDuplicates Tracking 433831 as yet unmatched pairs. 13159 records in RAM.
INFO 2026-06-08 07:59:17 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 3s. Last read position: chr3:142,422,824
INFO 2026-06-08 07:59:17 MarkDuplicates Tracking 431101 as yet unmatched pairs. 10428 records in RAM.
INFO 2026-06-08 07:59:20 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 3s. Last read position: chr3:170,303,055
INFO 2026-06-08 07:59:20 MarkDuplicates Tracking 428969 as yet unmatched pairs. 8296 records in RAM.
INFO 2026-06-08 07:59:24 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 3s. Last read position: chr3:186,857,044
INFO 2026-06-08 07:59:24 MarkDuplicates Tracking 426348 as yet unmatched pairs. 5675 records in RAM.
INFO 2026-06-08 07:59:26 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr3:195,780,155
INFO 2026-06-08 07:59:26 MarkDuplicates Tracking 426581 as yet unmatched pairs. 5906 records in RAM.
INFO 2026-06-08 07:59:28 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr3:195,782,946
INFO 2026-06-08 07:59:28 MarkDuplicates Tracking 426158 as yet unmatched pairs. 5478 records in RAM.
INFO 2026-06-08 07:59:30 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr3:195,786,361
INFO 2026-06-08 07:59:30 MarkDuplicates Tracking 424170 as yet unmatched pairs. 3489 records in RAM.
INFO 2026-06-08 07:59:33 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr4:958,411
INFO 2026-06-08 07:59:33 MarkDuplicates Tracking 420365 as yet unmatched pairs. 13662 records in RAM.
INFO 2026-06-08 07:59:36 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr4:7,030,354
INFO 2026-06-08 07:59:36 MarkDuplicates Tracking 417255 as yet unmatched pairs. 10552 records in RAM.
INFO 2026-06-08 07:59:38 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr4:39,454,920
INFO 2026-06-08 07:59:38 MarkDuplicates Tracking 415007 as yet unmatched pairs. 8301 records in RAM.
INFO 2026-06-08 07:59:39 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr4:77,726,310
INFO 2026-06-08 07:59:39 MarkDuplicates Tracking 412734 as yet unmatched pairs. 6026 records in RAM.
INFO 2026-06-08 07:59:42 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr4:113,214,101
INFO 2026-06-08 07:59:42 MarkDuplicates Tracking 410415 as yet unmatched pairs. 3704 records in RAM.
INFO 2026-06-08 07:59:45 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr4:165,464,389
INFO 2026-06-08 07:59:45 MarkDuplicates Tracking 408138 as yet unmatched pairs. 1422 records in RAM.
INFO 2026-06-08 07:59:48 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 3s. Last read position: chr5:14,290,998
INFO 2026-06-08 07:59:48 MarkDuplicates Tracking 405597 as yet unmatched pairs. 24561 records in RAM.
INFO 2026-06-08 07:59:52 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 3s. Last read position: chr5:37,182,853
INFO 2026-06-08 07:59:52 MarkDuplicates Tracking 402867 as yet unmatched pairs. 21830 records in RAM.
INFO 2026-06-08 07:59:54 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr5:72,196,343
INFO 2026-06-08 07:59:54 MarkDuplicates Tracking 400904 as yet unmatched pairs. 19867 records in RAM.
INFO 2026-06-08 07:59:57 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr5:95,755,693
INFO 2026-06-08 07:59:57 MarkDuplicates Tracking 398655 as yet unmatched pairs. 17616 records in RAM.
INFO 2026-06-08 08:00:00 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr5:134,225,759
INFO 2026-06-08 08:00:00 MarkDuplicates Tracking 396362 as yet unmatched pairs. 15321 records in RAM.
INFO 2026-06-08 08:00:02 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr5:141,123,416
INFO 2026-06-08 08:00:02 MarkDuplicates Tracking 394065 as yet unmatched pairs. 13003 records in RAM.
INFO 2026-06-08 08:00:03 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr5:150,126,520
INFO 2026-06-08 08:00:03 MarkDuplicates Tracking 391880 as yet unmatched pairs. 10809 records in RAM.
INFO 2026-06-08 08:00:06 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr5:150,649,509
INFO 2026-06-08 08:00:06 MarkDuplicates Tracking 389076 as yet unmatched pairs. 8004 records in RAM.
INFO 2026-06-08 08:00:09 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr5:171,390,104
INFO 2026-06-08 08:00:09 MarkDuplicates Tracking 387721 as yet unmatched pairs. 6648 records in RAM.
INFO 2026-06-08 08:00:12 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 3s. Last read position: chr5:177,459,673
INFO 2026-06-08 08:00:12 MarkDuplicates Tracking 384366 as yet unmatched pairs. 3291 records in RAM.
INFO 2026-06-08 08:00:15 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 3s. Last read position: chr5:180,791,839
INFO 2026-06-08 08:00:15 MarkDuplicates Tracking 381662 as yet unmatched pairs. 587 records in RAM.
INFO 2026-06-08 08:00:19 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 3s. Last read position: chr6:13,634,467
INFO 2026-06-08 08:00:19 MarkDuplicates Tracking 379018 as yet unmatched pairs. 22722 records in RAM.
INFO 2026-06-08 08:00:22 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 3s. Last read position: chr6:30,661,750
INFO 2026-06-08 08:00:22 MarkDuplicates Tracking 376854 as yet unmatched pairs. 20557 records in RAM.
INFO 2026-06-08 08:00:25 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr6:31,816,695
INFO 2026-06-08 08:00:25 MarkDuplicates Tracking 374550 as yet unmatched pairs. 18253 records in RAM.
INFO 2026-06-08 08:00:27 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr6:32,847,144
INFO 2026-06-08 08:00:27 MarkDuplicates Tracking 372391 as yet unmatched pairs. 16081 records in RAM.
INFO 2026-06-08 08:00:30 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr6:39,913,811
INFO 2026-06-08 08:00:30 MarkDuplicates Tracking 369891 as yet unmatched pairs. 13580 records in RAM.
INFO 2026-06-08 08:00:32 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr6:56,529,565
INFO 2026-06-08 08:00:32 MarkDuplicates Tracking 367405 as yet unmatched pairs. 11085 records in RAM.
INFO 2026-06-08 08:00:34 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr6:85,615,002
INFO 2026-06-08 08:00:34 MarkDuplicates Tracking 365055 as yet unmatched pairs. 8732 records in RAM.
INFO 2026-06-08 08:00:37 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr6:121,447,799
INFO 2026-06-08 08:00:37 MarkDuplicates Tracking 362700 as yet unmatched pairs. 6370 records in RAM.
INFO 2026-06-08 08:00:39 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr6:151,351,924
INFO 2026-06-08 08:00:39 MarkDuplicates Tracking 360149 as yet unmatched pairs. 3817 records in RAM.
INFO 2026-06-08 08:00:41 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr6:161,091,421
INFO 2026-06-08 08:00:41 MarkDuplicates Tracking 357753 as yet unmatched pairs. 1415 records in RAM.
INFO 2026-06-08 08:00:45 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 3s. Last read position: chr7:5,371,186
INFO 2026-06-08 08:00:45 MarkDuplicates Tracking 354918 as yet unmatched pairs. 24817 records in RAM.
INFO 2026-06-08 08:00:48 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr7:20,159,188
INFO 2026-06-08 08:00:48 MarkDuplicates Tracking 352200 as yet unmatched pairs. 22098 records in RAM.
INFO 2026-06-08 08:00:50 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr7:44,111,154
INFO 2026-06-08 08:00:50 MarkDuplicates Tracking 349925 as yet unmatched pairs. 19821 records in RAM.
INFO 2026-06-08 08:00:52 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr7:73,155,251
INFO 2026-06-08 08:00:52 MarkDuplicates Tracking 347632 as yet unmatched pairs. 17522 records in RAM.
INFO 2026-06-08 08:00:54 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr7:76,302,878
INFO 2026-06-08 08:00:54 MarkDuplicates Tracking 346135 as yet unmatched pairs. 16024 records in RAM.
INFO 2026-06-08 08:00:56 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr7:94,400,195
INFO 2026-06-08 08:00:56 MarkDuplicates Tracking 343510 as yet unmatched pairs. 13397 records in RAM.
INFO 2026-06-08 08:01:00 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 3s. Last read position: chr7:98,925,152
INFO 2026-06-08 08:01:00 MarkDuplicates Tracking 340613 as yet unmatched pairs. 10497 records in RAM.
INFO 2026-06-08 08:01:02 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr7:102,554,484
INFO 2026-06-08 08:01:02 MarkDuplicates Tracking 338283 as yet unmatched pairs. 8167 records in RAM.
INFO 2026-06-08 08:01:04 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr7:127,887,906
INFO 2026-06-08 08:01:04 MarkDuplicates Tracking 336435 as yet unmatched pairs. 6317 records in RAM.
INFO 2026-06-08 08:01:06 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr7:140,679,154
INFO 2026-06-08 08:01:06 MarkDuplicates Tracking 333492 as yet unmatched pairs. 3372 records in RAM.
INFO 2026-06-08 08:01:08 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr7:152,094,369
INFO 2026-06-08 08:01:08 MarkDuplicates Tracking 331117 as yet unmatched pairs. 996 records in RAM.
INFO 2026-06-08 08:01:10 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr8:20,214,823
INFO 2026-06-08 08:01:10 MarkDuplicates Tracking 328635 as yet unmatched pairs. 21957 records in RAM.
INFO 2026-06-08 08:01:13 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr8:38,413,708
INFO 2026-06-08 08:01:13 MarkDuplicates Tracking 326248 as yet unmatched pairs. 19569 records in RAM.
INFO 2026-06-08 08:01:15 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr8:55,999,440
INFO 2026-06-08 08:01:15 MarkDuplicates Tracking 322954 as yet unmatched pairs. 16275 records in RAM.
INFO 2026-06-08 08:01:18 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr8:82,292,212
INFO 2026-06-08 08:01:18 MarkDuplicates Tracking 320729 as yet unmatched pairs. 14048 records in RAM.
INFO 2026-06-08 08:01:21 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr8:100,721,483
INFO 2026-06-08 08:01:21 MarkDuplicates Tracking 318618 as yet unmatched pairs. 11936 records in RAM.
INFO 2026-06-08 08:01:24 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr8:125,433,496
INFO 2026-06-08 08:01:24 MarkDuplicates Tracking 315896 as yet unmatched pairs. 9209 records in RAM.
INFO 2026-06-08 08:01:27 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 3s. Last read position: chr8:143,806,983
INFO 2026-06-08 08:01:27 MarkDuplicates Tracking 312989 as yet unmatched pairs. 6283 records in RAM.
INFO 2026-06-08 08:01:29 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr8:143,863,937
INFO 2026-06-08 08:01:29 MarkDuplicates Tracking 311709 as yet unmatched pairs. 5003 records in RAM.
INFO 2026-06-08 08:01:31 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr8:143,932,910
INFO 2026-06-08 08:01:31 MarkDuplicates Tracking 309442 as yet unmatched pairs. 2736 records in RAM.
INFO 2026-06-08 08:01:33 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 2s. Last read position: chr9:3,828,259
INFO 2026-06-08 08:01:33 MarkDuplicates Tracking 306463 as yet unmatched pairs. 20241 records in RAM.
INFO 2026-06-08 08:01:36 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr9:35,090,145
INFO 2026-06-08 08:01:36 MarkDuplicates Tracking 304036 as yet unmatched pairs. 17814 records in RAM.
INFO 2026-06-08 08:01:39 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr9:77,316,379
INFO 2026-06-08 08:01:39 MarkDuplicates Tracking 301855 as yet unmatched pairs. 15626 records in RAM.
INFO 2026-06-08 08:01:41 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr9:99,049,705
INFO 2026-06-08 08:01:41 MarkDuplicates Tracking 299353 as yet unmatched pairs. 13122 records in RAM.
INFO 2026-06-08 08:01:43 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 2s. Last read position: chr9:115,073,603
INFO 2026-06-08 08:01:43 MarkDuplicates Tracking 297090 as yet unmatched pairs. 10858 records in RAM.
INFO 2026-06-08 08:01:46 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 3s. Last read position: chr9:127,450,743
INFO 2026-06-08 08:01:46 MarkDuplicates Tracking 294585 as yet unmatched pairs. 8353 records in RAM.
INFO 2026-06-08 08:01:49 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr9:130,885,019
INFO 2026-06-08 08:01:49 MarkDuplicates Tracking 291638 as yet unmatched pairs. 5404 records in RAM.
INFO 2026-06-08 08:01:50 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr9:134,824,588
INFO 2026-06-08 08:01:50 MarkDuplicates Tracking 288883 as yet unmatched pairs. 2648 records in RAM.
INFO 2026-06-08 08:01:53 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 2s. Last read position: chr10:3,784,959
INFO 2026-06-08 08:01:53 MarkDuplicates Tracking 285873 as yet unmatched pairs. 16192 records in RAM.
INFO 2026-06-08 08:01:56 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 3s. Last read position: chr10:29,533,237
INFO 2026-06-08 08:01:56 MarkDuplicates Tracking 283488 as yet unmatched pairs. 13805 records in RAM.
INFO 2026-06-08 08:01:59 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr10:49,019,737
INFO 2026-06-08 08:01:59 MarkDuplicates Tracking 281315 as yet unmatched pairs. 11630 records in RAM.
INFO 2026-06-08 08:02:02 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr10:71,811,992
INFO 2026-06-08 08:02:02 MarkDuplicates Tracking 278730 as yet unmatched pairs. 9042 records in RAM.
INFO 2026-06-08 08:02:05 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: chr10:89,008,984
INFO 2026-06-08 08:02:05 MarkDuplicates Tracking 276723 as yet unmatched pairs. 7034 records in RAM.
INFO 2026-06-08 08:02:08 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr10:102,655,199
INFO 2026-06-08 08:02:08 MarkDuplicates Tracking 274291 as yet unmatched pairs. 4595 records in RAM.
INFO 2026-06-08 08:02:10 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr10:119,838,688
INFO 2026-06-08 08:02:10 MarkDuplicates Tracking 271789 as yet unmatched pairs. 2087 records in RAM.
INFO 2026-06-08 08:02:13 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr11:319,879
INFO 2026-06-08 08:02:13 MarkDuplicates Tracking 269986 as yet unmatched pairs. 31192 records in RAM.
INFO 2026-06-08 08:02:16 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr11:1,245,154
INFO 2026-06-08 08:02:16 MarkDuplicates Tracking 267545 as yet unmatched pairs. 28749 records in RAM.
INFO 2026-06-08 08:02:18 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr11:1,761,391
INFO 2026-06-08 08:02:18 MarkDuplicates Tracking 266101 as yet unmatched pairs. 27305 records in RAM.
INFO 2026-06-08 08:02:21 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 2s. Last read position: chr11:14,262,728
INFO 2026-06-08 08:02:21 MarkDuplicates Tracking 263493 as yet unmatched pairs. 24696 records in RAM.
INFO 2026-06-08 08:02:23 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr11:45,870,847
INFO 2026-06-08 08:02:23 MarkDuplicates Tracking 260682 as yet unmatched pairs. 21884 records in RAM.
INFO 2026-06-08 08:02:25 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr11:58,579,265
INFO 2026-06-08 08:02:25 MarkDuplicates Tracking 258265 as yet unmatched pairs. 19467 records in RAM.
INFO 2026-06-08 08:02:27 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr11:62,530,797
INFO 2026-06-08 08:02:27 MarkDuplicates Tracking 255946 as yet unmatched pairs. 17147 records in RAM.
INFO 2026-06-08 08:02:29 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr11:65,182,842
INFO 2026-06-08 08:02:29 MarkDuplicates Tracking 253016 as yet unmatched pairs. 14217 records in RAM.
INFO 2026-06-08 08:02:32 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr11:66,858,181
INFO 2026-06-08 08:02:32 MarkDuplicates Tracking 250104 as yet unmatched pairs. 11302 records in RAM.
INFO 2026-06-08 08:02:34 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr11:72,295,607
INFO 2026-06-08 08:02:34 MarkDuplicates Tracking 247435 as yet unmatched pairs. 8632 records in RAM.
INFO 2026-06-08 08:02:37 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr11:94,799,584
INFO 2026-06-08 08:02:37 MarkDuplicates Tracking 244927 as yet unmatched pairs. 6121 records in RAM.
INFO 2026-06-08 08:02:40 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr11:118,396,328
INFO 2026-06-08 08:02:40 MarkDuplicates Tracking 242500 as yet unmatched pairs. 3693 records in RAM.
INFO 2026-06-08 08:02:41 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr11:125,080,645
INFO 2026-06-08 08:02:41 MarkDuplicates Tracking 240015 as yet unmatched pairs. 1207 records in RAM.
INFO 2026-06-08 08:02:44 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chr12:6,537,120
INFO 2026-06-08 08:02:44 MarkDuplicates Tracking 237518 as yet unmatched pairs. 20501 records in RAM.
INFO 2026-06-08 08:02:47 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: chr12:14,770,769
INFO 2026-06-08 08:02:47 MarkDuplicates Tracking 235123 as yet unmatched pairs. 18106 records in RAM.
INFO 2026-06-08 08:02:51 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 3s. Last read position: chr12:49,027,135
INFO 2026-06-08 08:02:51 MarkDuplicates Tracking 232742 as yet unmatched pairs. 15722 records in RAM.
INFO 2026-06-08 08:02:54 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 3s. Last read position: chr12:53,049,154
INFO 2026-06-08 08:02:54 MarkDuplicates Tracking 230430 as yet unmatched pairs. 13408 records in RAM.
INFO 2026-06-08 08:02:57 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr12:56,615,239
INFO 2026-06-08 08:02:57 MarkDuplicates Tracking 228120 as yet unmatched pairs. 11098 records in RAM.
INFO 2026-06-08 08:03:00 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr12:62,965,320
INFO 2026-06-08 08:03:00 MarkDuplicates Tracking 225515 as yet unmatched pairs. 8492 records in RAM.
INFO 2026-06-08 08:03:02 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr12:98,601,175
INFO 2026-06-08 08:03:02 MarkDuplicates Tracking 223471 as yet unmatched pairs. 6446 records in RAM.
INFO 2026-06-08 08:03:05 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 2s. Last read position: chr12:113,320,603
INFO 2026-06-08 08:03:05 MarkDuplicates Tracking 221131 as yet unmatched pairs. 4106 records in RAM.
INFO 2026-06-08 08:03:08 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 2s. Last read position: chr12:124,372,331
INFO 2026-06-08 08:03:08 MarkDuplicates Tracking 218492 as yet unmatched pairs. 1464 records in RAM.
INFO 2026-06-08 08:03:11 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr13:27,583,168
INFO 2026-06-08 08:03:11 MarkDuplicates Tracking 215907 as yet unmatched pairs. 7143 records in RAM.
INFO 2026-06-08 08:03:13 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 2s. Last read position: chr13:51,369,019
INFO 2026-06-08 08:03:13 MarkDuplicates Tracking 213638 as yet unmatched pairs. 4873 records in RAM.
INFO 2026-06-08 08:03:15 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr13:109,783,999
INFO 2026-06-08 08:03:15 MarkDuplicates Tracking 211186 as yet unmatched pairs. 2420 records in RAM.
INFO 2026-06-08 08:03:18 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 2s. Last read position: chr14:21,211,451
INFO 2026-06-08 08:03:18 MarkDuplicates Tracking 208363 as yet unmatched pairs. 14641 records in RAM.
INFO 2026-06-08 08:03:21 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 3s. Last read position: chr14:31,026,041
INFO 2026-06-08 08:03:21 MarkDuplicates Tracking 205718 as yet unmatched pairs. 11994 records in RAM.
INFO 2026-06-08 08:03:24 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 2s. Last read position: chr14:55,138,330
INFO 2026-06-08 08:03:24 MarkDuplicates Tracking 203438 as yet unmatched pairs. 9710 records in RAM.
INFO 2026-06-08 08:03:26 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr14:69,768,879
INFO 2026-06-08 08:03:26 MarkDuplicates Tracking 200875 as yet unmatched pairs. 7147 records in RAM.
INFO 2026-06-08 08:03:28 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr14:92,577,212
INFO 2026-06-08 08:03:28 MarkDuplicates Tracking 198155 as yet unmatched pairs. 4425 records in RAM.
INFO 2026-06-08 08:03:31 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr14:104,893,521
INFO 2026-06-08 08:03:31 MarkDuplicates Tracking 195384 as yet unmatched pairs. 1648 records in RAM.
INFO 2026-06-08 08:03:33 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr15:28,206,263
INFO 2026-06-08 08:03:33 MarkDuplicates Tracking 193327 as yet unmatched pairs. 12317 records in RAM.
INFO 2026-06-08 08:03:36 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr15:42,529,809
INFO 2026-06-08 08:03:36 MarkDuplicates Tracking 191335 as yet unmatched pairs. 10323 records in RAM.
INFO 2026-06-08 08:03:38 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr15:56,921,051
INFO 2026-06-08 08:03:38 MarkDuplicates Tracking 188962 as yet unmatched pairs. 7946 records in RAM.
INFO 2026-06-08 08:03:40 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 2s. Last read position: chr15:68,992,846
INFO 2026-06-08 08:03:40 MarkDuplicates Tracking 186205 as yet unmatched pairs. 5188 records in RAM.
INFO 2026-06-08 08:03:42 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 2s. Last read position: chr15:77,181,765
INFO 2026-06-08 08:03:42 MarkDuplicates Tracking 183616 as yet unmatched pairs. 2599 records in RAM.
INFO 2026-06-08 08:03:45 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 2s. Last read position: chr15:98,896,815
INFO 2026-06-08 08:03:45 MarkDuplicates Tracking 181410 as yet unmatched pairs. 390 records in RAM.
INFO 2026-06-08 08:03:47 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr16:2,760,451
INFO 2026-06-08 08:03:47 MarkDuplicates Tracking 178534 as yet unmatched pairs. 20092 records in RAM.
INFO 2026-06-08 08:03:49 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr16:11,897,841
INFO 2026-06-08 08:03:49 MarkDuplicates Tracking 175755 as yet unmatched pairs. 17311 records in RAM.
INFO 2026-06-08 08:03:51 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr16:17,117,965
INFO 2026-06-08 08:03:51 MarkDuplicates Tracking 174553 as yet unmatched pairs. 16109 records in RAM.
INFO 2026-06-08 08:03:53 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 2s. Last read position: chr16:21,404,887
INFO 2026-06-08 08:03:53 MarkDuplicates Tracking 173829 as yet unmatched pairs. 15385 records in RAM.
INFO 2026-06-08 08:03:56 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 2s. Last read position: chr16:22,523,929
INFO 2026-06-08 08:03:56 MarkDuplicates Tracking 172357 as yet unmatched pairs. 13913 records in RAM.
INFO 2026-06-08 08:03:58 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 2s. Last read position: chr16:28,714,905
INFO 2026-06-08 08:03:58 MarkDuplicates Tracking 170906 as yet unmatched pairs. 12459 records in RAM.
INFO 2026-06-08 08:04:00 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr16:29,878,363
INFO 2026-06-08 08:04:00 MarkDuplicates Tracking 169356 as yet unmatched pairs. 10909 records in RAM.
INFO 2026-06-08 08:04:02 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 2s. Last read position: chr16:30,738,400
INFO 2026-06-08 08:04:02 MarkDuplicates Tracking 167513 as yet unmatched pairs. 9066 records in RAM.
INFO 2026-06-08 08:04:04 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 1s. Last read position: chr16:55,509,211
INFO 2026-06-08 08:04:04 MarkDuplicates Tracking 165193 as yet unmatched pairs. 6744 records in RAM.
INFO 2026-06-08 08:04:06 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chr16:69,693,825
INFO 2026-06-08 08:04:06 MarkDuplicates Tracking 162763 as yet unmatched pairs. 4313 records in RAM.
INFO 2026-06-08 08:04:09 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 2s. Last read position: chr16:88,433,327
INFO 2026-06-08 08:04:09 MarkDuplicates Tracking 160061 as yet unmatched pairs. 1606 records in RAM.
INFO 2026-06-08 08:04:12 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 2s. Last read position: chr17:1,650,937
INFO 2026-06-08 08:04:12 MarkDuplicates Tracking 157298 as yet unmatched pairs. 59184 records in RAM.
INFO 2026-06-08 08:04:14 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 2s. Last read position: chr17:7,012,677
INFO 2026-06-08 08:04:14 MarkDuplicates Tracking 155139 as yet unmatched pairs. 57025 records in RAM.
INFO 2026-06-08 08:04:17 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr17:7,898,040
INFO 2026-06-08 08:04:17 MarkDuplicates Tracking 152252 as yet unmatched pairs. 54138 records in RAM.
INFO 2026-06-08 08:04:19 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr17:21,028,596
INFO 2026-06-08 08:04:19 MarkDuplicates Tracking 149889 as yet unmatched pairs. 51773 records in RAM.
INFO 2026-06-08 08:04:22 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 3s. Last read position: chr17:36,242,268
INFO 2026-06-08 08:04:22 MarkDuplicates Tracking 147468 as yet unmatched pairs. 49348 records in RAM.
INFO 2026-06-08 08:04:25 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 2s. Last read position: chr17:40,487,310
INFO 2026-06-08 08:04:25 MarkDuplicates Tracking 145248 as yet unmatched pairs. 47127 records in RAM.
INFO 2026-06-08 08:04:27 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr17:44,558,320
INFO 2026-06-08 08:04:27 MarkDuplicates Tracking 142552 as yet unmatched pairs. 44431 records in RAM.
INFO 2026-06-08 08:04:30 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr17:50,185,480
INFO 2026-06-08 08:04:30 MarkDuplicates Tracking 147039 as yet unmatched pairs. 48917 records in RAM.
INFO 2026-06-08 08:04:33 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,875
INFO 2026-06-08 08:04:33 MarkDuplicates Tracking 141060 as yet unmatched pairs. 42938 records in RAM.
INFO 2026-06-08 08:04:36 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,132
INFO 2026-06-08 08:04:36 MarkDuplicates Tracking 137345 as yet unmatched pairs. 39223 records in RAM.
INFO 2026-06-08 08:04:38 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,419
INFO 2026-06-08 08:04:38 MarkDuplicates Tracking 135189 as yet unmatched pairs. 37067 records in RAM.
INFO 2026-06-08 08:04:41 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,041
INFO 2026-06-08 08:04:41 MarkDuplicates Tracking 137303 as yet unmatched pairs. 39180 records in RAM.
INFO 2026-06-08 08:04:44 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 2s. Last read position: chr17:50,191,871
INFO 2026-06-08 08:04:44 MarkDuplicates Tracking 131792 as yet unmatched pairs. 33669 records in RAM.
INFO 2026-06-08 08:04:46 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,018
INFO 2026-06-08 08:04:46 MarkDuplicates Tracking 129021 as yet unmatched pairs. 30898 records in RAM.
INFO 2026-06-08 08:04:49 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,056
INFO 2026-06-08 08:04:49 MarkDuplicates Tracking 124178 as yet unmatched pairs. 26055 records in RAM.
INFO 2026-06-08 08:04:52 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 3s. Last read position: chr17:50,196,185
INFO 2026-06-08 08:04:52 MarkDuplicates Tracking 125775 as yet unmatched pairs. 27651 records in RAM.
INFO 2026-06-08 08:04:55 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 3s. Last read position: chr17:50,197,212
INFO 2026-06-08 08:04:55 MarkDuplicates Tracking 119411 as yet unmatched pairs. 21287 records in RAM.
INFO 2026-06-08 08:04:58 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 3s. Last read position: chr17:50,199,433
INFO 2026-06-08 08:04:58 MarkDuplicates Tracking 113329 as yet unmatched pairs. 15204 records in RAM.
INFO 2026-06-08 08:05:00 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr17:58,312,216
INFO 2026-06-08 08:05:00 MarkDuplicates Tracking 108573 as yet unmatched pairs. 10448 records in RAM.
INFO 2026-06-08 08:05:02 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr17:64,502,464
INFO 2026-06-08 08:05:02 MarkDuplicates Tracking 106140 as yet unmatched pairs. 8015 records in RAM.
INFO 2026-06-08 08:05:04 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 2s. Last read position: chr17:75,731,870
INFO 2026-06-08 08:05:04 MarkDuplicates Tracking 103620 as yet unmatched pairs. 5495 records in RAM.
INFO 2026-06-08 08:05:06 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr17:80,347,603
INFO 2026-06-08 08:05:06 MarkDuplicates Tracking 101020 as yet unmatched pairs. 2895 records in RAM.
INFO 2026-06-08 08:05:08 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 2s. Last read position: chr18:2,697,112
INFO 2026-06-08 08:05:08 MarkDuplicates Tracking 97946 as yet unmatched pairs. 4134 records in RAM.
INFO 2026-06-08 08:05:11 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr18:47,896,594
INFO 2026-06-08 08:05:11 MarkDuplicates Tracking 95633 as yet unmatched pairs. 1814 records in RAM.
INFO 2026-06-08 08:05:13 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 2s. Last read position: chr19:1,085,793
INFO 2026-06-08 08:05:13 MarkDuplicates Tracking 93079 as yet unmatched pairs. 38949 records in RAM.
INFO 2026-06-08 08:05:16 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 2s. Last read position: chr19:5,212,416
INFO 2026-06-08 08:05:16 MarkDuplicates Tracking 90028 as yet unmatched pairs. 35897 records in RAM.
INFO 2026-06-08 08:05:18 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr19:8,895,993
INFO 2026-06-08 08:05:18 MarkDuplicates Tracking 87289 as yet unmatched pairs. 33158 records in RAM.
INFO 2026-06-08 08:05:20 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 2s. Last read position: chr19:8,951,174
INFO 2026-06-08 08:05:20 MarkDuplicates Tracking 85013 as yet unmatched pairs. 30882 records in RAM.
INFO 2026-06-08 08:05:22 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 2s. Last read position: chr19:8,963,885
INFO 2026-06-08 08:05:22 MarkDuplicates Tracking 82825 as yet unmatched pairs. 28694 records in RAM.
INFO 2026-06-08 08:05:24 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr19:10,350,888
INFO 2026-06-08 08:05:24 MarkDuplicates Tracking 80361 as yet unmatched pairs. 26230 records in RAM.
INFO 2026-06-08 08:05:27 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 2s. Last read position: chr19:14,515,947
INFO 2026-06-08 08:05:27 MarkDuplicates Tracking 78092 as yet unmatched pairs. 23961 records in RAM.
INFO 2026-06-08 08:05:29 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 2s. Last read position: chr19:16,893,154
INFO 2026-06-08 08:05:29 MarkDuplicates Tracking 74933 as yet unmatched pairs. 20802 records in RAM.
INFO 2026-06-08 08:05:32 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 2s. Last read position: chr19:19,794,728
INFO 2026-06-08 08:05:32 MarkDuplicates Tracking 72034 as yet unmatched pairs. 17900 records in RAM.
INFO 2026-06-08 08:05:35 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr19:38,162,389
INFO 2026-06-08 08:05:35 MarkDuplicates Tracking 69454 as yet unmatched pairs. 15319 records in RAM.
INFO 2026-06-08 08:05:37 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr19:41,001,988
INFO 2026-06-08 08:05:37 MarkDuplicates Tracking 66938 as yet unmatched pairs. 12803 records in RAM.
INFO 2026-06-08 08:05:39 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr19:44,820,705
INFO 2026-06-08 08:05:39 MarkDuplicates Tracking 64341 as yet unmatched pairs. 10199 records in RAM.
INFO 2026-06-08 08:05:40 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr19:48,617,327
INFO 2026-06-08 08:05:40 MarkDuplicates Tracking 61415 as yet unmatched pairs. 7273 records in RAM.
INFO 2026-06-08 08:05:42 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr19:50,323,094
INFO 2026-06-08 08:05:42 MarkDuplicates Tracking 58631 as yet unmatched pairs. 4489 records in RAM.
INFO 2026-06-08 08:05:44 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr19:55,236,929
INFO 2026-06-08 08:05:44 MarkDuplicates Tracking 56253 as yet unmatched pairs. 2111 records in RAM.
INFO 2026-06-08 08:05:46 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 2s. Last read position: chr20:3,035,673
INFO 2026-06-08 08:05:46 MarkDuplicates Tracking 53509 as yet unmatched pairs. 15248 records in RAM.
INFO 2026-06-08 08:05:48 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr20:32,309,743
INFO 2026-06-08 08:05:48 MarkDuplicates Tracking 51127 as yet unmatched pairs. 12866 records in RAM.
INFO 2026-06-08 08:05:50 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr20:41,174,139
INFO 2026-06-08 08:05:50 MarkDuplicates Tracking 48749 as yet unmatched pairs. 10488 records in RAM.
INFO 2026-06-08 08:05:52 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 2s. Last read position: chr20:49,661,123
INFO 2026-06-08 08:05:52 MarkDuplicates Tracking 46187 as yet unmatched pairs. 7925 records in RAM.
INFO 2026-06-08 08:05:55 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 2s. Last read position: chr20:58,909,391
INFO 2026-06-08 08:05:55 MarkDuplicates Tracking 43933 as yet unmatched pairs. 5670 records in RAM.
INFO 2026-06-08 08:05:57 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 2s. Last read position: chr20:62,813,232
INFO 2026-06-08 08:05:57 MarkDuplicates Tracking 40392 as yet unmatched pairs. 2128 records in RAM.
INFO 2026-06-08 08:05:59 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,907
INFO 2026-06-08 08:05:59 MarkDuplicates Tracking 37744 as yet unmatched pairs. 8548 records in RAM.
INFO 2026-06-08 08:06:01 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 2s. Last read position: chr21:31,671,772
INFO 2026-06-08 08:06:01 MarkDuplicates Tracking 36303 as yet unmatched pairs. 7105 records in RAM.
INFO 2026-06-08 08:06:04 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 3s. Last read position: chr21:44,117,887
INFO 2026-06-08 08:06:04 MarkDuplicates Tracking 33670 as yet unmatched pairs. 4472 records in RAM.
INFO 2026-06-08 08:06:08 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 3s. Last read position: chr21:46,003,816
INFO 2026-06-08 08:06:08 MarkDuplicates Tracking 30993 as yet unmatched pairs. 1795 records in RAM.
INFO 2026-06-08 08:06:11 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 3s. Last read position: chr22:23,180,948
INFO 2026-06-08 08:06:11 MarkDuplicates Tracking 28061 as yet unmatched pairs. 10324 records in RAM.
INFO 2026-06-08 08:06:13 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 2s. Last read position: chr22:30,337,739
INFO 2026-06-08 08:06:13 MarkDuplicates Tracking 25264 as yet unmatched pairs. 7527 records in RAM.
INFO 2026-06-08 08:06:15 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr22:37,805,674
INFO 2026-06-08 08:06:15 MarkDuplicates Tracking 22507 as yet unmatched pairs. 4770 records in RAM.
INFO 2026-06-08 08:06:17 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr22:45,205,660
INFO 2026-06-08 08:06:17 MarkDuplicates Tracking 19842 as yet unmatched pairs. 2105 records in RAM.
INFO 2026-06-08 08:06:20 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: chrX:3,323,071
INFO 2026-06-08 08:06:20 MarkDuplicates Tracking 16893 as yet unmatched pairs. 13405 records in RAM.
INFO 2026-06-08 08:06:22 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 2s. Last read position: chrX:45,059,103
INFO 2026-06-08 08:06:22 MarkDuplicates Tracking 14470 as yet unmatched pairs. 10981 records in RAM.
INFO 2026-06-08 08:06:24 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chrX:53,592,603
INFO 2026-06-08 08:06:24 MarkDuplicates Tracking 11989 as yet unmatched pairs. 8500 records in RAM.
INFO 2026-06-08 08:06:26 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 2s. Last read position: chrX:77,857,481
INFO 2026-06-08 08:06:26 MarkDuplicates Tracking 9465 as yet unmatched pairs. 5976 records in RAM.
INFO 2026-06-08 08:06:28 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 2s. Last read position: chrX:133,671,243
INFO 2026-06-08 08:06:28 MarkDuplicates Tracking 7298 as yet unmatched pairs. 3809 records in RAM.
INFO 2026-06-08 08:06:31 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 2s. Last read position: chrX:154,362,718
INFO 2026-06-08 08:06:31 MarkDuplicates Tracking 4713 as yet unmatched pairs. 1224 records in RAM.
INFO 2026-06-08 08:06:33 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,159
INFO 2026-06-08 08:06:33 MarkDuplicates Tracking 2826 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-08 08:06:34 MarkDuplicates Read 228824512 records. 0 pairs never matched.
INFO 2026-06-08 08:06:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 36055946080; totalMemory: 62142808064; maxMemory: 63585648640
INFO 2026-06-08 08:06:51 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:06:58 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder Large duplicate set. size = 2363
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,287
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,030
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder Large duplicate set. size = 1059
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,898
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder Large duplicate set. size = 1063
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,964
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder Large duplicate set. size = 1188
INFO 2026-06-08 08:07:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,686
INFO 2026-06-08 08:07:16 OpticalDuplicateFinder Large duplicate set. size = 1086
INFO 2026-06-08 08:07:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,665
INFO 2026-06-08 08:07:16 OpticalDuplicateFinder Large duplicate set. size = 1367
INFO 2026-06-08 08:07:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,401
INFO 2026-06-08 08:07:16 OpticalDuplicateFinder Large duplicate set. size = 1061
INFO 2026-06-08 08:07:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,234
INFO 2026-06-08 08:07:31 OpticalDuplicateFinder Large duplicate set. size = 1041
INFO 2026-06-08 08:07:31 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,091
INFO 2026-06-08 08:07:31 OpticalDuplicateFinder Large duplicate set. size = 1025
INFO 2026-06-08 08:07:31 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,798
INFO 2026-06-08 08:07:31 OpticalDuplicateFinder Large duplicate set. size = 1001
INFO 2026-06-08 08:07:31 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,815
INFO 2026-06-08 08:07:31 OpticalDuplicateFinder Large duplicate set. size = 1273
INFO 2026-06-08 08:07:31 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,977
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1274
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,259
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1574
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,359
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1011
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,079
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1227
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,544
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1161
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,248
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1029
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,651
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1203
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,751
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1534
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,344
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1361
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,254
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1201
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,746
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1562
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,967
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1008
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,786
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 1340
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,715
INFO 2026-06-08 08:07:32 OpticalDuplicateFinder Large duplicate set. size = 2935
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,461
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,123
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1167
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,455
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1285
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,739
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1718
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,169
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1371
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,966
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1244
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,737
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1065
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,505
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1257
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,380
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1484
INFO 2026-06-08 08:07:33 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 08:07:33 OpticalDuplicateFinder Large duplicate set. size = 1945
INFO 2026-06-08 08:07:33 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,307
INFO 2026-06-08 08:07:38 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 08:08:00 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:08:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300757736; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:08:08 MarkDuplicates Marking 152421992 records as duplicates.
INFO 2026-06-08 08:08:08 MarkDuplicates Found 5604653 optical duplicate clusters.
INFO 2026-06-08 08:08:08 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:08:31 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:23s. Time for last 10,000,000: 23s. Last read position: chr1:145,957,637
INFO 2026-06-08 08:08:52 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:44s. Time for last 10,000,000: 21s. Last read position: chr2:6,897,017
INFO 2026-06-08 08:09:14 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:06s. Time for last 10,000,000: 22s. Last read position: chr2:130,152,656
INFO 2026-06-08 08:09:37 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:29s. Time for last 10,000,000: 22s. Last read position: chr2:215,409,680
INFO 2026-06-08 08:10:00 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:52s. Time for last 10,000,000: 22s. Last read position: chr3:99,849,278
INFO 2026-06-08 08:10:23 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:15s. Time for last 10,000,000: 22s. Last read position: chr4:7,030,354
INFO 2026-06-08 08:10:45 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:37s. Time for last 10,000,000: 22s. Last read position: chr5:141,123,416
INFO 2026-06-08 08:11:07 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:59s. Time for last 10,000,000: 21s. Last read position: chr6:39,913,811
INFO 2026-06-08 08:11:27 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:19s. Time for last 10,000,000: 19s. Last read position: chr7:76,302,878
INFO 2026-06-08 08:11:49 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:41s. Time for last 10,000,000: 22s. Last read position: chr8:82,292,212
INFO 2026-06-08 08:12:09 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:01s. Time for last 10,000,000: 20s. Last read position: chr9:115,073,603
INFO 2026-06-08 08:12:31 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:23s. Time for last 10,000,000: 21s. Last read position: chr10:119,838,688
INFO 2026-06-08 08:12:52 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:43s. Time for last 10,000,000: 20s. Last read position: chr11:72,295,607
INFO 2026-06-08 08:13:12 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:04s. Time for last 10,000,000: 20s. Last read position: chr12:98,601,175
INFO 2026-06-08 08:13:30 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:22s. Time for last 10,000,000: 18s. Last read position: chr14:92,577,212
INFO 2026-06-08 08:13:49 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:41s. Time for last 10,000,000: 19s. Last read position: chr16:17,117,965
INFO 2026-06-08 08:14:08 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:06:00s. Time for last 10,000,000: 18s. Last read position: chr17:7,012,677
INFO 2026-06-08 08:14:29 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:06:20s. Time for last 10,000,000: 20s. Last read position: chr17:50,190,041
INFO 2026-06-08 08:14:48 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:06:40s. Time for last 10,000,000: 19s. Last read position: chr17:80,347,603
INFO 2026-06-08 08:15:08 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:06:59s. Time for last 10,000,000: 19s. Last read position: chr19:16,893,154
INFO 2026-06-08 08:15:28 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:07:20s. Time for last 10,000,000: 20s. Last read position: chr20:41,174,139
INFO 2026-06-08 08:15:46 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:07:38s. Time for last 10,000,000: 17s. Last read position: chr22:37,805,674
INFO 2026-06-08 08:16:05 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:07:57s. Time for last 10,000,000: 19s. Last read position: */*
INFO 2026-06-08 08:16:07 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:16:07 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:16:07 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:16:07 MarkDuplicates Before output close freeMemory: 201955656; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:16:07 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:16:07 MarkDuplicates After output close freeMemory: 104226872; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:16:07 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 19.48 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory