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-2ca847-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:24:59.763 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 08:24:59 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-2ca847-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-2ca847-R1_A23WJ53LT4_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 08:24:59 GMT 2026] Executing as ?@nf-c0a6cf6e461a5618bdcc9b6f0f4ee877-6be11-x95t4 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 08:24:59 MarkDuplicates Start of doWork freeMemory: 105491880; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:24:59 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:24:59 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:25:05 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:1,542,149
INFO 2026-06-08 08:25:05 MarkDuplicates Tracking 2013 as yet unmatched pairs. 117 records in RAM.
INFO 2026-06-08 08:25:08 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:8,866,456
INFO 2026-06-08 08:25:08 MarkDuplicates Tracking 3832 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-08 08:25:11 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:15,934,419
INFO 2026-06-08 08:25:11 MarkDuplicates Tracking 5532 as yet unmatched pairs. 189 records in RAM.
INFO 2026-06-08 08:25:15 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:20,773,453
INFO 2026-06-08 08:25:15 MarkDuplicates Tracking 6871 as yet unmatched pairs. 65 records in RAM.
INFO 2026-06-08 08:25:18 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:21,887,470
INFO 2026-06-08 08:25:18 MarkDuplicates Tracking 8830 as yet unmatched pairs. 356 records in RAM.
INFO 2026-06-08 08:25:22 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr1:26,696,552
INFO 2026-06-08 08:25:22 MarkDuplicates Tracking 10103 as yet unmatched pairs. 49 records in RAM.
INFO 2026-06-08 08:25:24 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:31,426,706
INFO 2026-06-08 08:25:24 MarkDuplicates Tracking 12153 as yet unmatched pairs. 247 records in RAM.
INFO 2026-06-08 08:25:26 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:32,895,557
INFO 2026-06-08 08:25:26 MarkDuplicates Tracking 13985 as yet unmatched pairs. 113 records in RAM.
INFO 2026-06-08 08:25:29 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr1:39,334,635
INFO 2026-06-08 08:25:29 MarkDuplicates Tracking 15590 as yet unmatched pairs. 135 records in RAM.
INFO 2026-06-08 08:25:31 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:43,960,312
INFO 2026-06-08 08:25:31 MarkDuplicates Tracking 17097 as yet unmatched pairs. 54 records in RAM.
INFO 2026-06-08 08:25:34 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:53,210,486
INFO 2026-06-08 08:25:34 MarkDuplicates Tracking 18740 as yet unmatched pairs. 31 records in RAM.
INFO 2026-06-08 08:25:36 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:84,164,981
INFO 2026-06-08 08:25:36 MarkDuplicates Tracking 20894 as yet unmatched pairs. 733 records in RAM.
INFO 2026-06-08 08:25:38 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:109,229,549
INFO 2026-06-08 08:25:38 MarkDuplicates Tracking 21603 as yet unmatched pairs. 38 records in RAM.
INFO 2026-06-08 08:25:40 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:114,723,978
INFO 2026-06-08 08:25:40 MarkDuplicates Tracking 23605 as yet unmatched pairs. 493 records in RAM.
INFO 2026-06-08 08:25:42 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:120,451,093
INFO 2026-06-08 08:25:42 MarkDuplicates Tracking 24558 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:25:44 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:146,142,680
INFO 2026-06-08 08:25:44 MarkDuplicates Tracking 25357 as yet unmatched pairs. 116 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:149,075,719
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 26365 as yet unmatched pairs. 369 records in RAM.
INFO 2026-06-08 08:25:48 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:150,511,160
INFO 2026-06-08 08:25:48 MarkDuplicates Tracking 27363 as yet unmatched pairs. 326 records in RAM.
INFO 2026-06-08 08:25:50 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:151,428,001
INFO 2026-06-08 08:25:50 MarkDuplicates Tracking 28750 as yet unmatched pairs. 146 records in RAM.
INFO 2026-06-08 08:25:53 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:154,172,964
INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 31558 as yet unmatched pairs. 1511 records in RAM.
INFO 2026-06-08 08:25:54 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:155,062,279
INFO 2026-06-08 08:25:54 MarkDuplicates Tracking 31919 as yet unmatched pairs. 504 records in RAM.
INFO 2026-06-08 08:25:57 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:155,717,097
INFO 2026-06-08 08:25:57 MarkDuplicates Tracking 33120 as yet unmatched pairs. 367 records in RAM.
INFO 2026-06-08 08:25:59 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr1:156,249,566
INFO 2026-06-08 08:25:59 MarkDuplicates Tracking 34739 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:26:01 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:160,314,116
INFO 2026-06-08 08:26:01 MarkDuplicates Tracking 36598 as yet unmatched pairs. 160 records in RAM.
INFO 2026-06-08 08:26:03 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:168,068,367
INFO 2026-06-08 08:26:03 MarkDuplicates Tracking 38017 as yet unmatched pairs. 112 records in RAM.
INFO 2026-06-08 08:26:05 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:180,194,330
INFO 2026-06-08 08:26:05 MarkDuplicates Tracking 39669 as yet unmatched pairs. 324 records in RAM.
INFO 2026-06-08 08:26:07 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:190,295,258
INFO 2026-06-08 08:26:07 MarkDuplicates Tracking 40923 as yet unmatched pairs. 130 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:203,712,016
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 42481 as yet unmatched pairs. 60 records in RAM.
INFO 2026-06-08 08:26:11 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr1:207,886,747
INFO 2026-06-08 08:26:11 MarkDuplicates Tracking 44393 as yet unmatched pairs. 421 records in RAM.
INFO 2026-06-08 08:26:13 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:223,712,771
INFO 2026-06-08 08:26:13 MarkDuplicates Tracking 45792 as yet unmatched pairs. 380 records in RAM.
INFO 2026-06-08 08:26:16 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:228,244,549
INFO 2026-06-08 08:26:16 MarkDuplicates Tracking 47025 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:26:18 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr1:236,552,076
INFO 2026-06-08 08:26:18 MarkDuplicates Tracking 48884 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-08 08:26:21 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: chr2:3,651,325
INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 50425 as yet unmatched pairs. 50312 records in RAM.
INFO 2026-06-08 08:26:23 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr2:24,821,550
INFO 2026-06-08 08:26:23 MarkDuplicates Tracking 51959 as yet unmatched pairs. 51846 records in RAM.
INFO 2026-06-08 08:26:24 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr2:32,547,990
INFO 2026-06-08 08:26:24 MarkDuplicates Tracking 53679 as yet unmatched pairs. 53565 records in RAM.
INFO 2026-06-08 08:26:27 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:26:27 MarkDuplicates Tracking 483302 as yet unmatched pairs. 38711 records in RAM.
INFO 2026-06-08 08:26:28 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr2:38,781,746
INFO 2026-06-08 08:26:28 MarkDuplicates Tracking 517763 as yet unmatched pairs. 37133 records in RAM.
INFO 2026-06-08 08:26:30 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr2:48,495,698
INFO 2026-06-08 08:26:30 MarkDuplicates Tracking 516131 as yet unmatched pairs. 35501 records in RAM.
INFO 2026-06-08 08:26:32 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:61,325,393
INFO 2026-06-08 08:26:32 MarkDuplicates Tracking 514724 as yet unmatched pairs. 34093 records in RAM.
INFO 2026-06-08 08:26:34 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr2:70,991,835
INFO 2026-06-08 08:26:34 MarkDuplicates Tracking 513185 as yet unmatched pairs. 32551 records in RAM.
INFO 2026-06-08 08:26:35 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr2:74,460,444
INFO 2026-06-08 08:26:35 MarkDuplicates Tracking 512125 as yet unmatched pairs. 31491 records in RAM.
INFO 2026-06-08 08:26:37 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr2:86,914,418
INFO 2026-06-08 08:26:37 MarkDuplicates Tracking 509925 as yet unmatched pairs. 29280 records in RAM.
INFO 2026-06-08 08:26:39 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:97,671,389
INFO 2026-06-08 08:26:39 MarkDuplicates Tracking 508496 as yet unmatched pairs. 27851 records in RAM.
INFO 2026-06-08 08:26:41 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:108,766,915
INFO 2026-06-08 08:26:41 MarkDuplicates Tracking 507253 as yet unmatched pairs. 26605 records in RAM.
INFO 2026-06-08 08:26:43 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:119,372,271
INFO 2026-06-08 08:26:43 MarkDuplicates Tracking 506253 as yet unmatched pairs. 25603 records in RAM.
INFO 2026-06-08 08:26:45 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:131,484,203
INFO 2026-06-08 08:26:45 MarkDuplicates Tracking 505453 as yet unmatched pairs. 24802 records in RAM.
INFO 2026-06-08 08:26:46 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:148,783,663
INFO 2026-06-08 08:26:46 MarkDuplicates Tracking 503770 as yet unmatched pairs. 23119 records in RAM.
INFO 2026-06-08 08:26:48 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr2:171,976,156
INFO 2026-06-08 08:26:48 MarkDuplicates Tracking 502348 as yet unmatched pairs. 21697 records in RAM.
INFO 2026-06-08 08:26:50 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:181,922,349
INFO 2026-06-08 08:26:50 MarkDuplicates Tracking 501982 as yet unmatched pairs. 21329 records in RAM.
INFO 2026-06-08 08:26:52 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr2:189,008,937
INFO 2026-06-08 08:26:52 MarkDuplicates Tracking 499741 as yet unmatched pairs. 19088 records in RAM.
INFO 2026-06-08 08:26:54 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:200,815,420
INFO 2026-06-08 08:26:54 MarkDuplicates Tracking 497683 as yet unmatched pairs. 17030 records in RAM.
INFO 2026-06-08 08:26:55 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:215,361,515
INFO 2026-06-08 08:26:55 MarkDuplicates Tracking 502063 as yet unmatched pairs. 21409 records in RAM.
