Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT BVT_FFPE_TRNA_brn_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_brn_01_A23WKFTLT4_3.md.bam --METRICS_FILE BVT_FFPE_TRNA_brn_01_A23WKFTLT4_3.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:19:22.603 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 08:19:22 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_brn_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_brn_01_A23WKFTLT4_3.md.bam --METRICS_FILE BVT_FFPE_TRNA_brn_01_A23WKFTLT4_3.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:19:22 GMT 2026] Executing as ?@nf-e2aad2cfe85c66262e2c9237c8f4ea54-ebdb4-tqpsb 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 08:19:22 MarkDuplicates Start of doWork freeMemory: 105492528; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:19:22 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:19:22 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:19:26 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:6,554,181
INFO 2026-06-08 08:19:26 MarkDuplicates Tracking 2786 as yet unmatched pairs. 52 records in RAM.
INFO 2026-06-08 08:19:28 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:11,925,421
INFO 2026-06-08 08:19:28 MarkDuplicates Tracking 5275 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 08:19:30 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:16,986,092
INFO 2026-06-08 08:19:30 MarkDuplicates Tracking 7816 as yet unmatched pairs. 302 records in RAM.
INFO 2026-06-08 08:19:32 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:21,852,792
INFO 2026-06-08 08:19:32 MarkDuplicates Tracking 10106 as yet unmatched pairs. 32 records in RAM.
INFO 2026-06-08 08:19:34 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:26,697,290
INFO 2026-06-08 08:19:34 MarkDuplicates Tracking 12863 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 08:19:36 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:30,992,511
INFO 2026-06-08 08:19:36 MarkDuplicates Tracking 15226 as yet unmatched pairs. 100 records in RAM.
INFO 2026-06-08 08:19:38 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:33,334,175
INFO 2026-06-08 08:19:38 MarkDuplicates Tracking 18041 as yet unmatched pairs. 240 records in RAM.
INFO 2026-06-08 08:19:40 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:37,931,956
INFO 2026-06-08 08:19:40 MarkDuplicates Tracking 20274 as yet unmatched pairs. 71 records in RAM.
INFO 2026-06-08 08:19:42 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:40,770,468
INFO 2026-06-08 08:19:42 MarkDuplicates Tracking 22844 as yet unmatched pairs. 88 records in RAM.
INFO 2026-06-08 08:19:45 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:44,776,709
INFO 2026-06-08 08:19:45 MarkDuplicates Tracking 25715 as yet unmatched pairs. 288 records in RAM.
INFO 2026-06-08 08:19:48 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:54,216,225
INFO 2026-06-08 08:19:48 MarkDuplicates Tracking 28301 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-08 08:19:49 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:81,943,394
INFO 2026-06-08 08:19:49 MarkDuplicates Tracking 30669 as yet unmatched pairs. 29 records in RAM.
INFO 2026-06-08 08:19:51 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:109,250,564
INFO 2026-06-08 08:19:51 MarkDuplicates Tracking 33175 as yet unmatched pairs. 392 records in RAM.
INFO 2026-06-08 08:19:53 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:113,391,170
INFO 2026-06-08 08:19:53 MarkDuplicates Tracking 35595 as yet unmatched pairs. 73 records in RAM.
INFO 2026-06-08 08:19:55 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:119,922,320
INFO 2026-06-08 08:19:55 MarkDuplicates Tracking 38517 as yet unmatched pairs. 465 records in RAM.
INFO 2026-06-08 08:19:57 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:120,827,115
INFO 2026-06-08 08:19:57 MarkDuplicates Tracking 40582 as yet unmatched pairs. 303 records in RAM.
INFO 2026-06-08 08:19:59 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:146,963,105
INFO 2026-06-08 08:19:59 MarkDuplicates Tracking 41318 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:20:01 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:149,390,757
INFO 2026-06-08 08:20:01 MarkDuplicates Tracking 42347 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:20:03 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:150,949,367
INFO 2026-06-08 08:20:03 MarkDuplicates Tracking 44088 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 08:20:04 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:154,251,244
INFO 2026-06-08 08:20:04 MarkDuplicates Tracking 46765 as yet unmatched pairs. 122 records in RAM.
INFO 2026-06-08 08:20:06 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:155,765,903
INFO 2026-06-08 08:20:06 MarkDuplicates Tracking 49237 as yet unmatched pairs. 345 records in RAM.
INFO 2026-06-08 08:20:07 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:156,652,452
INFO 2026-06-08 08:20:07 MarkDuplicates Tracking 54264 as yet unmatched pairs. 2676 records in RAM.
INFO 2026-06-08 08:20:09 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr1:156,671,593
INFO 2026-06-08 08:20:09 MarkDuplicates Tracking 54908 as yet unmatched pairs. 760 records in RAM.
INFO 2026-06-08 08:20:11 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:160,139,669
INFO 2026-06-08 08:20:11 MarkDuplicates Tracking 57882 as yet unmatched pairs. 957 records in RAM.
INFO 2026-06-08 08:20:12 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:171,541,513
INFO 2026-06-08 08:20:12 MarkDuplicates Tracking 59442 as yet unmatched pairs. 86 records in RAM.
INFO 2026-06-08 08:20:14 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr1:183,121,923
INFO 2026-06-08 08:20:14 MarkDuplicates Tracking 61899 as yet unmatched pairs. 84 records in RAM.
INFO 2026-06-08 08:20:17 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:201,788,504
INFO 2026-06-08 08:20:17 MarkDuplicates Tracking 64486 as yet unmatched pairs. 416 records in RAM.
INFO 2026-06-08 08:20:19 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:204,981,855
INFO 2026-06-08 08:20:19 MarkDuplicates Tracking 66683 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-08 08:20:21 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:220,033,568
INFO 2026-06-08 08:20:21 MarkDuplicates Tracking 69086 as yet unmatched pairs. 45 records in RAM.
INFO 2026-06-08 08:20:22 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:228,493,884
INFO 2026-06-08 08:20:22 MarkDuplicates Tracking 71881 as yet unmatched pairs. 311 records in RAM.
INFO 2026-06-08 08:20:24 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:236,686,750
INFO 2026-06-08 08:20:24 MarkDuplicates Tracking 74576 as yet unmatched pairs. 115 records in RAM.
INFO 2026-06-08 08:20:25 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:246,482,229
INFO 2026-06-08 08:20:25 MarkDuplicates Tracking 76974 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:20:28 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr2:12,724,587
INFO 2026-06-08 08:20:28 MarkDuplicates Tracking 80355 as yet unmatched pairs. 79228 records in RAM.
INFO 2026-06-08 08:20:29 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr2:27,055,155
INFO 2026-06-08 08:20:29 MarkDuplicates Tracking 82330 as yet unmatched pairs. 81170 records in RAM.
INFO 2026-06-08 08:20:31 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr2:32,464,731
INFO 2026-06-08 08:20:31 MarkDuplicates Tracking 85728 as yet unmatched pairs. 84538 records in RAM.
INFO 2026-06-08 08:20:33 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:20:33 MarkDuplicates Tracking 481500 as yet unmatched pairs. 61034 records in RAM.
INFO 2026-06-08 08:20:35 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:20:35 MarkDuplicates Tracking 754447 as yet unmatched pairs. 44777 records in RAM.
INFO 2026-06-08 08:20:37 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr2:42,284,680
INFO 2026-06-08 08:20:37 MarkDuplicates Tracking 798166 as yet unmatched pairs. 41493 records in RAM.
INFO 2026-06-08 08:20:39 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr2:54,526,426
INFO 2026-06-08 08:20:39 MarkDuplicates Tracking 796044 as yet unmatched pairs. 39302 records in RAM.
INFO 2026-06-08 08:20:41 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr2:61,394,881
INFO 2026-06-08 08:20:41 MarkDuplicates Tracking 793047 as yet unmatched pairs. 36273 records in RAM.
INFO 2026-06-08 08:20:42 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr2:74,156,632
INFO 2026-06-08 08:20:42 MarkDuplicates Tracking 790812 as yet unmatched pairs. 34010 records in RAM.
INFO 2026-06-08 08:20:44 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr2:95,087,409
INFO 2026-06-08 08:20:44 MarkDuplicates Tracking 788760 as yet unmatched pairs. 31902 records in RAM.
INFO 2026-06-08 08:20:46 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr2:101,887,143
INFO 2026-06-08 08:20:46 MarkDuplicates Tracking 786399 as yet unmatched pairs. 29491 records in RAM.
INFO 2026-06-08 08:20:47 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr2:112,389,779
INFO 2026-06-08 08:20:47 MarkDuplicates Tracking 784191 as yet unmatched pairs. 27260 records in RAM.
INFO 2026-06-08 08:20:49 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr2:130,931,027
INFO 2026-06-08 08:20:49 MarkDuplicates Tracking 782337 as yet unmatched pairs. 25384 records in RAM.
INFO 2026-06-08 08:20:51 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr2:158,621,081
INFO 2026-06-08 08:20:51 MarkDuplicates Tracking 779926 as yet unmatched pairs. 22946 records in RAM.
INFO 2026-06-08 08:20:53 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr2:177,222,539
INFO 2026-06-08 08:20:53 MarkDuplicates Tracking 777990 as yet unmatched pairs. 20988 records in RAM.
INFO 2026-06-08 08:20:54 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:195,708,672
INFO 2026-06-08 08:20:54 MarkDuplicates Tracking 775260 as yet unmatched pairs. 18219 records in RAM.
INFO 2026-06-08 08:20:56 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr2:208,248,378
INFO 2026-06-08 08:20:56 MarkDuplicates Tracking 772835 as yet unmatched pairs. 15637 records in RAM.
INFO 2026-06-08 08:20:57 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr2:215,379,258
INFO 2026-06-08 08:20:57 MarkDuplicates Tracking 771923 as yet unmatched pairs. 14707 records in RAM.
INFO 2026-06-08 08:20:59 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:215,435,672
INFO 2026-06-08 08:20:59 MarkDuplicates Tracking 770746 as yet unmatched pairs. 13514 records in RAM.
INFO 2026-06-08 08:21:00 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:219,172,784
INFO 2026-06-08 08:21:00 MarkDuplicates Tracking 764969 as yet unmatched pairs. 7651 records in RAM.
INFO 2026-06-08 08:21:02 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:227,347,319
INFO 2026-06-08 08:21:02 MarkDuplicates Tracking 761890 as yet unmatched pairs. 4540 records in RAM.
INFO 2026-06-08 08:21:03 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:238,184,047
INFO 2026-06-08 08:21:03 MarkDuplicates Tracking 759462 as yet unmatched pairs. 2065 records in RAM.
INFO 2026-06-08 08:21:05 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr3:8,990,729
INFO 2026-06-08 08:21:05 MarkDuplicates Tracking 756951 as yet unmatched pairs. 36343 records in RAM.
INFO 2026-06-08 08:21:07 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr3:12,839,456
INFO 2026-06-08 08:21:07 MarkDuplicates Tracking 755127 as yet unmatched pairs. 34441 records in RAM.
INFO 2026-06-08 08:21:09 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr3:37,050,549
INFO 2026-06-08 08:21:09 MarkDuplicates Tracking 751998 as yet unmatched pairs. 31268 records in RAM.
INFO 2026-06-08 08:21:10 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr3:46,436,134
INFO 2026-06-08 08:21:10 MarkDuplicates Tracking 749384 as yet unmatched pairs. 28622 records in RAM.
INFO 2026-06-08 08:21:12 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr3:48,418,222
INFO 2026-06-08 08:21:12 MarkDuplicates Tracking 746906 as yet unmatched pairs. 26103 records in RAM.
INFO 2026-06-08 08:21:14 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr3:49,357,414
INFO 2026-06-08 08:21:14 MarkDuplicates Tracking 744290 as yet unmatched pairs. 23458 records in RAM.
INFO 2026-06-08 08:21:16 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr3:51,969,553
INFO 2026-06-08 08:21:16 MarkDuplicates Tracking 741004 as yet unmatched pairs. 20168 records in RAM.
INFO 2026-06-08 08:21:18 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr3:62,267,711
INFO 2026-06-08 08:21:18 MarkDuplicates Tracking 738703 as yet unmatched pairs. 17851 records in RAM.
INFO 2026-06-08 08:21:19 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr3:101,681,148
INFO 2026-06-08 08:21:19 MarkDuplicates Tracking 737064 as yet unmatched pairs. 16159 records in RAM.
INFO 2026-06-08 08:21:21 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr3:122,718,643
INFO 2026-06-08 08:21:21 MarkDuplicates Tracking 734371 as yet unmatched pairs. 13413 records in RAM.
INFO 2026-06-08 08:21:23 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr3:129,393,289
INFO 2026-06-08 08:21:23 MarkDuplicates Tracking 731846 as yet unmatched pairs. 10798 records in RAM.
INFO 2026-06-08 08:21:25 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr3:148,986,655
INFO 2026-06-08 08:21:25 MarkDuplicates Tracking 729403 as yet unmatched pairs. 8302 records in RAM.
INFO 2026-06-08 08:21:26 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr3:171,110,781
INFO 2026-06-08 08:21:26 MarkDuplicates Tracking 727339 as yet unmatched pairs. 6184 records in RAM.
INFO 2026-06-08 08:21:28 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr3:184,321,652
INFO 2026-06-08 08:21:28 MarkDuplicates Tracking 724964 as yet unmatched pairs. 3749 records in RAM.
INFO 2026-06-08 08:21:30 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr3:194,137,844
INFO 2026-06-08 08:21:30 MarkDuplicates Tracking 722820 as yet unmatched pairs. 1521 records in RAM.
INFO 2026-06-08 08:21:32 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr4:1,236,641
INFO 2026-06-08 08:21:32 MarkDuplicates Tracking 720704 as yet unmatched pairs. 21425 records in RAM.
INFO 2026-06-08 08:21:33 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr4:2,066,975
INFO 2026-06-08 08:21:33 MarkDuplicates Tracking 717611 as yet unmatched pairs. 18314 records in RAM.
INFO 2026-06-08 08:21:35 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr4:8,475,824
INFO 2026-06-08 08:21:35 MarkDuplicates Tracking 715046 as yet unmatched pairs. 15746 records in RAM.
INFO 2026-06-08 08:21:37 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr4:47,031,607
INFO 2026-06-08 08:21:37 MarkDuplicates Tracking 712470 as yet unmatched pairs. 13076 records in RAM.
INFO 2026-06-08 08:21:39 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr4:73,085,425
INFO 2026-06-08 08:21:39 MarkDuplicates Tracking 710368 as yet unmatched pairs. 10812 records in RAM.
INFO 2026-06-08 08:21:40 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr4:86,772,384
INFO 2026-06-08 08:21:40 MarkDuplicates Tracking 708000 as yet unmatched pairs. 8438 records in RAM.
INFO 2026-06-08 08:21:42 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr4:109,530,338
INFO 2026-06-08 08:21:42 MarkDuplicates Tracking 705669 as yet unmatched pairs. 6104 records in RAM.
INFO 2026-06-08 08:21:43 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr4:143,468,969
INFO 2026-06-08 08:21:43 MarkDuplicates Tracking 703508 as yet unmatched pairs. 3936 records in RAM.
INFO 2026-06-08 08:21:45 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr4:175,635,002
INFO 2026-06-08 08:21:45 MarkDuplicates Tracking 701113 as yet unmatched pairs. 1517 records in RAM.
INFO 2026-06-08 08:21:47 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr5:10,415,503
INFO 2026-06-08 08:21:47 MarkDuplicates Tracking 698356 as yet unmatched pairs. 40082 records in RAM.
INFO 2026-06-08 08:21:48 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr5:14,487,679
INFO 2026-06-08 08:21:48 MarkDuplicates Tracking 696684 as yet unmatched pairs. 38349 records in RAM.
INFO 2026-06-08 08:21:50 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr5:32,101,116
INFO 2026-06-08 08:21:50 MarkDuplicates Tracking 692169 as yet unmatched pairs. 33806 records in RAM.
INFO 2026-06-08 08:21:52 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr5:55,344,549
INFO 2026-06-08 08:21:52 MarkDuplicates Tracking 690074 as yet unmatched pairs. 31685 records in RAM.
INFO 2026-06-08 08:21:53 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr5:72,196,006
INFO 2026-06-08 08:21:53 MarkDuplicates Tracking 688166 as yet unmatched pairs. 29756 records in RAM.
INFO 2026-06-08 08:21:55 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr5:83,541,265
INFO 2026-06-08 08:21:55 MarkDuplicates Tracking 685840 as yet unmatched pairs. 27390 records in RAM.
INFO 2026-06-08 08:21:57 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr5:113,053,947
INFO 2026-06-08 08:21:57 MarkDuplicates Tracking 683560 as yet unmatched pairs. 25075 records in RAM.
INFO 2026-06-08 08:21:58 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr5:134,157,710
INFO 2026-06-08 08:21:58 MarkDuplicates Tracking 681459 as yet unmatched pairs. 22917 records in RAM.
INFO 2026-06-08 08:22:00 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr5:139,680,474
INFO 2026-06-08 08:22:00 MarkDuplicates Tracking 678959 as yet unmatched pairs. 20415 records in RAM.
INFO 2026-06-08 08:22:01 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr5:141,178,632
INFO 2026-06-08 08:22:01 MarkDuplicates Tracking 676713 as yet unmatched pairs. 18112 records in RAM.
INFO 2026-06-08 08:22:03 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr5:141,389,941
INFO 2026-06-08 08:22:03 MarkDuplicates Tracking 674901 as yet unmatched pairs. 16250 records in RAM.
INFO 2026-06-08 08:22:04 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr5:141,864,855
INFO 2026-06-08 08:22:04 MarkDuplicates Tracking 671613 as yet unmatched pairs. 12886 records in RAM.
INFO 2026-06-08 08:22:06 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr5:150,115,859
INFO 2026-06-08 08:22:06 MarkDuplicates Tracking 669171 as yet unmatched pairs. 10389 records in RAM.
INFO 2026-06-08 08:22:07 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr5:151,671,645
INFO 2026-06-08 08:22:07 MarkDuplicates Tracking 666599 as yet unmatched pairs. 7810 records in RAM.
INFO 2026-06-08 08:22:09 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr5:172,234,228
INFO 2026-06-08 08:22:09 MarkDuplicates Tracking 663961 as yet unmatched pairs. 5106 records in RAM.
INFO 2026-06-08 08:22:10 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr5:179,616,125
INFO 2026-06-08 08:22:10 MarkDuplicates Tracking 661659 as yet unmatched pairs. 2752 records in RAM.
INFO 2026-06-08 08:22:12 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr6:144,530
INFO 2026-06-08 08:22:12 MarkDuplicates Tracking 658922 as yet unmatched pairs. 37320 records in RAM.
INFO 2026-06-08 08:22:14 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr6:7,297,952
INFO 2026-06-08 08:22:14 MarkDuplicates Tracking 656989 as yet unmatched pairs. 35321 records in RAM.
INFO 2026-06-08 08:22:16 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr6:26,217,051
INFO 2026-06-08 08:22:16 MarkDuplicates Tracking 654480 as yet unmatched pairs. 32799 records in RAM.
INFO 2026-06-08 08:22:17 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr6:30,622,831
INFO 2026-06-08 08:22:17 MarkDuplicates Tracking 651967 as yet unmatched pairs. 30250 records in RAM.
INFO 2026-06-08 08:22:19 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr6:31,540,409
INFO 2026-06-08 08:22:19 MarkDuplicates Tracking 649725 as yet unmatched pairs. 27963 records in RAM.
INFO 2026-06-08 08:22:22 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr6:31,829,476
INFO 2026-06-08 08:22:22 MarkDuplicates Tracking 647419 as yet unmatched pairs. 25649 records in RAM.
INFO 2026-06-08 08:22:23 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr6:32,974,715
INFO 2026-06-08 08:22:23 MarkDuplicates Tracking 644871 as yet unmatched pairs. 23071 records in RAM.
INFO 2026-06-08 08:22:25 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr6:35,576,993
INFO 2026-06-08 08:22:25 MarkDuplicates Tracking 642404 as yet unmatched pairs. 20571 records in RAM.
INFO 2026-06-08 08:22:26 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr6:43,305,861
INFO 2026-06-08 08:22:26 MarkDuplicates Tracking 639564 as yet unmatched pairs. 17627 records in RAM.
INFO 2026-06-08 08:22:28 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr6:56,593,965
INFO 2026-06-08 08:22:28 MarkDuplicates Tracking 637218 as yet unmatched pairs. 15262 records in RAM.
INFO 2026-06-08 08:22:30 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr6:88,142,052
INFO 2026-06-08 08:22:30 MarkDuplicates Tracking 635168 as yet unmatched pairs. 13166 records in RAM.
INFO 2026-06-08 08:22:31 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr6:110,209,202
INFO 2026-06-08 08:22:31 MarkDuplicates Tracking 632099 as yet unmatched pairs. 10096 records in RAM.
INFO 2026-06-08 08:22:33 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr6:130,869,812
INFO 2026-06-08 08:22:33 MarkDuplicates Tracking 629944 as yet unmatched pairs. 7922 records in RAM.
INFO 2026-06-08 08:22:34 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr6:151,348,728
INFO 2026-06-08 08:22:34 MarkDuplicates Tracking 628048 as yet unmatched pairs. 5982 records in RAM.
INFO 2026-06-08 08:22:36 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr6:158,785,515
INFO 2026-06-08 08:22:36 MarkDuplicates Tracking 624956 as yet unmatched pairs. 2879 records in RAM.
INFO 2026-06-08 08:22:38 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr6:169,668,628
INFO 2026-06-08 08:22:38 MarkDuplicates Tracking 622483 as yet unmatched pairs. 397 records in RAM.
INFO 2026-06-08 08:22:40 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr7:2,540,995
INFO 2026-06-08 08:22:40 MarkDuplicates Tracking 619507 as yet unmatched pairs. 104069 records in RAM.
INFO 2026-06-08 08:22:42 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr7:5,362,686
INFO 2026-06-08 08:22:42 MarkDuplicates Tracking 616755 as yet unmatched pairs. 101315 records in RAM.
INFO 2026-06-08 08:22:44 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,267
INFO 2026-06-08 08:22:44 MarkDuplicates Tracking 616351 as yet unmatched pairs. 100904 records in RAM.
INFO 2026-06-08 08:22:45 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr7:13,906,468
INFO 2026-06-08 08:22:45 MarkDuplicates Tracking 612418 as yet unmatched pairs. 96931 records in RAM.
INFO 2026-06-08 08:22:47 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr7:26,197,001
INFO 2026-06-08 08:22:47 MarkDuplicates Tracking 609756 as yet unmatched pairs. 94233 records in RAM.
INFO 2026-06-08 08:22:49 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr7:39,997,519
INFO 2026-06-08 08:22:49 MarkDuplicates Tracking 606351 as yet unmatched pairs. 90806 records in RAM.
INFO 2026-06-08 08:22:50 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr7:43,987,700
INFO 2026-06-08 08:22:50 MarkDuplicates Tracking 604650 as yet unmatched pairs. 89077 records in RAM.
INFO 2026-06-08 08:22:52 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr7:44,014,442
INFO 2026-06-08 08:22:52 MarkDuplicates Tracking 604195 as yet unmatched pairs. 88589 records in RAM.
INFO 2026-06-08 08:22:54 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr7:44,058,916
INFO 2026-06-08 08:22:54 MarkDuplicates Tracking 604849 as yet unmatched pairs. 89243 records in RAM.
INFO 2026-06-08 08:22:56 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr7:44,079,574
INFO 2026-06-08 08:22:56 MarkDuplicates Tracking 598558 as yet unmatched pairs. 82909 records in RAM.
INFO 2026-06-08 08:22:58 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr7:44,108,065
INFO 2026-06-08 08:22:58 MarkDuplicates Tracking 596954 as yet unmatched pairs. 81302 records in RAM.
INFO 2026-06-08 08:23:00 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: chr7:44,112,032
INFO 2026-06-08 08:23:00 MarkDuplicates Tracking 595072 as yet unmatched pairs. 79415 records in RAM.
INFO 2026-06-08 08:23:02 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr7:44,114,014
INFO 2026-06-08 08:23:02 MarkDuplicates Tracking 593922 as yet unmatched pairs. 78231 records in RAM.
INFO 2026-06-08 08:23:03 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr7:44,115,873
INFO 2026-06-08 08:23:03 MarkDuplicates Tracking 598661 as yet unmatched pairs. 82948 records in RAM.
INFO 2026-06-08 08:23:05 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr7:44,117,167
INFO 2026-06-08 08:23:05 MarkDuplicates Tracking 589007 as yet unmatched pairs. 73282 records in RAM.
INFO 2026-06-08 08:23:07 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr7:44,696,968
INFO 2026-06-08 08:23:07 MarkDuplicates Tracking 581854 as yet unmatched pairs. 66126 records in RAM.
INFO 2026-06-08 08:23:08 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr7:55,019,230
INFO 2026-06-08 08:23:08 MarkDuplicates Tracking 589439 as yet unmatched pairs. 73700 records in RAM.
INFO 2026-06-08 08:23:10 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr7:55,151,293
INFO 2026-06-08 08:23:10 MarkDuplicates Tracking 581439 as yet unmatched pairs. 65691 records in RAM.
INFO 2026-06-08 08:23:12 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr7:55,160,323
INFO 2026-06-08 08:23:12 MarkDuplicates Tracking 577469 as yet unmatched pairs. 61721 records in RAM.
INFO 2026-06-08 08:23:13 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr7:55,165,386
INFO 2026-06-08 08:23:13 MarkDuplicates Tracking 577917 as yet unmatched pairs. 62166 records in RAM.
INFO 2026-06-08 08:23:15 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr7:55,181,404
INFO 2026-06-08 08:23:15 MarkDuplicates Tracking 574178 as yet unmatched pairs. 58407 records in RAM.
INFO 2026-06-08 08:23:17 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr7:55,200,346
INFO 2026-06-08 08:23:17 MarkDuplicates Tracking 582800 as yet unmatched pairs. 67017 records in RAM.
INFO 2026-06-08 08:23:18 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr7:55,202,541
INFO 2026-06-08 08:23:18 MarkDuplicates Tracking 587210 as yet unmatched pairs. 71427 records in RAM.
INFO 2026-06-08 08:23:20 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr7:55,205,411
INFO 2026-06-08 08:23:20 MarkDuplicates Tracking 573395 as yet unmatched pairs. 57612 records in RAM.
INFO 2026-06-08 08:23:22 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr7:72,925,565
INFO 2026-06-08 08:23:22 MarkDuplicates Tracking 558855 as yet unmatched pairs. 43061 records in RAM.
INFO 2026-06-08 08:23:24 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr7:73,301,120
INFO 2026-06-08 08:23:24 MarkDuplicates Tracking 557972 as yet unmatched pairs. 42155 records in RAM.
INFO 2026-06-08 08:23:25 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr7:74,909,399
INFO 2026-06-08 08:23:25 MarkDuplicates Tracking 555533 as yet unmatched pairs. 39708 records in RAM.
INFO 2026-06-08 08:23:27 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr7:75,557,663
INFO 2026-06-08 08:23:27 MarkDuplicates Tracking 554130 as yet unmatched pairs. 38304 records in RAM.
INFO 2026-06-08 08:23:29 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr7:88,206,405
INFO 2026-06-08 08:23:29 MarkDuplicates Tracking 552838 as yet unmatched pairs. 37012 records in RAM.
INFO 2026-06-08 08:23:31 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr7:98,281,875
INFO 2026-06-08 08:23:31 MarkDuplicates Tracking 549913 as yet unmatched pairs. 34068 records in RAM.
INFO 2026-06-08 08:23:32 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr7:100,313,161
INFO 2026-06-08 08:23:32 MarkDuplicates Tracking 547496 as yet unmatched pairs. 31619 records in RAM.
INFO 2026-06-08 08:23:34 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr7:101,216,186
INFO 2026-06-08 08:23:34 MarkDuplicates Tracking 544695 as yet unmatched pairs. 28780 records in RAM.
INFO 2026-06-08 08:23:35 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr7:102,555,819
INFO 2026-06-08 08:23:35 MarkDuplicates Tracking 543537 as yet unmatched pairs. 27619 records in RAM.
INFO 2026-06-08 08:23:36 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr7:102,667,111
INFO 2026-06-08 08:23:36 MarkDuplicates Tracking 542510 as yet unmatched pairs. 26576 records in RAM.
INFO 2026-06-08 08:23:38 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr7:117,724,644
INFO 2026-06-08 08:23:38 MarkDuplicates Tracking 540274 as yet unmatched pairs. 24306 records in RAM.
INFO 2026-06-08 08:23:39 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr7:121,997,892
INFO 2026-06-08 08:23:39 MarkDuplicates Tracking 544081 as yet unmatched pairs. 28112 records in RAM.
INFO 2026-06-08 08:23:41 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr7:122,011,345
INFO 2026-06-08 08:23:41 MarkDuplicates Tracking 543508 as yet unmatched pairs. 27478 records in RAM.
INFO 2026-06-08 08:23:43 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr7:122,028,609
INFO 2026-06-08 08:23:43 MarkDuplicates Tracking 539561 as yet unmatched pairs. 23531 records in RAM.
INFO 2026-06-08 08:23:44 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr7:122,051,441
INFO 2026-06-08 08:23:44 MarkDuplicates Tracking 546236 as yet unmatched pairs. 30189 records in RAM.
INFO 2026-06-08 08:23:46 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr7:127,701,164
INFO 2026-06-08 08:23:46 MarkDuplicates Tracking 530062 as yet unmatched pairs. 13984 records in RAM.
INFO 2026-06-08 08:23:48 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr7:134,960,556
INFO 2026-06-08 08:23:48 MarkDuplicates Tracking 527052 as yet unmatched pairs. 10950 records in RAM.
INFO 2026-06-08 08:23:49 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr7:139,376,128
INFO 2026-06-08 08:23:49 MarkDuplicates Tracking 524805 as yet unmatched pairs. 8702 records in RAM.
INFO 2026-06-08 08:23:51 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr7:143,382,970
INFO 2026-06-08 08:23:51 MarkDuplicates Tracking 523554 as yet unmatched pairs. 7386 records in RAM.
INFO 2026-06-08 08:23:53 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr7:151,033,646
INFO 2026-06-08 08:23:53 MarkDuplicates Tracking 519630 as yet unmatched pairs. 3439 records in RAM.
INFO 2026-06-08 08:23:55 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr7:155,745,499
INFO 2026-06-08 08:23:55 MarkDuplicates Tracking 516805 as yet unmatched pairs. 590 records in RAM.
INFO 2026-06-08 08:23:56 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr8:17,280,419
INFO 2026-06-08 08:23:56 MarkDuplicates Tracking 514462 as yet unmatched pairs. 23582 records in RAM.
INFO 2026-06-08 08:23:59 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr8:26,508,566
INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 511760 as yet unmatched pairs. 20849 records in RAM.
INFO 2026-06-08 08:24:01 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chr8:37,697,879
INFO 2026-06-08 08:24:01 MarkDuplicates Tracking 509421 as yet unmatched pairs. 18490 records in RAM.
INFO 2026-06-08 08:24:02 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr8:43,122,167
INFO 2026-06-08 08:24:02 MarkDuplicates Tracking 506799 as yet unmatched pairs. 15847 records in RAM.
INFO 2026-06-08 08:24:04 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr8:70,128,892
INFO 2026-06-08 08:24:04 MarkDuplicates Tracking 504197 as yet unmatched pairs. 13242 records in RAM.
INFO 2026-06-08 08:24:06 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr8:99,156,608
INFO 2026-06-08 08:24:06 MarkDuplicates Tracking 501889 as yet unmatched pairs. 10918 records in RAM.
INFO 2026-06-08 08:24:07 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr8:127,736,334
INFO 2026-06-08 08:24:07 MarkDuplicates Tracking 499627 as yet unmatched pairs. 8609 records in RAM.
INFO 2026-06-08 08:24:09 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr8:143,380,563
INFO 2026-06-08 08:24:09 MarkDuplicates Tracking 496792 as yet unmatched pairs. 5736 records in RAM.
INFO 2026-06-08 08:24:10 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr8:144,082,733
INFO 2026-06-08 08:24:10 MarkDuplicates Tracking 493883 as yet unmatched pairs. 2791 records in RAM.
INFO 2026-06-08 08:24:12 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr9:3,277,422
INFO 2026-06-08 08:24:12 MarkDuplicates Tracking 490705 as yet unmatched pairs. 27224 records in RAM.
INFO 2026-06-08 08:24:14 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr9:35,091,243
INFO 2026-06-08 08:24:14 MarkDuplicates Tracking 488697 as yet unmatched pairs. 25127 records in RAM.
INFO 2026-06-08 08:24:16 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr9:79,627,372
INFO 2026-06-08 08:24:16 MarkDuplicates Tracking 486640 as yet unmatched pairs. 23051 records in RAM.
INFO 2026-06-08 08:24:17 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr9:93,556,511
INFO 2026-06-08 08:24:17 MarkDuplicates Tracking 484332 as yet unmatched pairs. 20712 records in RAM.
INFO 2026-06-08 08:24:19 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr9:111,444,440
INFO 2026-06-08 08:24:19 MarkDuplicates Tracking 481812 as yet unmatched pairs. 18187 records in RAM.
INFO 2026-06-08 08:24:20 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr9:121,328,942
INFO 2026-06-08 08:24:20 MarkDuplicates Tracking 479444 as yet unmatched pairs. 15790 records in RAM.
INFO 2026-06-08 08:24:22 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr9:128,166,260
INFO 2026-06-08 08:24:22 MarkDuplicates Tracking 477035 as yet unmatched pairs. 13355 records in RAM.
INFO 2026-06-08 08:24:23 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr9:130,048,186
INFO 2026-06-08 08:24:23 MarkDuplicates Tracking 474357 as yet unmatched pairs. 10653 records in RAM.
INFO 2026-06-08 08:24:26 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr9:132,677,977
INFO 2026-06-08 08:24:26 MarkDuplicates Tracking 472141 as yet unmatched pairs. 8429 records in RAM.
INFO 2026-06-08 08:24:27 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr9:136,438,924
INFO 2026-06-08 08:24:27 MarkDuplicates Tracking 469466 as yet unmatched pairs. 5751 records in RAM.
INFO 2026-06-08 08:24:29 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr9:136,925,806
INFO 2026-06-08 08:24:29 MarkDuplicates Tracking 466305 as yet unmatched pairs. 2580 records in RAM.
INFO 2026-06-08 08:24:31 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr10:3,109,375
INFO 2026-06-08 08:24:31 MarkDuplicates Tracking 463586 as yet unmatched pairs. 14277 records in RAM.
INFO 2026-06-08 08:24:33 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr10:25,598,533
INFO 2026-06-08 08:24:33 MarkDuplicates Tracking 460976 as yet unmatched pairs. 11667 records in RAM.
INFO 2026-06-08 08:24:35 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr10:50,008,791
INFO 2026-06-08 08:24:35 MarkDuplicates Tracking 459141 as yet unmatched pairs. 9805 records in RAM.
INFO 2026-06-08 08:24:36 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr10:74,977,346
INFO 2026-06-08 08:24:36 MarkDuplicates Tracking 456506 as yet unmatched pairs. 7166 records in RAM.
INFO 2026-06-08 08:24:38 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr10:95,414,632
INFO 2026-06-08 08:24:38 MarkDuplicates Tracking 454301 as yet unmatched pairs. 4943 records in RAM.
INFO 2026-06-08 08:24:40 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr10:110,118,699
INFO 2026-06-08 08:24:40 MarkDuplicates Tracking 451614 as yet unmatched pairs. 2249 records in RAM.
INFO 2026-06-08 08:24:41 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr10:133,459,064
INFO 2026-06-08 08:24:41 MarkDuplicates Tracking 449504 as yet unmatched pairs. 120 records in RAM.
INFO 2026-06-08 08:24:43 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr11:1,753,820
INFO 2026-06-08 08:24:43 MarkDuplicates Tracking 446729 as yet unmatched pairs. 41826 records in RAM.
INFO 2026-06-08 08:24:45 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr11:6,640,255
INFO 2026-06-08 08:24:45 MarkDuplicates Tracking 443951 as yet unmatched pairs. 39047 records in RAM.
INFO 2026-06-08 08:24:47 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr11:17,145,680
INFO 2026-06-08 08:24:47 MarkDuplicates Tracking 441297 as yet unmatched pairs. 36388 records in RAM.
INFO 2026-06-08 08:24:48 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr11:35,618,661
INFO 2026-06-08 08:24:48 MarkDuplicates Tracking 438885 as yet unmatched pairs. 33964 records in RAM.
INFO 2026-06-08 08:24:50 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr11:47,165,445
INFO 2026-06-08 08:24:50 MarkDuplicates Tracking 436249 as yet unmatched pairs. 31311 records in RAM.
INFO 2026-06-08 08:24:52 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr11:60,936,096
INFO 2026-06-08 08:24:52 MarkDuplicates Tracking 434036 as yet unmatched pairs. 29097 records in RAM.
INFO 2026-06-08 08:24:53 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr11:62,647,606
INFO 2026-06-08 08:24:53 MarkDuplicates Tracking 431451 as yet unmatched pairs. 26509 records in RAM.
INFO 2026-06-08 08:24:54 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr11:64,767,619
INFO 2026-06-08 08:24:54 MarkDuplicates Tracking 429012 as yet unmatched pairs. 24041 records in RAM.
INFO 2026-06-08 08:24:57 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr11:65,650,637
INFO 2026-06-08 08:24:57 MarkDuplicates Tracking 425262 as yet unmatched pairs. 20262 records in RAM.
INFO 2026-06-08 08:24:59 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr11:66,857,894
INFO 2026-06-08 08:24:59 MarkDuplicates Tracking 422813 as yet unmatched pairs. 17778 records in RAM.
INFO 2026-06-08 08:25:00 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr11:72,004,241
INFO 2026-06-08 08:25:00 MarkDuplicates Tracking 420192 as yet unmatched pairs. 15142 records in RAM.
INFO 2026-06-08 08:25:03 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr11:75,608,188
INFO 2026-06-08 08:25:03 MarkDuplicates Tracking 417749 as yet unmatched pairs. 12681 records in RAM.
INFO 2026-06-08 08:25:04 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr11:93,687,668
INFO 2026-06-08 08:25:04 MarkDuplicates Tracking 414898 as yet unmatched pairs. 9830 records in RAM.
INFO 2026-06-08 08:25:06 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr11:113,255,922
INFO 2026-06-08 08:25:06 MarkDuplicates Tracking 413023 as yet unmatched pairs. 7929 records in RAM.
INFO 2026-06-08 08:25:07 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr11:118,645,487
INFO 2026-06-08 08:25:07 MarkDuplicates Tracking 410242 as yet unmatched pairs. 5140 records in RAM.
INFO 2026-06-08 08:25:09 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr11:124,919,652
INFO 2026-06-08 08:25:09 MarkDuplicates Tracking 408438 as yet unmatched pairs. 3328 records in RAM.
INFO 2026-06-08 08:25:11 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr12:753,530
INFO 2026-06-08 08:25:11 MarkDuplicates Tracking 405426 as yet unmatched pairs. 41114 records in RAM.
INFO 2026-06-08 08:25:12 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr12:6,587,775
INFO 2026-06-08 08:25:12 MarkDuplicates Tracking 402266 as yet unmatched pairs. 37939 records in RAM.
INFO 2026-06-08 08:25:14 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr12:8,773,405
INFO 2026-06-08 08:25:14 MarkDuplicates Tracking 399814 as yet unmatched pairs. 35476 records in RAM.
INFO 2026-06-08 08:25:16 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr12:26,065,060
INFO 2026-06-08 08:25:16 MarkDuplicates Tracking 397424 as yet unmatched pairs. 33081 records in RAM.
INFO 2026-06-08 08:25:17 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr12:48,834,328
INFO 2026-06-08 08:25:17 MarkDuplicates Tracking 394884 as yet unmatched pairs. 30536 records in RAM.
INFO 2026-06-08 08:25:19 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr12:49,185,530
INFO 2026-06-08 08:25:19 MarkDuplicates Tracking 393137 as yet unmatched pairs. 28785 records in RAM.
INFO 2026-06-08 08:25:20 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr12:53,027,854
INFO 2026-06-08 08:25:20 MarkDuplicates Tracking 390160 as yet unmatched pairs. 25799 records in RAM.
INFO 2026-06-08 08:25:22 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr12:55,683,944
INFO 2026-06-08 08:25:22 MarkDuplicates Tracking 388550 as yet unmatched pairs. 24189 records in RAM.
INFO 2026-06-08 08:25:24 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr12:56,327,380
INFO 2026-06-08 08:25:24 MarkDuplicates Tracking 385662 as yet unmatched pairs. 21295 records in RAM.
INFO 2026-06-08 08:25:25 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr12:57,173,167
INFO 2026-06-08 08:25:25 MarkDuplicates Tracking 383853 as yet unmatched pairs. 19485 records in RAM.
INFO 2026-06-08 08:25:27 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr12:57,234,002
INFO 2026-06-08 08:25:27 MarkDuplicates Tracking 380280 as yet unmatched pairs. 15908 records in RAM.
INFO 2026-06-08 08:25:29 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr12:71,636,846
INFO 2026-06-08 08:25:29 MarkDuplicates Tracking 378007 as yet unmatched pairs. 13620 records in RAM.
INFO 2026-06-08 08:25:31 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: chr12:101,383,267
INFO 2026-06-08 08:25:31 MarkDuplicates Tracking 375310 as yet unmatched pairs. 10920 records in RAM.
INFO 2026-06-08 08:25:32 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr12:111,581,429
INFO 2026-06-08 08:25:32 MarkDuplicates Tracking 373115 as yet unmatched pairs. 8697 records in RAM.
INFO 2026-06-08 08:25:34 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr12:120,197,468
INFO 2026-06-08 08:25:34 MarkDuplicates Tracking 370709 as yet unmatched pairs. 6289 records in RAM.
INFO 2026-06-08 08:25:36 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 2s. Last read position: chr12:123,423,042
INFO 2026-06-08 08:25:36 MarkDuplicates Tracking 367633 as yet unmatched pairs. 3193 records in RAM.
INFO 2026-06-08 08:25:38 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr12:132,569,963
INFO 2026-06-08 08:25:38 MarkDuplicates Tracking 365463 as yet unmatched pairs. 988 records in RAM.
INFO 2026-06-08 08:25:40 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr13:25,171,094
INFO 2026-06-08 08:25:40 MarkDuplicates Tracking 363093 as yet unmatched pairs. 11587 records in RAM.
INFO 2026-06-08 08:25:41 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr13:42,303,436
INFO 2026-06-08 08:25:41 MarkDuplicates Tracking 360337 as yet unmatched pairs. 8806 records in RAM.
INFO 2026-06-08 08:25:43 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr13:67,228,296
INFO 2026-06-08 08:25:43 MarkDuplicates Tracking 358141 as yet unmatched pairs. 6603 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr13:109,782,957
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 356166 as yet unmatched pairs. 4598 records in RAM.
INFO 2026-06-08 08:25:46 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr13:112,690,405
INFO 2026-06-08 08:25:46 MarkDuplicates Tracking 352389 as yet unmatched pairs. 815 records in RAM.
INFO 2026-06-08 08:25:48 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr14:21,522,842
INFO 2026-06-08 08:25:48 MarkDuplicates Tracking 350234 as yet unmatched pairs. 21512 records in RAM.
INFO 2026-06-08 08:25:50 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr14:24,240,237
INFO 2026-06-08 08:25:50 MarkDuplicates Tracking 347324 as yet unmatched pairs. 18577 records in RAM.
INFO 2026-06-08 08:25:51 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr14:35,627,916
INFO 2026-06-08 08:25:51 MarkDuplicates Tracking 344600 as yet unmatched pairs. 15824 records in RAM.
INFO 2026-06-08 08:25:53 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr14:58,131,511
INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 342145 as yet unmatched pairs. 13262 records in RAM.
INFO 2026-06-08 08:25:55 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr14:69,053,955
INFO 2026-06-08 08:25:55 MarkDuplicates Tracking 340014 as yet unmatched pairs. 11120 records in RAM.
INFO 2026-06-08 08:25:56 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr14:74,809,455
INFO 2026-06-08 08:25:56 MarkDuplicates Tracking 337760 as yet unmatched pairs. 8843 records in RAM.
INFO 2026-06-08 08:25:57 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr14:92,706,614
INFO 2026-06-08 08:25:57 MarkDuplicates Tracking 335141 as yet unmatched pairs. 6172 records in RAM.
INFO 2026-06-08 08:26:00 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 2s. Last read position: chr14:102,209,393
INFO 2026-06-08 08:26:00 MarkDuplicates Tracking 332474 as yet unmatched pairs. 3492 records in RAM.
INFO 2026-06-08 08:26:01 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr14:105,463,206
INFO 2026-06-08 08:26:01 MarkDuplicates Tracking 329428 as yet unmatched pairs. 445 records in RAM.
INFO 2026-06-08 08:26:03 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr15:29,762,351
INFO 2026-06-08 08:26:03 MarkDuplicates Tracking 327708 as yet unmatched pairs. 21718 records in RAM.
INFO 2026-06-08 08:26:05 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr15:39,594,319
INFO 2026-06-08 08:26:05 MarkDuplicates Tracking 325410 as yet unmatched pairs. 19420 records in RAM.
INFO 2026-06-08 08:26:07 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr15:43,329,952
INFO 2026-06-08 08:26:07 MarkDuplicates Tracking 322746 as yet unmatched pairs. 16753 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr15:50,300,789
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 320322 as yet unmatched pairs. 14310 records in RAM.
INFO 2026-06-08 08:26:11 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr15:61,925,485
INFO 2026-06-08 08:26:11 MarkDuplicates Tracking 318396 as yet unmatched pairs. 12380 records in RAM.
INFO 2026-06-08 08:26:12 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 1s. Last read position: chr15:69,455,198
INFO 2026-06-08 08:26:12 MarkDuplicates Tracking 316648 as yet unmatched pairs. 10630 records in RAM.
INFO 2026-06-08 08:26:14 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr15:75,639,566
INFO 2026-06-08 08:26:14 MarkDuplicates Tracking 312918 as yet unmatched pairs. 6886 records in RAM.
INFO 2026-06-08 08:26:15 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 1s. Last read position: chr15:84,669,950
INFO 2026-06-08 08:26:15 MarkDuplicates Tracking 310719 as yet unmatched pairs. 4686 records in RAM.
INFO 2026-06-08 08:26:17 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr15:90,441,581
INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 308062 as yet unmatched pairs. 2029 records in RAM.
INFO 2026-06-08 08:26:19 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 2s. Last read position: chr16:377,036
INFO 2026-06-08 08:26:19 MarkDuplicates Tracking 305751 as yet unmatched pairs. 46925 records in RAM.
INFO 2026-06-08 08:26:21 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr16:1,445,503
INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 301942 as yet unmatched pairs. 43091 records in RAM.
INFO 2026-06-08 08:26:22 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr16:2,108,860
INFO 2026-06-08 08:26:22 MarkDuplicates Tracking 299103 as yet unmatched pairs. 40246 records in RAM.
INFO 2026-06-08 08:26:24 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr16:2,763,710
INFO 2026-06-08 08:26:24 MarkDuplicates Tracking 295946 as yet unmatched pairs. 37089 records in RAM.
INFO 2026-06-08 08:26:25 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr16:3,977,538
INFO 2026-06-08 08:26:25 MarkDuplicates Tracking 293089 as yet unmatched pairs. 34232 records in RAM.
INFO 2026-06-08 08:26:27 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: chr16:14,725,919
INFO 2026-06-08 08:26:27 MarkDuplicates Tracking 290646 as yet unmatched pairs. 31781 records in RAM.
INFO 2026-06-08 08:26:28 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr16:15,363,909
INFO 2026-06-08 08:26:28 MarkDuplicates Tracking 289403 as yet unmatched pairs. 30538 records in RAM.
INFO 2026-06-08 08:26:30 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr16:16,374,659
INFO 2026-06-08 08:26:30 MarkDuplicates Tracking 288394 as yet unmatched pairs. 29529 records in RAM.
INFO 2026-06-08 08:26:31 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr16:18,424,360
INFO 2026-06-08 08:26:31 MarkDuplicates Tracking 287327 as yet unmatched pairs. 28460 records in RAM.
INFO 2026-06-08 08:26:33 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr16:21,406,667
INFO 2026-06-08 08:26:33 MarkDuplicates Tracking 285816 as yet unmatched pairs. 26948 records in RAM.
INFO 2026-06-08 08:26:34 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr16:22,533,635
INFO 2026-06-08 08:26:34 MarkDuplicates Tracking 284991 as yet unmatched pairs. 26121 records in RAM.
INFO 2026-06-08 08:26:36 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr16:27,740,690
INFO 2026-06-08 08:26:36 MarkDuplicates Tracking 283765 as yet unmatched pairs. 24895 records in RAM.
INFO 2026-06-08 08:26:38 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr16:29,453,491
INFO 2026-06-08 08:26:38 MarkDuplicates Tracking 282019 as yet unmatched pairs. 23149 records in RAM.
INFO 2026-06-08 08:27:38 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 59s. Last read position: chr16:30,095,388
INFO 2026-06-08 08:27:38 MarkDuplicates Tracking 279930 as yet unmatched pairs. 21040 records in RAM.
INFO 2026-06-08 08:27:39 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr16:30,738,969
INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 278362 as yet unmatched pairs. 19472 records in RAM.
INFO 2026-06-08 08:27:41 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr16:47,696,427
INFO 2026-06-08 08:27:41 MarkDuplicates Tracking 275731 as yet unmatched pairs. 16840 records in RAM.
INFO 2026-06-08 08:27:43 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr16:56,589,869
INFO 2026-06-08 08:27:43 MarkDuplicates Tracking 276982 as yet unmatched pairs. 18089 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr16:58,508,985
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 271209 as yet unmatched pairs. 12306 records in RAM.
INFO 2026-06-08 08:27:46 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr16:69,120,198
INFO 2026-06-08 08:27:46 MarkDuplicates Tracking 268165 as yet unmatched pairs. 9244 records in RAM.
INFO 2026-06-08 08:27:48 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr16:71,849,726
INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 265524 as yet unmatched pairs. 6603 records in RAM.
INFO 2026-06-08 08:27:49 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr16:84,183,454
INFO 2026-06-08 08:27:49 MarkDuplicates Tracking 263345 as yet unmatched pairs. 4423 records in RAM.
INFO 2026-06-08 08:27:51 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr16:89,560,956
INFO 2026-06-08 08:27:51 MarkDuplicates Tracking 260623 as yet unmatched pairs. 1698 records in RAM.
INFO 2026-06-08 08:27:53 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr17:1,661,617
INFO 2026-06-08 08:27:53 MarkDuplicates Tracking 257391 as yet unmatched pairs. 57690 records in RAM.
INFO 2026-06-08 08:27:55 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr17:4,944,886
INFO 2026-06-08 08:27:55 MarkDuplicates Tracking 255029 as yet unmatched pairs. 55328 records in RAM.
INFO 2026-06-08 08:27:56 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr17:7,415,691
INFO 2026-06-08 08:27:56 MarkDuplicates Tracking 252021 as yet unmatched pairs. 52313 records in RAM.
INFO 2026-06-08 08:27:58 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 2s. Last read position: chr17:7,902,940
INFO 2026-06-08 08:27:58 MarkDuplicates Tracking 249474 as yet unmatched pairs. 49766 records in RAM.
INFO 2026-06-08 08:28:00 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,137
INFO 2026-06-08 08:28:00 MarkDuplicates Tracking 247641 as yet unmatched pairs. 47912 records in RAM.
INFO 2026-06-08 08:28:02 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr17:19,416,076
INFO 2026-06-08 08:28:02 MarkDuplicates Tracking 244345 as yet unmatched pairs. 44596 records in RAM.
INFO 2026-06-08 08:28:03 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr17:28,759,399
INFO 2026-06-08 08:28:03 MarkDuplicates Tracking 242014 as yet unmatched pairs. 42265 records in RAM.
INFO 2026-06-08 08:28:05 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr17:35,608,271
INFO 2026-06-08 08:28:05 MarkDuplicates Tracking 239680 as yet unmatched pairs. 39929 records in RAM.
INFO 2026-06-08 08:28:06 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr17:38,712,743
INFO 2026-06-08 08:28:06 MarkDuplicates Tracking 237666 as yet unmatched pairs. 37903 records in RAM.
INFO 2026-06-08 08:28:07 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr17:40,404,200
INFO 2026-06-08 08:28:07 MarkDuplicates Tracking 235284 as yet unmatched pairs. 35521 records in RAM.
INFO 2026-06-08 08:28:09 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr17:43,095,846
INFO 2026-06-08 08:28:09 MarkDuplicates Tracking 232426 as yet unmatched pairs. 32662 records in RAM.
INFO 2026-06-08 08:28:10 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr17:44,911,372
INFO 2026-06-08 08:28:10 MarkDuplicates Tracking 231474 as yet unmatched pairs. 31697 records in RAM.
INFO 2026-06-08 08:28:12 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr17:46,330,518
INFO 2026-06-08 08:28:12 MarkDuplicates Tracking 227362 as yet unmatched pairs. 27585 records in RAM.
INFO 2026-06-08 08:28:14 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,718
INFO 2026-06-08 08:28:14 MarkDuplicates Tracking 225961 as yet unmatched pairs. 26168 records in RAM.
INFO 2026-06-08 08:28:15 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,408
INFO 2026-06-08 08:28:15 MarkDuplicates Tracking 223929 as yet unmatched pairs. 24135 records in RAM.
INFO 2026-06-08 08:28:17 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr17:50,990,493
INFO 2026-06-08 08:28:17 MarkDuplicates Tracking 219149 as yet unmatched pairs. 19355 records in RAM.
INFO 2026-06-08 08:28:18 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr17:59,693,763
INFO 2026-06-08 08:28:18 MarkDuplicates Tracking 216525 as yet unmatched pairs. 16701 records in RAM.
INFO 2026-06-08 08:28:20 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr17:64,749,880
INFO 2026-06-08 08:28:20 MarkDuplicates Tracking 213835 as yet unmatched pairs. 14011 records in RAM.
INFO 2026-06-08 08:28:22 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr17:73,227,183
INFO 2026-06-08 08:28:22 MarkDuplicates Tracking 211506 as yet unmatched pairs. 11682 records in RAM.
INFO 2026-06-08 08:28:23 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr17:75,923,265
INFO 2026-06-08 08:28:23 MarkDuplicates Tracking 208593 as yet unmatched pairs. 8766 records in RAM.
INFO 2026-06-08 08:28:25 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr17:78,997,483
INFO 2026-06-08 08:28:25 MarkDuplicates Tracking 205992 as yet unmatched pairs. 6162 records in RAM.
INFO 2026-06-08 08:28:26 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr17:81,696,637
INFO 2026-06-08 08:28:26 MarkDuplicates Tracking 203034 as yet unmatched pairs. 3203 records in RAM.
INFO 2026-06-08 08:28:28 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr18:158,593
INFO 2026-06-08 08:28:28 MarkDuplicates Tracking 199879 as yet unmatched pairs. 9961 records in RAM.
INFO 2026-06-08 08:28:30 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr18:26,032,419
INFO 2026-06-08 08:28:30 MarkDuplicates Tracking 197910 as yet unmatched pairs. 7983 records in RAM.
INFO 2026-06-08 08:28:32 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr18:44,701,386
INFO 2026-06-08 08:28:32 MarkDuplicates Tracking 195737 as yet unmatched pairs. 5796 records in RAM.
INFO 2026-06-08 08:28:34 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr18:62,187,633
INFO 2026-06-08 08:28:34 MarkDuplicates Tracking 193510 as yet unmatched pairs. 3568 records in RAM.
INFO 2026-06-08 08:28:35 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 1s. Last read position: chr18:80,046,025
INFO 2026-06-08 08:28:35 MarkDuplicates Tracking 190081 as yet unmatched pairs. 126 records in RAM.
INFO 2026-06-08 08:28:37 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 2s. Last read position: chr19:1,206,925
INFO 2026-06-08 08:28:37 MarkDuplicates Tracking 187153 as yet unmatched pairs. 94280 records in RAM.
INFO 2026-06-08 08:28:39 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr19:1,467,341
INFO 2026-06-08 08:28:39 MarkDuplicates Tracking 185023 as yet unmatched pairs. 92150 records in RAM.
INFO 2026-06-08 08:28:40 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr19:2,041,160
INFO 2026-06-08 08:28:40 MarkDuplicates Tracking 179987 as yet unmatched pairs. 87114 records in RAM.
INFO 2026-06-08 08:28:42 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr19:2,733,290
INFO 2026-06-08 08:28:42 MarkDuplicates Tracking 177132 as yet unmatched pairs. 84258 records in RAM.
INFO 2026-06-08 08:28:43 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr19:4,452,396
INFO 2026-06-08 08:28:43 MarkDuplicates Tracking 174320 as yet unmatched pairs. 81446 records in RAM.
INFO 2026-06-08 08:28:45 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr19:5,286,053
INFO 2026-06-08 08:28:45 MarkDuplicates Tracking 171460 as yet unmatched pairs. 78583 records in RAM.
INFO 2026-06-08 08:28:46 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr19:7,519,340
INFO 2026-06-08 08:28:46 MarkDuplicates Tracking 168311 as yet unmatched pairs. 75433 records in RAM.
INFO 2026-06-08 08:28:48 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr19:9,974,186
INFO 2026-06-08 08:28:48 MarkDuplicates Tracking 165042 as yet unmatched pairs. 72164 records in RAM.
INFO 2026-06-08 08:28:50 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr19:10,873,866
INFO 2026-06-08 08:28:50 MarkDuplicates Tracking 162248 as yet unmatched pairs. 69370 records in RAM.
INFO 2026-06-08 08:28:51 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr19:12,715,158
INFO 2026-06-08 08:28:51 MarkDuplicates Tracking 159810 as yet unmatched pairs. 66932 records in RAM.
INFO 2026-06-08 08:28:53 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr19:14,106,757
INFO 2026-06-08 08:28:53 MarkDuplicates Tracking 156943 as yet unmatched pairs. 64065 records in RAM.
INFO 2026-06-08 08:28:54 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr19:15,239,696
INFO 2026-06-08 08:28:54 MarkDuplicates Tracking 155699 as yet unmatched pairs. 62821 records in RAM.
INFO 2026-06-08 08:28:56 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 2s. Last read position: chr19:16,523,193
INFO 2026-06-08 08:28:56 MarkDuplicates Tracking 151774 as yet unmatched pairs. 58894 records in RAM.
INFO 2026-06-08 08:28:58 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr19:17,862,986
INFO 2026-06-08 08:28:58 MarkDuplicates Tracking 149192 as yet unmatched pairs. 56310 records in RAM.
INFO 2026-06-08 08:29:00 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr19:18,870,109
INFO 2026-06-08 08:29:00 MarkDuplicates Tracking 147339 as yet unmatched pairs. 54431 records in RAM.
INFO 2026-06-08 08:29:01 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr19:19,630,286
INFO 2026-06-08 08:29:01 MarkDuplicates Tracking 142426 as yet unmatched pairs. 49518 records in RAM.
INFO 2026-06-08 08:29:03 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 2s. Last read position: chr19:35,131,265
INFO 2026-06-08 08:29:03 MarkDuplicates Tracking 139832 as yet unmatched pairs. 46924 records in RAM.
INFO 2026-06-08 08:29:05 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr19:36,017,426
INFO 2026-06-08 08:29:05 MarkDuplicates Tracking 135358 as yet unmatched pairs. 42450 records in RAM.
INFO 2026-06-08 08:29:06 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr19:38,883,687
INFO 2026-06-08 08:29:06 MarkDuplicates Tracking 132607 as yet unmatched pairs. 39676 records in RAM.
INFO 2026-06-08 08:29:07 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr19:39,885,741
INFO 2026-06-08 08:29:07 MarkDuplicates Tracking 130277 as yet unmatched pairs. 37322 records in RAM.
INFO 2026-06-08 08:29:09 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr19:40,739,342
INFO 2026-06-08 08:29:09 MarkDuplicates Tracking 127179 as yet unmatched pairs. 34224 records in RAM.
INFO 2026-06-08 08:29:10 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr19:42,269,320
INFO 2026-06-08 08:29:10 MarkDuplicates Tracking 124761 as yet unmatched pairs. 31774 records in RAM.
INFO 2026-06-08 08:29:12 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr19:42,323,948
INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 121643 as yet unmatched pairs. 28656 records in RAM.
INFO 2026-06-08 08:29:13 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr19:44,865,636
INFO 2026-06-08 08:29:13 MarkDuplicates Tracking 118791 as yet unmatched pairs. 25802 records in RAM.
INFO 2026-06-08 08:29:15 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr19:45,785,991
INFO 2026-06-08 08:29:15 MarkDuplicates Tracking 116162 as yet unmatched pairs. 23167 records in RAM.
INFO 2026-06-08 08:29:16 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr19:47,320,476
INFO 2026-06-08 08:29:16 MarkDuplicates Tracking 112480 as yet unmatched pairs. 19484 records in RAM.
INFO 2026-06-08 08:29:18 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr19:48,873,996
INFO 2026-06-08 08:29:18 MarkDuplicates Tracking 109807 as yet unmatched pairs. 16811 records in RAM.
INFO 2026-06-08 08:29:19 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr19:49,599,923
INFO 2026-06-08 08:29:19 MarkDuplicates Tracking 107056 as yet unmatched pairs. 14060 records in RAM.
INFO 2026-06-08 08:29:21 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr19:50,382,453
INFO 2026-06-08 08:29:21 MarkDuplicates Tracking 103925 as yet unmatched pairs. 10923 records in RAM.
INFO 2026-06-08 08:29:22 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr19:54,250,879
INFO 2026-06-08 08:29:22 MarkDuplicates Tracking 101140 as yet unmatched pairs. 8137 records in RAM.
INFO 2026-06-08 08:29:24 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr19:55,266,148
INFO 2026-06-08 08:29:24 MarkDuplicates Tracking 98635 as yet unmatched pairs. 5623 records in RAM.
INFO 2026-06-08 08:29:26 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 2s. Last read position: chr19:57,444,892
INFO 2026-06-08 08:29:26 MarkDuplicates Tracking 95825 as yet unmatched pairs. 2813 records in RAM.
INFO 2026-06-08 08:29:28 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr19:58,563,271
INFO 2026-06-08 08:29:28 MarkDuplicates Tracking 93362 as yet unmatched pairs. 348 records in RAM.
INFO 2026-06-08 08:29:30 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr20:3,697,177
INFO 2026-06-08 08:29:30 MarkDuplicates Tracking 90318 as yet unmatched pairs. 25939 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr20:17,660,307
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 87938 as yet unmatched pairs. 23559 records in RAM.
INFO 2026-06-08 08:29:33 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr20:32,149,754
INFO 2026-06-08 08:29:33 MarkDuplicates Tracking 85238 as yet unmatched pairs. 20839 records in RAM.
INFO 2026-06-08 08:29:34 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr20:35,653,298
INFO 2026-06-08 08:29:34 MarkDuplicates Tracking 82775 as yet unmatched pairs. 18376 records in RAM.
INFO 2026-06-08 08:29:36 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr20:41,173,749
INFO 2026-06-08 08:29:36 MarkDuplicates Tracking 80596 as yet unmatched pairs. 16190 records in RAM.
INFO 2026-06-08 08:29:37 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr20:45,904,963
INFO 2026-06-08 08:29:37 MarkDuplicates Tracking 77978 as yet unmatched pairs. 13541 records in RAM.
INFO 2026-06-08 08:29:39 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr20:50,893,635
INFO 2026-06-08 08:29:39 MarkDuplicates Tracking 75431 as yet unmatched pairs. 10994 records in RAM.
INFO 2026-06-08 08:29:40 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr20:58,903,537
INFO 2026-06-08 08:29:40 MarkDuplicates Tracking 73691 as yet unmatched pairs. 9253 records in RAM.
INFO 2026-06-08 08:29:42 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr20:62,813,314
INFO 2026-06-08 08:29:42 MarkDuplicates Tracking 69804 as yet unmatched pairs. 5366 records in RAM.
INFO 2026-06-08 08:29:43 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr20:63,566,861
INFO 2026-06-08 08:29:43 MarkDuplicates Tracking 66226 as yet unmatched pairs. 1788 records in RAM.
INFO 2026-06-08 08:29:45 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr21:8,215,013
INFO 2026-06-08 08:29:45 MarkDuplicates Tracking 63945 as yet unmatched pairs. 11697 records in RAM.
INFO 2026-06-08 08:29:46 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 0s. Last read position: chr21:8,399,101
INFO 2026-06-08 08:29:46 MarkDuplicates Tracking 62933 as yet unmatched pairs. 10679 records in RAM.
INFO 2026-06-08 08:29:47 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr21:8,987,953
INFO 2026-06-08 08:29:47 MarkDuplicates Tracking 60690 as yet unmatched pairs. 8428 records in RAM.
INFO 2026-06-08 08:29:48 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr21:33,559,727
INFO 2026-06-08 08:29:48 MarkDuplicates Tracking 58070 as yet unmatched pairs. 5808 records in RAM.
INFO 2026-06-08 08:29:50 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr21:44,364,113
INFO 2026-06-08 08:29:50 MarkDuplicates Tracking 55328 as yet unmatched pairs. 3066 records in RAM.
INFO 2026-06-08 08:29:51 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr21:46,602,289
INFO 2026-06-08 08:29:51 MarkDuplicates Tracking 52526 as yet unmatched pairs. 257 records in RAM.
INFO 2026-06-08 08:29:53 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr22:20,799,245
INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 49780 as yet unmatched pairs. 19066 records in RAM.