INFO 2026-06-08 08:26:57 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:215,372,154
INFO 2026-06-08 08:26:57 MarkDuplicates Tracking 504032 as yet unmatched pairs. 23366 records in RAM.
INFO 2026-06-08 08:26:59 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:215,379,206
INFO 2026-06-08 08:26:59 MarkDuplicates Tracking 500881 as yet unmatched pairs. 20208 records in RAM.
INFO 2026-06-08 08:27:01 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:215,394,528
INFO 2026-06-08 08:27:01 MarkDuplicates Tracking 495467 as yet unmatched pairs. 14793 records in RAM.
INFO 2026-06-08 08:27:03 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr2:215,408,305
INFO 2026-06-08 08:27:03 MarkDuplicates Tracking 496939 as yet unmatched pairs. 16264 records in RAM.
INFO 2026-06-08 08:27:05 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr2:215,425,219
INFO 2026-06-08 08:27:05 MarkDuplicates Tracking 490944 as yet unmatched pairs. 10265 records in RAM.
INFO 2026-06-08 08:27:07 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr2:217,813,688
INFO 2026-06-08 08:27:07 MarkDuplicates Tracking 487179 as yet unmatched pairs. 6499 records in RAM.
INFO 2026-06-08 08:27:09 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr2:224,845,295
INFO 2026-06-08 08:27:09 MarkDuplicates Tracking 485340 as yet unmatched pairs. 4648 records in RAM.
INFO 2026-06-08 08:27:11 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:237,334,671
INFO 2026-06-08 08:27:11 MarkDuplicates Tracking 484150 as yet unmatched pairs. 3458 records in RAM.
INFO 2026-06-08 08:27:12 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:238,081,750
INFO 2026-06-08 08:27:12 MarkDuplicates Tracking 482257 as yet unmatched pairs. 1565 records in RAM.
INFO 2026-06-08 08:27:15 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr3:4,983,198
INFO 2026-06-08 08:27:15 MarkDuplicates Tracking 480721 as yet unmatched pairs. 23946 records in RAM.
INFO 2026-06-08 08:27:16 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr3:12,604,274
INFO 2026-06-08 08:27:16 MarkDuplicates Tracking 479426 as yet unmatched pairs. 22651 records in RAM.
INFO 2026-06-08 08:27:18 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr3:30,650,439
INFO 2026-06-08 08:27:18 MarkDuplicates Tracking 477444 as yet unmatched pairs. 20666 records in RAM.
INFO 2026-06-08 08:27:20 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr3:41,234,177
INFO 2026-06-08 08:27:20 MarkDuplicates Tracking 476130 as yet unmatched pairs. 19351 records in RAM.
INFO 2026-06-08 08:27:21 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr3:47,875,851
INFO 2026-06-08 08:27:21 MarkDuplicates Tracking 474403 as yet unmatched pairs. 17624 records in RAM.
INFO 2026-06-08 08:27:23 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr3:49,122,896
INFO 2026-06-08 08:27:23 MarkDuplicates Tracking 472680 as yet unmatched pairs. 15897 records in RAM.
INFO 2026-06-08 08:27:26 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr3:52,051,024
INFO 2026-06-08 08:27:26 MarkDuplicates Tracking 470949 as yet unmatched pairs. 14165 records in RAM.
INFO 2026-06-08 08:27:27 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr3:63,996,292
INFO 2026-06-08 08:27:27 MarkDuplicates Tracking 469266 as yet unmatched pairs. 12480 records in RAM.
INFO 2026-06-08 08:27:29 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr3:101,853,113
INFO 2026-06-08 08:27:29 MarkDuplicates Tracking 468375 as yet unmatched pairs. 11587 records in RAM.
INFO 2026-06-08 08:27:31 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr3:122,463,975
INFO 2026-06-08 08:27:31 MarkDuplicates Tracking 466552 as yet unmatched pairs. 9763 records in RAM.
INFO 2026-06-08 08:27:32 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr3:129,170,389
INFO 2026-06-08 08:27:32 MarkDuplicates Tracking 464817 as yet unmatched pairs. 8024 records in RAM.
INFO 2026-06-08 08:27:34 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr3:140,566,233
INFO 2026-06-08 08:27:34 MarkDuplicates Tracking 463020 as yet unmatched pairs. 6225 records in RAM.
INFO 2026-06-08 08:27:35 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr3:150,742,339
INFO 2026-06-08 08:27:35 MarkDuplicates Tracking 461771 as yet unmatched pairs. 4968 records in RAM.
INFO 2026-06-08 08:27:37 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr3:179,615,040
INFO 2026-06-08 08:27:37 MarkDuplicates Tracking 460320 as yet unmatched pairs. 3516 records in RAM.
INFO 2026-06-08 08:27:39 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr3:185,600,843
INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 458672 as yet unmatched pairs. 1868 records in RAM.
INFO 2026-06-08 08:27:40 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr3:196,885,773
INFO 2026-06-08 08:27:40 MarkDuplicates Tracking 457126 as yet unmatched pairs. 314 records in RAM.
INFO 2026-06-08 08:27:42 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr4:1,728,006
INFO 2026-06-08 08:27:42 MarkDuplicates Tracking 455532 as yet unmatched pairs. 14341 records in RAM.
INFO 2026-06-08 08:27:43 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr4:3,316,581
INFO 2026-06-08 08:27:43 MarkDuplicates Tracking 453447 as yet unmatched pairs. 12255 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr4:16,505,925
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 451775 as yet unmatched pairs. 10578 records in RAM.
INFO 2026-06-08 08:27:47 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr4:48,522,923
INFO 2026-06-08 08:27:47 MarkDuplicates Tracking 450294 as yet unmatched pairs. 9093 records in RAM.
INFO 2026-06-08 08:27:48 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr4:73,153,901
INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 448779 as yet unmatched pairs. 7577 records in RAM.
INFO 2026-06-08 08:27:50 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr4:87,493,881
INFO 2026-06-08 08:27:50 MarkDuplicates Tracking 447499 as yet unmatched pairs. 6296 records in RAM.
INFO 2026-06-08 08:27:52 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr4:109,463,271
INFO 2026-06-08 08:27:52 MarkDuplicates Tracking 445817 as yet unmatched pairs. 4611 records in RAM.
INFO 2026-06-08 08:27:53 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr4:139,725,702
INFO 2026-06-08 08:27:53 MarkDuplicates Tracking 444220 as yet unmatched pairs. 3014 records in RAM.
INFO 2026-06-08 08:27:54 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr4:158,170,739
INFO 2026-06-08 08:27:54 MarkDuplicates Tracking 443621 as yet unmatched pairs. 2400 records in RAM.
INFO 2026-06-08 08:27:56 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr5:466,833
INFO 2026-06-08 08:27:56 MarkDuplicates Tracking 441184 as yet unmatched pairs. 25929 records in RAM.
INFO 2026-06-08 08:27:58 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr5:14,388,661
INFO 2026-06-08 08:27:58 MarkDuplicates Tracking 439995 as yet unmatched pairs. 24740 records in RAM.
INFO 2026-06-08 08:28:00 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr5:35,065,965
INFO 2026-06-08 08:28:00 MarkDuplicates Tracking 438095 as yet unmatched pairs. 22840 records in RAM.
INFO 2026-06-08 08:28:01 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr5:56,938,912
INFO 2026-06-08 08:28:01 MarkDuplicates Tracking 436478 as yet unmatched pairs. 21220 records in RAM.
INFO 2026-06-08 08:28:03 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr5:70,984,901
INFO 2026-06-08 08:28:03 MarkDuplicates Tracking 435679 as yet unmatched pairs. 20420 records in RAM.
INFO 2026-06-08 08:28:05 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr5:80,058,772
INFO 2026-06-08 08:28:05 MarkDuplicates Tracking 434033 as yet unmatched pairs. 18774 records in RAM.
INFO 2026-06-08 08:28:07 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr5:96,736,188
INFO 2026-06-08 08:28:07 MarkDuplicates Tracking 432600 as yet unmatched pairs. 17339 records in RAM.
INFO 2026-06-08 08:28:08 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr5:128,083,874
INFO 2026-06-08 08:28:08 MarkDuplicates Tracking 431073 as yet unmatched pairs. 15810 records in RAM.
INFO 2026-06-08 08:28:11 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr5:136,055,723
INFO 2026-06-08 08:28:11 MarkDuplicates Tracking 429234 as yet unmatched pairs. 13957 records in RAM.
INFO 2026-06-08 08:28:12 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr5:140,539,566
INFO 2026-06-08 08:28:12 MarkDuplicates Tracking 427681 as yet unmatched pairs. 12345 records in RAM.
INFO 2026-06-08 08:28:14 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr5:141,357,261
INFO 2026-06-08 08:28:14 MarkDuplicates Tracking 426444 as yet unmatched pairs. 11108 records in RAM.
INFO 2026-06-08 08:28:16 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr5:149,351,147
INFO 2026-06-08 08:28:16 MarkDuplicates Tracking 424891 as yet unmatched pairs. 9552 records in RAM.
INFO 2026-06-08 08:28:17 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr5:150,403,154
INFO 2026-06-08 08:28:17 MarkDuplicates Tracking 428214 as yet unmatched pairs. 12874 records in RAM.
INFO 2026-06-08 08:28:19 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr5:151,129,407
INFO 2026-06-08 08:28:19 MarkDuplicates Tracking 421782 as yet unmatched pairs. 6441 records in RAM.
INFO 2026-06-08 08:28:21 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr5:171,387,877
INFO 2026-06-08 08:28:21 MarkDuplicates Tracking 421181 as yet unmatched pairs. 5839 records in RAM.
INFO 2026-06-08 08:28:23 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr5:177,280,656
INFO 2026-06-08 08:28:23 MarkDuplicates Tracking 418778 as yet unmatched pairs. 3434 records in RAM.
INFO 2026-06-08 08:28:25 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr5:179,726,733
INFO 2026-06-08 08:28:25 MarkDuplicates Tracking 417950 as yet unmatched pairs. 2600 records in RAM.
INFO 2026-06-08 08:28:27 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr5:181,260,693
INFO 2026-06-08 08:28:27 MarkDuplicates Tracking 415401 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 08:28:28 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr6:7,585,756
INFO 2026-06-08 08:28:28 MarkDuplicates Tracking 413910 as yet unmatched pairs. 27357 records in RAM.
INFO 2026-06-08 08:28:30 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr6:26,184,075
INFO 2026-06-08 08:28:30 MarkDuplicates Tracking 412064 as yet unmatched pairs. 25507 records in RAM.
INFO 2026-06-08 08:28:31 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr6:30,602,185
INFO 2026-06-08 08:28:31 MarkDuplicates Tracking 410754 as yet unmatched pairs. 24195 records in RAM.
INFO 2026-06-08 08:28:33 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr6:31,623,767
INFO 2026-06-08 08:28:33 MarkDuplicates Tracking 409037 as yet unmatched pairs. 22478 records in RAM.
INFO 2026-06-08 08:28:34 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr6:31,829,384
INFO 2026-06-08 08:28:34 MarkDuplicates Tracking 407672 as yet unmatched pairs. 21113 records in RAM.
INFO 2026-06-08 08:28:36 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr6:31,994,624
INFO 2026-06-08 08:28:36 MarkDuplicates Tracking 410796 as yet unmatched pairs. 24237 records in RAM.
INFO 2026-06-08 08:28:38 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr6:32,026,982
INFO 2026-06-08 08:28:38 MarkDuplicates Tracking 408903 as yet unmatched pairs. 22343 records in RAM.
INFO 2026-06-08 08:28:39 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr6:32,118,841
INFO 2026-06-08 08:28:39 MarkDuplicates Tracking 404382 as yet unmatched pairs. 17822 records in RAM.
INFO 2026-06-08 08:28:40 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr6:33,293,180
INFO 2026-06-08 08:28:40 MarkDuplicates Tracking 403608 as yet unmatched pairs. 17046 records in RAM.
INFO 2026-06-08 08:28:43 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr6:35,424,531
INFO 2026-06-08 08:28:43 MarkDuplicates Tracking 400905 as yet unmatched pairs. 14343 records in RAM.
INFO 2026-06-08 08:28:44 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr6:43,046,902
INFO 2026-06-08 08:28:44 MarkDuplicates Tracking 399175 as yet unmatched pairs. 12613 records in RAM.
INFO 2026-06-08 08:28:46 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr6:52,420,449
INFO 2026-06-08 08:28:46 MarkDuplicates Tracking 397543 as yet unmatched pairs. 10981 records in RAM.
INFO 2026-06-08 08:28:48 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr6:75,886,067
INFO 2026-06-08 08:28:48 MarkDuplicates Tracking 396220 as yet unmatched pairs. 9657 records in RAM.
INFO 2026-06-08 08:28:49 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr6:110,967,628
INFO 2026-06-08 08:28:49 MarkDuplicates Tracking 394609 as yet unmatched pairs. 8038 records in RAM.
INFO 2026-06-08 08:28:51 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr6:134,172,693
INFO 2026-06-08 08:28:51 MarkDuplicates Tracking 393011 as yet unmatched pairs. 6438 records in RAM.
INFO 2026-06-08 08:28:52 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr6:144,797,895
INFO 2026-06-08 08:28:52 MarkDuplicates Tracking 391310 as yet unmatched pairs. 4732 records in RAM.
INFO 2026-06-08 08:28:54 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr6:152,061,075
INFO 2026-06-08 08:28:54 MarkDuplicates Tracking 390413 as yet unmatched pairs. 3835 records in RAM.
INFO 2026-06-08 08:28:56 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr6:159,232,996
INFO 2026-06-08 08:28:56 MarkDuplicates Tracking 388108 as yet unmatched pairs. 1530 records in RAM.
INFO 2026-06-08 08:28:57 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr7:838,879
INFO 2026-06-08 08:28:57 MarkDuplicates Tracking 386744 as yet unmatched pairs. 23901 records in RAM.
INFO 2026-06-08 08:28:59 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr7:5,332,963
INFO 2026-06-08 08:28:59 MarkDuplicates Tracking 384648 as yet unmatched pairs. 21797 records in RAM.
INFO 2026-06-08 08:29:01 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr7:5,529,546
INFO 2026-06-08 08:29:01 MarkDuplicates Tracking 386190 as yet unmatched pairs. 23339 records in RAM.
INFO 2026-06-08 08:29:02 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr7:23,260,740
INFO 2026-06-08 08:29:02 MarkDuplicates Tracking 381582 as yet unmatched pairs. 18710 records in RAM.
INFO 2026-06-08 08:29:04 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr7:43,640,647
INFO 2026-06-08 08:29:04 MarkDuplicates Tracking 379815 as yet unmatched pairs. 16933 records in RAM.
INFO 2026-06-08 08:29:07 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr7:45,713,819
INFO 2026-06-08 08:29:07 MarkDuplicates Tracking 378169 as yet unmatched pairs. 15283 records in RAM.
INFO 2026-06-08 08:29:08 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr7:73,082,826
INFO 2026-06-08 08:29:08 MarkDuplicates Tracking 376852 as yet unmatched pairs. 13957 records in RAM.
INFO 2026-06-08 08:29:10 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr7:75,416,670
INFO 2026-06-08 08:29:10 MarkDuplicates Tracking 375773 as yet unmatched pairs. 12878 records in RAM.
INFO 2026-06-08 08:29:12 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr7:80,744,918
INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 374252 as yet unmatched pairs. 11355 records in RAM.
INFO 2026-06-08 08:29:13 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr7:94,409,589
INFO 2026-06-08 08:29:13 MarkDuplicates Tracking 374263 as yet unmatched pairs. 11366 records in RAM.
INFO 2026-06-08 08:29:15 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr7:94,664,831
INFO 2026-06-08 08:29:15 MarkDuplicates Tracking 371413 as yet unmatched pairs. 8516 records in RAM.
INFO 2026-06-08 08:29:17 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr7:100,603,984
INFO 2026-06-08 08:29:17 MarkDuplicates Tracking 369766 as yet unmatched pairs. 6860 records in RAM.
INFO 2026-06-08 08:29:18 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr7:105,814,383
INFO 2026-06-08 08:29:18 MarkDuplicates Tracking 368082 as yet unmatched pairs. 5175 records in RAM.
INFO 2026-06-08 08:29:20 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr7:130,129,486
INFO 2026-06-08 08:29:20 MarkDuplicates Tracking 366693 as yet unmatched pairs. 3779 records in RAM.
INFO 2026-06-08 08:29:21 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr7:143,382,994
INFO 2026-06-08 08:29:21 MarkDuplicates Tracking 365440 as yet unmatched pairs. 2524 records in RAM.
INFO 2026-06-08 08:29:23 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr7:152,144,810
INFO 2026-06-08 08:29:23 MarkDuplicates Tracking 363710 as yet unmatched pairs. 783 records in RAM.
INFO 2026-06-08 08:29:24 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr8:16,168,801
INFO 2026-06-08 08:29:24 MarkDuplicates Tracking 362376 as yet unmatched pairs. 20123 records in RAM.
INFO 2026-06-08 08:29:26 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr8:23,681,269
INFO 2026-06-08 08:29:26 MarkDuplicates Tracking 360664 as yet unmatched pairs. 18410 records in RAM.
INFO 2026-06-08 08:29:27 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr8:38,417,870
INFO 2026-06-08 08:29:27 MarkDuplicates Tracking 359182 as yet unmatched pairs. 16928 records in RAM.
INFO 2026-06-08 08:29:29 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr8:54,010,480
INFO 2026-06-08 08:29:29 MarkDuplicates Tracking 357604 as yet unmatched pairs. 15334 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr8:74,350,405
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 356107 as yet unmatched pairs. 13818 records in RAM.
INFO 2026-06-08 08:29:32 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr8:98,294,031
INFO 2026-06-08 08:29:32 MarkDuplicates Tracking 354720 as yet unmatched pairs. 12428 records in RAM.
INFO 2026-06-08 08:29:34 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr8:102,828,571
INFO 2026-06-08 08:29:34 MarkDuplicates Tracking 353548 as yet unmatched pairs. 11255 records in RAM.
INFO 2026-06-08 08:29:35 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr8:124,330,775
INFO 2026-06-08 08:29:35 MarkDuplicates Tracking 351616 as yet unmatched pairs. 9322 records in RAM.
INFO 2026-06-08 08:29:38 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr8:143,376,572
INFO 2026-06-08 08:29:38 MarkDuplicates Tracking 350241 as yet unmatched pairs. 7945 records in RAM.
INFO 2026-06-08 08:29:39 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,157
INFO 2026-06-08 08:29:39 MarkDuplicates Tracking 350236 as yet unmatched pairs. 7938 records in RAM.
INFO 2026-06-08 08:29:40 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,800
INFO 2026-06-08 08:29:40 MarkDuplicates Tracking 347671 as yet unmatched pairs. 5373 records in RAM.
INFO 2026-06-08 08:29:42 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,379
INFO 2026-06-08 08:29:42 MarkDuplicates Tracking 347260 as yet unmatched pairs. 4962 records in RAM.
INFO 2026-06-08 08:29:44 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr8:143,991,974
INFO 2026-06-08 08:29:44 MarkDuplicates Tracking 344721 as yet unmatched pairs. 2422 records in RAM.
INFO 2026-06-08 08:29:46 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr8:144,931,408
INFO 2026-06-08 08:29:46 MarkDuplicates Tracking 342349 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 08:29:48 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr9:22,005,214
INFO 2026-06-08 08:29:48 MarkDuplicates Tracking 340939 as yet unmatched pairs. 16677 records in RAM.
INFO 2026-06-08 08:29:49 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr9:35,717,207
INFO 2026-06-08 08:29:49 MarkDuplicates Tracking 339522 as yet unmatched pairs. 15260 records in RAM.
INFO 2026-06-08 08:29:51 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr9:83,842,283
INFO 2026-06-08 08:29:51 MarkDuplicates Tracking 337974 as yet unmatched pairs. 13699 records in RAM.
INFO 2026-06-08 08:29:53 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr9:95,107,188
INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 336399 as yet unmatched pairs. 12124 records in RAM.
INFO 2026-06-08 08:29:54 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr9:111,422,184
INFO 2026-06-08 08:29:54 MarkDuplicates Tracking 334854 as yet unmatched pairs. 10579 records in RAM.
INFO 2026-06-08 08:29:56 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr9:121,324,566
INFO 2026-06-08 08:29:56 MarkDuplicates Tracking 333245 as yet unmatched pairs. 8970 records in RAM.
INFO 2026-06-08 08:29:57 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr9:127,867,997
INFO 2026-06-08 08:29:57 MarkDuplicates Tracking 331443 as yet unmatched pairs. 7166 records in RAM.
INFO 2026-06-08 08:29:59 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr9:130,296,758
INFO 2026-06-08 08:29:59 MarkDuplicates Tracking 329825 as yet unmatched pairs. 5547 records in RAM.
INFO 2026-06-08 08:30:00 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr9:134,139,949
INFO 2026-06-08 08:30:00 MarkDuplicates Tracking 328225 as yet unmatched pairs. 3945 records in RAM.
INFO 2026-06-08 08:30:02 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr9:136,502,025
INFO 2026-06-08 08:30:02 MarkDuplicates Tracking 326419 as yet unmatched pairs. 2138 records in RAM.
INFO 2026-06-08 08:30:04 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr9:137,776,734
INFO 2026-06-08 08:30:04 MarkDuplicates Tracking 324410 as yet unmatched pairs. 119 records in RAM.
INFO 2026-06-08 08:30:05 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr10:8,073,902
INFO 2026-06-08 08:30:05 MarkDuplicates Tracking 323858 as yet unmatched pairs. 18108 records in RAM.
INFO 2026-06-08 08:30:07 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr10:24,544,384
INFO 2026-06-08 08:30:07 MarkDuplicates Tracking 321207 as yet unmatched pairs. 15456 records in RAM.
INFO 2026-06-08 08:30:08 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr10:32,922,332
INFO 2026-06-08 08:30:08 MarkDuplicates Tracking 320298 as yet unmatched pairs. 14543 records in RAM.
INFO 2026-06-08 08:30:10 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr10:37,219,175
INFO 2026-06-08 08:30:10 MarkDuplicates Tracking 321192 as yet unmatched pairs. 15437 records in RAM.
INFO 2026-06-08 08:30:12 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr10:46,016,566
INFO 2026-06-08 08:30:12 MarkDuplicates Tracking 318776 as yet unmatched pairs. 13014 records in RAM.
INFO 2026-06-08 08:30:13 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr10:69,132,907
INFO 2026-06-08 08:30:13 MarkDuplicates Tracking 316442 as yet unmatched pairs. 10680 records in RAM.
INFO 2026-06-08 08:30:15 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr10:75,222,275
INFO 2026-06-08 08:30:15 MarkDuplicates Tracking 314954 as yet unmatched pairs. 9192 records in RAM.
INFO 2026-06-08 08:30:17 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr10:89,339,204
INFO 2026-06-08 08:30:17 MarkDuplicates Tracking 313323 as yet unmatched pairs. 7560 records in RAM.
INFO 2026-06-08 08:30:19 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr10:97,678,884
INFO 2026-06-08 08:30:19 MarkDuplicates Tracking 311644 as yet unmatched pairs. 5881 records in RAM.
INFO 2026-06-08 08:30:20 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr10:103,602,050
INFO 2026-06-08 08:30:20 MarkDuplicates Tracking 310248 as yet unmatched pairs. 4483 records in RAM.
INFO 2026-06-08 08:30:22 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr10:119,577,165
INFO 2026-06-08 08:30:22 MarkDuplicates Tracking 308728 as yet unmatched pairs. 2959 records in RAM.
INFO 2026-06-08 08:30:24 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr10:127,012,332
INFO 2026-06-08 08:30:24 MarkDuplicates Tracking 307163 as yet unmatched pairs. 1393 records in RAM.
INFO 2026-06-08 08:30:26 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr11:314,992
INFO 2026-06-08 08:30:26 MarkDuplicates Tracking 306845 as yet unmatched pairs. 37735 records in RAM.
INFO 2026-06-08 08:30:27 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr11:801,570
INFO 2026-06-08 08:30:27 MarkDuplicates Tracking 303573 as yet unmatched pairs. 34463 records in RAM.
INFO 2026-06-08 08:30:29 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr11:1,243,655
INFO 2026-06-08 08:30:29 MarkDuplicates Tracking 302390 as yet unmatched pairs. 33280 records in RAM.
INFO 2026-06-08 08:30:30 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr11:1,248,201
INFO 2026-06-08 08:30:30 MarkDuplicates Tracking 301715 as yet unmatched pairs. 32605 records in RAM.
INFO 2026-06-08 08:30:32 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr11:1,753,568
INFO 2026-06-08 08:30:32 MarkDuplicates Tracking 302449 as yet unmatched pairs. 33339 records in RAM.
INFO 2026-06-08 08:30:33 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr11:3,120,594
INFO 2026-06-08 08:30:33 MarkDuplicates Tracking 298249 as yet unmatched pairs. 29138 records in RAM.
INFO 2026-06-08 08:30:35 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr11:9,143,439
INFO 2026-06-08 08:30:35 MarkDuplicates Tracking 296637 as yet unmatched pairs. 27525 records in RAM.
INFO 2026-06-08 08:30:36 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr11:18,396,863
INFO 2026-06-08 08:30:36 MarkDuplicates Tracking 295805 as yet unmatched pairs. 26693 records in RAM.
INFO 2026-06-08 08:30:38 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr11:45,870,386
INFO 2026-06-08 08:30:38 MarkDuplicates Tracking 293501 as yet unmatched pairs. 24383 records in RAM.
INFO 2026-06-08 08:30:39 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr11:48,145,114
INFO 2026-06-08 08:30:39 MarkDuplicates Tracking 291852 as yet unmatched pairs. 22734 records in RAM.
INFO 2026-06-08 08:30:41 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr11:60,921,871
INFO 2026-06-08 08:30:41 MarkDuplicates Tracking 290553 as yet unmatched pairs. 21433 records in RAM.
INFO 2026-06-08 08:30:42 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr11:62,523,252
INFO 2026-06-08 08:30:42 MarkDuplicates Tracking 289459 as yet unmatched pairs. 20335 records in RAM.
INFO 2026-06-08 08:30:44 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr11:62,633,009
INFO 2026-06-08 08:30:44 MarkDuplicates Tracking 287862 as yet unmatched pairs. 18737 records in RAM.
INFO 2026-06-08 08:30:45 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr11:64,288,653
INFO 2026-06-08 08:30:45 MarkDuplicates Tracking 285817 as yet unmatched pairs. 16691 records in RAM.
INFO 2026-06-08 08:30:47 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr11:65,546,824
INFO 2026-06-08 08:30:47 MarkDuplicates Tracking 284041 as yet unmatched pairs. 14914 records in RAM.
INFO 2026-06-08 08:30:49 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr11:66,055,255
INFO 2026-06-08 08:30:49 MarkDuplicates Tracking 281905 as yet unmatched pairs. 12777 records in RAM.
INFO 2026-06-08 08:30:50 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr11:67,352,758
INFO 2026-06-08 08:30:50 MarkDuplicates Tracking 280889 as yet unmatched pairs. 11760 records in RAM.
INFO 2026-06-08 08:30:52 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr11:69,643,838
INFO 2026-06-08 08:30:52 MarkDuplicates Tracking 279449 as yet unmatched pairs. 10319 records in RAM.
INFO 2026-06-08 08:30:54 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr11:72,035,900
INFO 2026-06-08 08:30:54 MarkDuplicates Tracking 276921 as yet unmatched pairs. 7791 records in RAM.
INFO 2026-06-08 08:30:56 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr11:75,449,121
INFO 2026-06-08 08:30:56 MarkDuplicates Tracking 275343 as yet unmatched pairs. 6205 records in RAM.
INFO 2026-06-08 08:30:58 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr11:93,801,853
INFO 2026-06-08 08:30:58 MarkDuplicates Tracking 273832 as yet unmatched pairs. 4692 records in RAM.
INFO 2026-06-08 08:30:59 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr11:117,219,610
INFO 2026-06-08 08:30:59 MarkDuplicates Tracking 272301 as yet unmatched pairs. 3160 records in RAM.
INFO 2026-06-08 08:31:01 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr11:122,796,964
INFO 2026-06-08 08:31:01 MarkDuplicates Tracking 270665 as yet unmatched pairs. 1524 records in RAM.
INFO 2026-06-08 08:31:03 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr12:18,052
INFO 2026-06-08 08:31:03 MarkDuplicates Tracking 269185 as yet unmatched pairs. 30974 records in RAM.
INFO 2026-06-08 08:31:04 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr12:6,232,695
INFO 2026-06-08 08:31:04 MarkDuplicates Tracking 268192 as yet unmatched pairs. 29979 records in RAM.
INFO 2026-06-08 08:31:06 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr12:6,965,565
INFO 2026-06-08 08:31:06 MarkDuplicates Tracking 265828 as yet unmatched pairs. 27614 records in RAM.
INFO 2026-06-08 08:31:08 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr12:12,477,873
INFO 2026-06-08 08:31:08 MarkDuplicates Tracking 264253 as yet unmatched pairs. 26037 records in RAM.
INFO 2026-06-08 08:31:09 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr12:30,710,039
INFO 2026-06-08 08:31:09 MarkDuplicates Tracking 262736 as yet unmatched pairs. 24519 records in RAM.
INFO 2026-06-08 08:31:11 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr12:48,818,734
INFO 2026-06-08 08:31:11 MarkDuplicates Tracking 261348 as yet unmatched pairs. 23129 records in RAM.
INFO 2026-06-08 08:31:12 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr12:49,565,572
INFO 2026-06-08 08:31:12 MarkDuplicates Tracking 259803 as yet unmatched pairs. 21584 records in RAM.
INFO 2026-06-08 08:31:14 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr12:52,904,758
INFO 2026-06-08 08:31:14 MarkDuplicates Tracking 259000 as yet unmatched pairs. 20780 records in RAM.
INFO 2026-06-08 08:31:15 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr12:53,669,150
INFO 2026-06-08 08:31:15 MarkDuplicates Tracking 257321 as yet unmatched pairs. 19101 records in RAM.
INFO 2026-06-08 08:31:17 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr12:56,101,641
INFO 2026-06-08 08:31:17 MarkDuplicates Tracking 255186 as yet unmatched pairs. 16965 records in RAM.
INFO 2026-06-08 08:31:19 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr12:56,713,629
INFO 2026-06-08 08:31:19 MarkDuplicates Tracking 254114 as yet unmatched pairs. 15892 records in RAM.
INFO 2026-06-08 08:31:20 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr12:57,210,316
INFO 2026-06-08 08:31:20 MarkDuplicates Tracking 252113 as yet unmatched pairs. 13891 records in RAM.
INFO 2026-06-08 08:31:22 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr12:67,305,353
INFO 2026-06-08 08:31:22 MarkDuplicates Tracking 250532 as yet unmatched pairs. 12310 records in RAM.
INFO 2026-06-08 08:31:24 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr12:92,776,114
INFO 2026-06-08 08:31:24 MarkDuplicates Tracking 249034 as yet unmatched pairs. 10810 records in RAM.
INFO 2026-06-08 08:31:25 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr12:106,240,286
INFO 2026-06-08 08:31:25 MarkDuplicates Tracking 247656 as yet unmatched pairs. 9432 records in RAM.
INFO 2026-06-08 08:31:27 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr12:112,229,843
INFO 2026-06-08 08:31:27 MarkDuplicates Tracking 245867 as yet unmatched pairs. 7642 records in RAM.
INFO 2026-06-08 08:31:29 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr12:118,052,338
INFO 2026-06-08 08:31:29 MarkDuplicates Tracking 244370 as yet unmatched pairs. 6141 records in RAM.
INFO 2026-06-08 08:31:32 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr12:121,921,519
INFO 2026-06-08 08:31:32 MarkDuplicates Tracking 242485 as yet unmatched pairs. 4255 records in RAM.
INFO 2026-06-08 08:31:33 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr12:124,343,013
INFO 2026-06-08 08:31:33 MarkDuplicates Tracking 241080 as yet unmatched pairs. 2850 records in RAM.
INFO 2026-06-08 08:31:34 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr12:132,574,511
INFO 2026-06-08 08:31:34 MarkDuplicates Tracking 239431 as yet unmatched pairs. 1200 records in RAM.
INFO 2026-06-08 08:31:36 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr13:27,427,117
INFO 2026-06-08 08:31:36 MarkDuplicates Tracking 237551 as yet unmatched pairs. 6021 records in RAM.
INFO 2026-06-08 08:31:38 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr13:41,131,562
INFO 2026-06-08 08:31:38 MarkDuplicates Tracking 236061 as yet unmatched pairs. 4530 records in RAM.
INFO 2026-06-08 08:31:39 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr13:79,520,912
INFO 2026-06-08 08:31:39 MarkDuplicates Tracking 234545 as yet unmatched pairs. 3012 records in RAM.
INFO 2026-06-08 08:31:41 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr13:110,449,690
INFO 2026-06-08 08:31:41 MarkDuplicates Tracking 233266 as yet unmatched pairs. 1732 records in RAM.
INFO 2026-06-08 08:31:42 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr14:21,083,850
INFO 2026-06-08 08:31:42 MarkDuplicates Tracking 231259 as yet unmatched pairs. 16022 records in RAM.
INFO 2026-06-08 08:31:44 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr14:23,562,048
INFO 2026-06-08 08:31:44 MarkDuplicates Tracking 229583 as yet unmatched pairs. 14340 records in RAM.
INFO 2026-06-08 08:31:46 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr14:29,159,275
INFO 2026-06-08 08:31:46 MarkDuplicates Tracking 227817 as yet unmatched pairs. 12571 records in RAM.
INFO 2026-06-08 08:31:47 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr14:49,618,839
INFO 2026-06-08 08:31:47 MarkDuplicates Tracking 226537 as yet unmatched pairs. 11288 records in RAM.
INFO 2026-06-08 08:31:49 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr14:60,291,440
INFO 2026-06-08 08:31:49 MarkDuplicates Tracking 224900 as yet unmatched pairs. 9635 records in RAM.
INFO 2026-06-08 08:31:50 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr14:70,523,114
INFO 2026-06-08 08:31:50 MarkDuplicates Tracking 223259 as yet unmatched pairs. 7994 records in RAM.
INFO 2026-06-08 08:31:52 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr14:75,280,585
INFO 2026-06-08 08:31:52 MarkDuplicates Tracking 222147 as yet unmatched pairs. 6882 records in RAM.
INFO 2026-06-08 08:31:53 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr14:92,157,660
INFO 2026-06-08 08:31:53 MarkDuplicates Tracking 220233 as yet unmatched pairs. 4967 records in RAM.
INFO 2026-06-08 08:31:56 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr14:100,239,495
INFO 2026-06-08 08:31:56 MarkDuplicates Tracking 218664 as yet unmatched pairs. 3386 records in RAM.
INFO 2026-06-08 08:31:57 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr14:104,714,252
INFO 2026-06-08 08:31:57 MarkDuplicates Tracking 217076 as yet unmatched pairs. 1798 records in RAM.
INFO 2026-06-08 08:31:59 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr15:22,542,430
INFO 2026-06-08 08:31:59 MarkDuplicates Tracking 215271 as yet unmatched pairs. 14674 records in RAM.
INFO 2026-06-08 08:32:01 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 2s. Last read position: chr15:39,583,604
INFO 2026-06-08 08:32:01 MarkDuplicates Tracking 214086 as yet unmatched pairs. 13489 records in RAM.
INFO 2026-06-08 08:32:03 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr15:42,694,532
INFO 2026-06-08 08:32:03 MarkDuplicates Tracking 212414 as yet unmatched pairs. 11814 records in RAM.
INFO 2026-06-08 08:32:04 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr15:48,467,975
INFO 2026-06-08 08:32:04 MarkDuplicates Tracking 211021 as yet unmatched pairs. 10420 records in RAM.
INFO 2026-06-08 08:32:05 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr15:57,232,750
INFO 2026-06-08 08:32:05 MarkDuplicates Tracking 210243 as yet unmatched pairs. 9640 records in RAM.
INFO 2026-06-08 08:32:07 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr15:64,689,141
INFO 2026-06-08 08:32:07 MarkDuplicates Tracking 207842 as yet unmatched pairs. 7239 records in RAM.
INFO 2026-06-08 08:32:09 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr15:72,200,594
INFO 2026-06-08 08:32:09 MarkDuplicates Tracking 206433 as yet unmatched pairs. 5830 records in RAM.
INFO 2026-06-08 08:32:10 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr15:75,430,248
INFO 2026-06-08 08:32:10 MarkDuplicates Tracking 204412 as yet unmatched pairs. 3809 records in RAM.
INFO 2026-06-08 08:32:12 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr15:85,715,788
INFO 2026-06-08 08:32:12 MarkDuplicates Tracking 202894 as yet unmatched pairs. 2289 records in RAM.
INFO 2026-06-08 08:32:13 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr15:98,913,234
INFO 2026-06-08 08:32:13 MarkDuplicates Tracking 201187 as yet unmatched pairs. 582 records in RAM.
INFO 2026-06-08 08:32:15 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr16:651,646
INFO 2026-06-08 08:32:15 MarkDuplicates Tracking 199655 as yet unmatched pairs. 29804 records in RAM.
INFO 2026-06-08 08:32:17 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr16:1,363,030
INFO 2026-06-08 08:32:17 MarkDuplicates Tracking 197544 as yet unmatched pairs. 27693 records in RAM.
INFO 2026-06-08 08:32:18 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr16:2,088,081
INFO 2026-06-08 08:32:18 MarkDuplicates Tracking 195998 as yet unmatched pairs. 26147 records in RAM.
INFO 2026-06-08 08:32:20 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr16:2,762,497
INFO 2026-06-08 08:32:20 MarkDuplicates Tracking 193732 as yet unmatched pairs. 23881 records in RAM.
INFO 2026-06-08 08:32:21 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr16:3,484,819
INFO 2026-06-08 08:32:21 MarkDuplicates Tracking 192166 as yet unmatched pairs. 22312 records in RAM.
INFO 2026-06-08 08:32:23 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr16:10,533,076
INFO 2026-06-08 08:32:23 MarkDuplicates Tracking 190581 as yet unmatched pairs. 20727 records in RAM.
INFO 2026-06-08 08:33:25 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 61s. Last read position: chr16:14,926,055
INFO 2026-06-08 08:33:25 MarkDuplicates Tracking 189410 as yet unmatched pairs. 19556 records in RAM.
INFO 2026-06-08 08:33:27 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr16:16,316,805
INFO 2026-06-08 08:33:27 MarkDuplicates Tracking 188115 as yet unmatched pairs. 18261 records in RAM.
INFO 2026-06-08 08:33:28 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr16:18,345,442
INFO 2026-06-08 08:33:28 MarkDuplicates Tracking 187850 as yet unmatched pairs. 17996 records in RAM.
INFO 2026-06-08 08:33:29 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr16:19,114,490
INFO 2026-06-08 08:33:29 MarkDuplicates Tracking 187002 as yet unmatched pairs. 17148 records in RAM.
INFO 2026-06-08 08:33:30 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr16:21,835,402
INFO 2026-06-08 08:33:30 MarkDuplicates Tracking 186564 as yet unmatched pairs. 16710 records in RAM.
INFO 2026-06-08 08:33:31 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,708
INFO 2026-06-08 08:33:31 MarkDuplicates Tracking 185627 as yet unmatched pairs. 15773 records in RAM.
INFO 2026-06-08 08:33:33 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr16:28,638,395
INFO 2026-06-08 08:33:33 MarkDuplicates Tracking 184268 as yet unmatched pairs. 14414 records in RAM.
INFO 2026-06-08 08:33:34 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 1s. Last read position: chr16:29,483,971
INFO 2026-06-08 08:33:34 MarkDuplicates Tracking 183860 as yet unmatched pairs. 14006 records in RAM.
INFO 2026-06-08 08:33:36 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr16:30,069,348
INFO 2026-06-08 08:33:36 MarkDuplicates Tracking 182843 as yet unmatched pairs. 12989 records in RAM.
INFO 2026-06-08 08:33:37 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr16:30,555,553
INFO 2026-06-08 08:33:37 MarkDuplicates Tracking 180901 as yet unmatched pairs. 11046 records in RAM.
INFO 2026-06-08 08:33:38 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr16:31,184,259
INFO 2026-06-08 08:33:38 MarkDuplicates Tracking 179221 as yet unmatched pairs. 9365 records in RAM.
INFO 2026-06-08 08:33:40 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr16:53,826,282
INFO 2026-06-08 08:33:40 MarkDuplicates Tracking 177744 as yet unmatched pairs. 7885 records in RAM.
INFO 2026-06-08 08:33:42 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr16:67,166,570
INFO 2026-06-08 08:33:42 MarkDuplicates Tracking 176010 as yet unmatched pairs. 6150 records in RAM.
INFO 2026-06-08 08:33:43 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr16:70,259,057
INFO 2026-06-08 08:33:43 MarkDuplicates Tracking 174585 as yet unmatched pairs. 4724 records in RAM.
INFO 2026-06-08 08:33:45 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr16:84,183,441
INFO 2026-06-08 08:33:45 MarkDuplicates Tracking 172859 as yet unmatched pairs. 2997 records in RAM.
INFO 2026-06-08 08:33:48 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 2s. Last read position: chr16:88,901,550
INFO 2026-06-08 08:33:48 MarkDuplicates Tracking 170937 as yet unmatched pairs. 1075 records in RAM.
INFO 2026-06-08 08:33:51 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 3s. Last read position: chr17:1,635,526
INFO 2026-06-08 08:33:51 MarkDuplicates Tracking 169134 as yet unmatched pairs. 59062 records in RAM.
INFO 2026-06-08 08:33:53 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr17:4,946,738
INFO 2026-06-08 08:33:53 MarkDuplicates Tracking 168131 as yet unmatched pairs. 58058 records in RAM.
INFO 2026-06-08 08:33:54 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr17:7,513,348
INFO 2026-06-08 08:33:54 MarkDuplicates Tracking 166193 as yet unmatched pairs. 56119 records in RAM.
INFO 2026-06-08 08:33:56 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr17:12,054,889
INFO 2026-06-08 08:33:56 MarkDuplicates Tracking 164335 as yet unmatched pairs. 54260 records in RAM.
INFO 2026-06-08 08:33:58 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr17:18,671,495
INFO 2026-06-08 08:33:58 MarkDuplicates Tracking 162789 as yet unmatched pairs. 52712 records in RAM.
INFO 2026-06-08 08:34:00 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr17:30,379,335
INFO 2026-06-08 08:34:00 MarkDuplicates Tracking 161514 as yet unmatched pairs. 51437 records in RAM.
INFO 2026-06-08 08:34:01 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr17:38,122,805
INFO 2026-06-08 08:34:01 MarkDuplicates Tracking 160120 as yet unmatched pairs. 50041 records in RAM.
INFO 2026-06-08 08:34:03 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr17:39,727,321
INFO 2026-06-08 08:34:03 MarkDuplicates Tracking 159154 as yet unmatched pairs. 49075 records in RAM.
INFO 2026-06-08 08:34:05 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr17:41,905,527
INFO 2026-06-08 08:34:05 MarkDuplicates Tracking 156696 as yet unmatched pairs. 46617 records in RAM.
INFO 2026-06-08 08:34:06 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr17:44,350,524
INFO 2026-06-08 08:34:06 MarkDuplicates Tracking 155638 as yet unmatched pairs. 45557 records in RAM.
INFO 2026-06-08 08:34:08 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr17:48,874,836
INFO 2026-06-08 08:34:08 MarkDuplicates Tracking 153573 as yet unmatched pairs. 43492 records in RAM.
INFO 2026-06-08 08:34:10 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,689
INFO 2026-06-08 08:34:10 MarkDuplicates Tracking 155712 as yet unmatched pairs. 45631 records in RAM.
INFO 2026-06-08 08:34:12 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,931
INFO 2026-06-08 08:34:12 MarkDuplicates Tracking 168975 as yet unmatched pairs. 58894 records in RAM.
INFO 2026-06-08 08:34:13 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,770
INFO 2026-06-08 08:34:13 MarkDuplicates Tracking 165790 as yet unmatched pairs. 55709 records in RAM.
INFO 2026-06-08 08:34:15 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,491
INFO 2026-06-08 08:34:15 MarkDuplicates Tracking 164468 as yet unmatched pairs. 54387 records in RAM.
INFO 2026-06-08 08:34:17 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,086
INFO 2026-06-08 08:34:17 MarkDuplicates Tracking 169510 as yet unmatched pairs. 59429 records in RAM.
INFO 2026-06-08 08:34:19 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr17:50,191,474
INFO 2026-06-08 08:34:19 MarkDuplicates Tracking 157876 as yet unmatched pairs. 47795 records in RAM.
INFO 2026-06-08 08:34:22 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,796
INFO 2026-06-08 08:34:22 MarkDuplicates Tracking 164960 as yet unmatched pairs. 54879 records in RAM.
INFO 2026-06-08 08:34:24 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,133
INFO 2026-06-08 08:34:24 MarkDuplicates Tracking 168116 as yet unmatched pairs. 58035 records in RAM.
INFO 2026-06-08 08:34:26 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,765
INFO 2026-06-08 08:34:26 MarkDuplicates Tracking 158615 as yet unmatched pairs. 48533 records in RAM.
INFO 2026-06-08 08:34:27 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,603
INFO 2026-06-08 08:34:27 MarkDuplicates Tracking 170711 as yet unmatched pairs. 60629 records in RAM.
INFO 2026-06-08 08:34:29 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,333
INFO 2026-06-08 08:34:29 MarkDuplicates Tracking 160703 as yet unmatched pairs. 50621 records in RAM.
INFO 2026-06-08 08:34:31 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,205
INFO 2026-06-08 08:34:31 MarkDuplicates Tracking 161245 as yet unmatched pairs. 51163 records in RAM.
INFO 2026-06-08 08:34:33 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,238
INFO 2026-06-08 08:34:33 MarkDuplicates Tracking 147990 as yet unmatched pairs. 37908 records in RAM.
INFO 2026-06-08 08:34:35 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr17:50,201,489
INFO 2026-06-08 08:34:35 MarkDuplicates Tracking 129250 as yet unmatched pairs. 19168 records in RAM.
INFO 2026-06-08 08:34:36 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr17:58,543,026
INFO 2026-06-08 08:34:36 MarkDuplicates Tracking 127547 as yet unmatched pairs. 17465 records in RAM.
INFO 2026-06-08 08:34:38 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 2s. Last read position: chr17:60,391,925
INFO 2026-06-08 08:34:38 MarkDuplicates Tracking 126160 as yet unmatched pairs. 16078 records in RAM.
INFO 2026-06-08 08:34:40 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 1s. Last read position: chr17:64,500,158
INFO 2026-06-08 08:34:40 MarkDuplicates Tracking 124847 as yet unmatched pairs. 14765 records in RAM.
INFO 2026-06-08 08:34:42 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr17:68,530,351
INFO 2026-06-08 08:34:42 MarkDuplicates Tracking 124296 as yet unmatched pairs. 14214 records in RAM.
INFO 2026-06-08 08:34:44 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr17:75,502,177
INFO 2026-06-08 08:34:44 MarkDuplicates Tracking 121668 as yet unmatched pairs. 11585 records in RAM.
INFO 2026-06-08 08:34:46 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 2s. Last read position: chr17:76,270,383
INFO 2026-06-08 08:34:46 MarkDuplicates Tracking 119893 as yet unmatched pairs. 9810 records in RAM.
INFO 2026-06-08 08:34:47 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr17:78,971,799
INFO 2026-06-08 08:34:47 MarkDuplicates Tracking 118854 as yet unmatched pairs. 8771 records in RAM.
INFO 2026-06-08 08:34:49 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr17:80,340,334
INFO 2026-06-08 08:34:49 MarkDuplicates Tracking 116561 as yet unmatched pairs. 6478 records in RAM.
INFO 2026-06-08 08:34:51 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr17:81,547,868
INFO 2026-06-08 08:34:51 MarkDuplicates Tracking 114534 as yet unmatched pairs. 4450 records in RAM.
INFO 2026-06-08 08:34:52 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr17:82,054,012
INFO 2026-06-08 08:34:52 MarkDuplicates Tracking 112989 as yet unmatched pairs. 2903 records in RAM.
INFO 2026-06-08 08:34:54 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr17:82,472,565
INFO 2026-06-08 08:34:54 MarkDuplicates Tracking 110693 as yet unmatched pairs. 602 records in RAM.
INFO 2026-06-08 08:34:56 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr18:14,511,898
INFO 2026-06-08 08:34:56 MarkDuplicates Tracking 109225 as yet unmatched pairs. 3848 records in RAM.
INFO 2026-06-08 08:34:57 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr18:44,951,637
INFO 2026-06-08 08:34:57 MarkDuplicates Tracking 107697 as yet unmatched pairs. 2319 records in RAM.
INFO 2026-06-08 08:34:59 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr18:74,253,526
INFO 2026-06-08 08:34:59 MarkDuplicates Tracking 106406 as yet unmatched pairs. 1028 records in RAM.
INFO 2026-06-08 08:35:01 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 2s. Last read position: chr19:1,046,306
INFO 2026-06-08 08:35:01 MarkDuplicates Tracking 104107 as yet unmatched pairs. 42388 records in RAM.
INFO 2026-06-08 08:35:03 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr19:1,827,710
INFO 2026-06-08 08:35:03 MarkDuplicates Tracking 102205 as yet unmatched pairs. 40486 records in RAM.
INFO 2026-06-08 08:35:04 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr19:3,546,267
INFO 2026-06-08 08:35:04 MarkDuplicates Tracking 100338 as yet unmatched pairs. 38617 records in RAM.
INFO 2026-06-08 08:35:06 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr19:5,144,248
INFO 2026-06-08 08:35:06 MarkDuplicates Tracking 98378 as yet unmatched pairs. 36656 records in RAM.
INFO 2026-06-08 08:35:08 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr19:7,533,538
INFO 2026-06-08 08:35:08 MarkDuplicates Tracking 96686 as yet unmatched pairs. 34964 records in RAM.
INFO 2026-06-08 08:35:10 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr19:9,811,558
INFO 2026-06-08 08:35:10 MarkDuplicates Tracking 95028 as yet unmatched pairs. 33305 records in RAM.
INFO 2026-06-08 08:35:12 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr19:11,175,953
INFO 2026-06-08 08:35:12 MarkDuplicates Tracking 93373 as yet unmatched pairs. 31650 records in RAM.
INFO 2026-06-08 08:35:13 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr19:12,943,809
INFO 2026-06-08 08:35:13 MarkDuplicates Tracking 91808 as yet unmatched pairs. 30085 records in RAM.
INFO 2026-06-08 08:35:15 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr19:15,166,077
INFO 2026-06-08 08:35:15 MarkDuplicates Tracking 89930 as yet unmatched pairs. 28203 records in RAM.
INFO 2026-06-08 08:35:16 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr19:16,361,837
INFO 2026-06-08 08:35:16 MarkDuplicates Tracking 87760 as yet unmatched pairs. 26033 records in RAM.
INFO 2026-06-08 08:35:18 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr19:18,266,003
INFO 2026-06-08 08:35:18 MarkDuplicates Tracking 85938 as yet unmatched pairs. 24209 records in RAM.
INFO 2026-06-08 08:35:19 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr19:19,655,119
INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 84169 as yet unmatched pairs. 22440 records in RAM.
INFO 2026-06-08 08:35:21 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr19:35,269,875
INFO 2026-06-08 08:35:21 MarkDuplicates Tracking 82310 as yet unmatched pairs. 20581 records in RAM.
INFO 2026-06-08 08:35:23 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr19:38,635,036
INFO 2026-06-08 08:35:23 MarkDuplicates Tracking 80326 as yet unmatched pairs. 18597 records in RAM.
INFO 2026-06-08 08:35:25 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr19:40,235,298
INFO 2026-06-08 08:35:25 MarkDuplicates Tracking 79901 as yet unmatched pairs. 18172 records in RAM.
INFO 2026-06-08 08:35:26 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr19:41,506,547
INFO 2026-06-08 08:35:26 MarkDuplicates Tracking 76897 as yet unmatched pairs. 15168 records in RAM.
INFO 2026-06-08 08:35:28 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr19:42,509,183
INFO 2026-06-08 08:35:28 MarkDuplicates Tracking 75161 as yet unmatched pairs. 13428 records in RAM.
INFO 2026-06-08 08:35:30 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr19:45,380,067
INFO 2026-06-08 08:35:30 MarkDuplicates Tracking 73106 as yet unmatched pairs. 11373 records in RAM.
INFO 2026-06-08 08:35:31 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr19:47,271,338
INFO 2026-06-08 08:35:31 MarkDuplicates Tracking 71186 as yet unmatched pairs. 9453 records in RAM.
INFO 2026-06-08 08:35:33 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr19:49,015,817
INFO 2026-06-08 08:35:33 MarkDuplicates Tracking 69352 as yet unmatched pairs. 7619 records in RAM.
INFO 2026-06-08 08:35:35 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr19:49,830,773
INFO 2026-06-08 08:35:35 MarkDuplicates Tracking 67621 as yet unmatched pairs. 5888 records in RAM.
INFO 2026-06-08 08:35:37 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 2s. Last read position: chr19:54,107,032
INFO 2026-06-08 08:35:37 MarkDuplicates Tracking 65894 as yet unmatched pairs. 4161 records in RAM.
INFO 2026-06-08 08:35:38 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr19:55,602,718
INFO 2026-06-08 08:35:38 MarkDuplicates Tracking 63998 as yet unmatched pairs. 2265 records in RAM.
INFO 2026-06-08 08:35:39 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr19:58,206,733
INFO 2026-06-08 08:35:39 MarkDuplicates Tracking 62600 as yet unmatched pairs. 867 records in RAM.
INFO 2026-06-08 08:35:41 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr20:3,213,982
INFO 2026-06-08 08:35:41 MarkDuplicates Tracking 60779 as yet unmatched pairs. 16277 records in RAM.
INFO 2026-06-08 08:35:43 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr20:17,659,131
INFO 2026-06-08 08:35:43 MarkDuplicates Tracking 58903 as yet unmatched pairs. 14401 records in RAM.
INFO 2026-06-08 08:35:44 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr20:32,145,413
INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 57386 as yet unmatched pairs. 12884 records in RAM.
INFO 2026-06-08 08:35:46 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr20:35,725,040
INFO 2026-06-08 08:35:46 MarkDuplicates Tracking 55818 as yet unmatched pairs. 11316 records in RAM.
INFO 2026-06-08 08:35:47 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr20:43,459,830
INFO 2026-06-08 08:35:47 MarkDuplicates Tracking 54053 as yet unmatched pairs. 9549 records in RAM.
INFO 2026-06-08 08:35:49 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr20:46,726,882
INFO 2026-06-08 08:35:49 MarkDuplicates Tracking 52346 as yet unmatched pairs. 7842 records in RAM.
INFO 2026-06-08 08:35:50 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr20:51,718,484
INFO 2026-06-08 08:35:50 MarkDuplicates Tracking 50824 as yet unmatched pairs. 6320 records in RAM.
INFO 2026-06-08 08:35:52 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr20:59,032,224
INFO 2026-06-08 08:35:52 MarkDuplicates Tracking 48900 as yet unmatched pairs. 4396 records in RAM.
INFO 2026-06-08 08:35:53 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr20:62,813,532
INFO 2026-06-08 08:35:53 MarkDuplicates Tracking 47164 as yet unmatched pairs. 2660 records in RAM.
INFO 2026-06-08 08:35:55 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr20:63,869,429
INFO 2026-06-08 08:35:55 MarkDuplicates Tracking 45290 as yet unmatched pairs. 786 records in RAM.
INFO 2026-06-08 08:35:57 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,331
INFO 2026-06-08 08:35:57 MarkDuplicates Tracking 43897 as yet unmatched pairs. 9856 records in RAM.
INFO 2026-06-08 08:35:58 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr21:8,415,557
INFO 2026-06-08 08:35:58 MarkDuplicates Tracking 43355 as yet unmatched pairs. 9312 records in RAM.
INFO 2026-06-08 08:36:00 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr21:25,639,771
INFO 2026-06-08 08:36:00 MarkDuplicates Tracking 42045 as yet unmatched pairs. 8002 records in RAM.
INFO 2026-06-08 08:36:01 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr21:36,070,053
INFO 2026-06-08 08:36:01 MarkDuplicates Tracking 40270 as yet unmatched pairs. 6227 records in RAM.
INFO 2026-06-08 08:36:02 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr21:42,363,318
INFO 2026-06-08 08:36:02 MarkDuplicates Tracking 41000 as yet unmatched pairs. 6957 records in RAM.
INFO 2026-06-08 08:36:04 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr21:45,504,042
INFO 2026-06-08 08:36:04 MarkDuplicates Tracking 37015 as yet unmatched pairs. 2972 records in RAM.
INFO 2026-06-08 08:36:05 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 1s. Last read position: chr21:46,125,828
INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 35118 as yet unmatched pairs. 1075 records in RAM.
INFO 2026-06-08 08:36:07 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr22:20,704,031
INFO 2026-06-08 08:36:07 MarkDuplicates Tracking 33119 as yet unmatched pairs. 12188 records in RAM.
INFO 2026-06-08 08:36:09 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr22:24,650,781
INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 31160 as yet unmatched pairs. 10229 records in RAM.
INFO 2026-06-08 08:36:10 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr22:29,793,410
INFO 2026-06-08 08:36:10 MarkDuplicates Tracking 29569 as yet unmatched pairs. 8638 records in RAM.
INFO 2026-06-08 08:36:11 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr22:36,296,920
INFO 2026-06-08 08:36:11 MarkDuplicates Tracking 27951 as yet unmatched pairs. 7020 records in RAM.
INFO 2026-06-08 08:36:13 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr22:39,224,092
INFO 2026-06-08 08:36:13 MarkDuplicates Tracking 26228 as yet unmatched pairs. 5297 records in RAM.
INFO 2026-06-08 08:36:15 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr22:42,888,777
INFO 2026-06-08 08:36:15 MarkDuplicates Tracking 24580 as yet unmatched pairs. 3649 records in RAM.
INFO 2026-06-08 08:36:16 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr22:50,221,653
INFO 2026-06-08 08:36:16 MarkDuplicates Tracking 22615 as yet unmatched pairs. 1684 records in RAM.
INFO 2026-06-08 08:36:18 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chrX:2,490,148
INFO 2026-06-08 08:36:18 MarkDuplicates Tracking 20733 as yet unmatched pairs. 13966 records in RAM.
INFO 2026-06-08 08:36:19 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chrX:20,130,528
INFO 2026-06-08 08:36:19 MarkDuplicates Tracking 19316 as yet unmatched pairs. 12543 records in RAM.
INFO 2026-06-08 08:36:21 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chrX:47,210,847
INFO 2026-06-08 08:36:21 MarkDuplicates Tracking 17904 as yet unmatched pairs. 11128 records in RAM.
INFO 2026-06-08 08:36:22 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chrX:51,898,128
INFO 2026-06-08 08:36:22 MarkDuplicates Tracking 16503 as yet unmatched pairs. 9727 records in RAM.
INFO 2026-06-08 08:36:24 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chrX:57,908,525
INFO 2026-06-08 08:36:24 MarkDuplicates Tracking 14608 as yet unmatched pairs. 7832 records in RAM.
INFO 2026-06-08 08:36:26 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chrX:77,599,570
INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 13743 as yet unmatched pairs. 6966 records in RAM.
INFO 2026-06-08 08:36:28 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chrX:107,917,564
INFO 2026-06-08 08:36:28 MarkDuplicates Tracking 11845 as yet unmatched pairs. 5067 records in RAM.
INFO 2026-06-08 08:36:30 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 2s. Last read position: chrX:139,897,116
INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 10322 as yet unmatched pairs. 3544 records in RAM.
INFO 2026-06-08 08:36:31 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chrX:154,358,478
INFO 2026-06-08 08:36:31 MarkDuplicates Tracking 8675 as yet unmatched pairs. 1896 records in RAM.
INFO 2026-06-08 08:36:33 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 1s. Last read position: chrX:155,458,188
INFO 2026-06-08 08:36:33 MarkDuplicates Tracking 6795 as yet unmatched pairs. 16 records in RAM.
INFO 2026-06-08 08:36:34 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,122
INFO 2026-06-08 08:36:34 MarkDuplicates Tracking 4983 as yet unmatched pairs. 165 records in RAM.
INFO 2026-06-08 08:36:35 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,041
INFO 2026-06-08 08:36:35 MarkDuplicates Tracking 1135 as yet unmatched pairs. 1124 records in RAM.
INFO 2026-06-08 08:36:36 MarkDuplicates Read 363964443 records. 0 pairs never matched.
INFO 2026-06-08 08:37:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 32405629376; totalMemory: 46305116160; maxMemory: 63585648640
INFO 2026-06-08 08:37:10 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:37:19 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:37:51 OpticalDuplicateFinder Large duplicate set. size = 1009
INFO 2026-06-08 08:37:51 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,074
INFO 2026-06-08 08:37:51 OpticalDuplicateFinder Large duplicate set. size = 1113
INFO 2026-06-08 08:37:51 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,359
INFO 2026-06-08 08:37:51 OpticalDuplicateFinder Large duplicate set. size = 1211
INFO 2026-06-08 08:37:51 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,239
INFO 2026-06-08 08:37:52 OpticalDuplicateFinder Large duplicate set. size = 1138
INFO 2026-06-08 08:37:52 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,718
INFO 2026-06-08 08:37:52 OpticalDuplicateFinder Large duplicate set. size = 1023
INFO 2026-06-08 08:37:52 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,140
INFO 2026-06-08 08:37:52 OpticalDuplicateFinder Large duplicate set. size = 1101
INFO 2026-06-08 08:37:52 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,741
INFO 2026-06-08 08:37:52 OpticalDuplicateFinder Large duplicate set. size = 1455
INFO 2026-06-08 08:37:52 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,349
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1087
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,160
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1076
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,257
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1206
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,672
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1473
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,189
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1641
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,695
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1122
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,475
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1021
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,805
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1002
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,453
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1554
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,524
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1175
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,677
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder Large duplicate set. size = 1027
INFO 2026-06-08 08:37:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,152
INFO 2026-06-08 08:38:00 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:38:00 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:38:38 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:38:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300667192; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:38:48 MarkDuplicates Marking 231231299 records as duplicates.
INFO 2026-06-08 08:38:48 MarkDuplicates Found 7811103 optical duplicate clusters.
INFO 2026-06-08 08:38:48 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:39:03 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:15s. Time for last 10,000,000: 15s. Last read position: chr1:43,960,312
INFO 2026-06-08 08:39:19 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:31s. Time for last 10,000,000: 15s. Last read position: chr1:154,172,964
INFO 2026-06-08 08:39:35 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:47s. Time for last 10,000,000: 15s. Last read position: chr1:223,712,771
INFO 2026-06-08 08:39:51 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:03s. Time for last 10,000,000: 15s. Last read position: chr2:70,991,835
INFO 2026-06-08 08:40:07 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:19s. Time for last 10,000,000: 16s. Last read position: chr2:189,008,937
INFO 2026-06-08 08:40:23 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:35s. Time for last 10,000,000: 15s. Last read position: chr2:237,334,671
INFO 2026-06-08 08:40:39 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:51s. Time for last 10,000,000: 15s. Last read position: chr3:101,853,113
INFO 2026-06-08 08:40:55 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:06s. Time for last 10,000,000: 15s. Last read position: chr4:16,505,925
INFO 2026-06-08 08:41:11 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:22s. Time for last 10,000,000: 15s. Last read position: chr5:56,938,912
INFO 2026-06-08 08:41:26 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:38s. Time for last 10,000,000: 15s. Last read position: chr5:151,129,407
INFO 2026-06-08 08:41:42 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:54s. Time for last 10,000,000: 15s. Last read position: chr6:31,994,624
INFO 2026-06-08 08:41:58 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:10s. Time for last 10,000,000: 15s. Last read position: chr6:144,797,895
INFO 2026-06-08 08:42:14 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:25s. Time for last 10,000,000: 15s. Last read position: chr7:75,416,670
INFO 2026-06-08 08:42:29 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:41s. Time for last 10,000,000: 15s. Last read position: chr8:23,681,269
INFO 2026-06-08 08:42:44 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:56s. Time for last 10,000,000: 15s. Last read position: chr8:143,919,379
INFO 2026-06-08 08:43:00 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:12s. Time for last 10,000,000: 15s. Last read position: chr9:130,296,758
INFO 2026-06-08 08:43:16 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:27s. Time for last 10,000,000: 15s. Last read position: chr10:75,222,275
INFO 2026-06-08 08:43:31 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:43s. Time for last 10,000,000: 15s. Last read position: chr11:1,753,568
INFO 2026-06-08 08:43:46 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:58s. Time for last 10,000,000: 15s. Last read position: chr11:65,546,824
INFO 2026-06-08 08:44:02 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:14s. Time for last 10,000,000: 15s. Last read position: chr12:6,232,695
INFO 2026-06-08 08:44:17 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:28s. Time for last 10,000,000: 14s. Last read position: chr12:57,210,316
INFO 2026-06-08 08:44:32 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:44s. Time for last 10,000,000: 15s. Last read position: chr13:41,131,562
INFO 2026-06-08 08:44:48 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:00s. Time for last 10,000,000: 15s. Last read position: chr14:92,157,660
INFO 2026-06-08 08:45:04 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:16s. Time for last 10,000,000: 16s. Last read position: chr15:75,430,248
INFO 2026-06-08 08:45:21 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:32s. Time for last 10,000,000: 16s. Last read position: chr16:16,316,805
INFO 2026-06-08 08:45:36 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:48s. Time for last 10,000,000: 15s. Last read position: chr16:53,826,282
INFO 2026-06-08 08:45:53 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:05s. Time for last 10,000,000: 16s. Last read position: chr17:30,379,335
INFO 2026-06-08 08:46:09 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:21s. Time for last 10,000,000: 16s. Last read position: chr17:50,190,086
INFO 2026-06-08 08:46:25 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:37s. Time for last 10,000,000: 15s. Last read position: chr17:58,543,026
INFO 2026-06-08 08:46:41 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:53s. Time for last 10,000,000: 15s. Last read position: chr17:82,472,565
INFO 2026-06-08 08:46:57 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:09s. Time for last 10,000,000: 16s. Last read position: chr19:11,175,953
INFO 2026-06-08 08:47:13 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:25s. Time for last 10,000,000: 15s. Last read position: chr19:42,509,183
INFO 2026-06-08 08:47:29 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:41s. Time for last 10,000,000: 15s. Last read position: chr20:32,145,413
INFO 2026-06-08 08:47:45 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:56s. Time for last 10,000,000: 15s. Last read position: chr21:25,639,771
INFO 2026-06-08 08:48:00 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:12s. Time for last 10,000,000: 15s. Last read position: chr22:42,888,777
INFO 2026-06-08 08:48:16 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:28s. Time for last 10,000,000: 15s. Last read position: chrX:154,358,478
INFO 2026-06-08 08:48:27 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:48:27 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:48:27 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:48:27 MarkDuplicates Before output close freeMemory: 201350848; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:48:27 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:48:27 MarkDuplicates After output close freeMemory: 104132272; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:48:27 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 23.46 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory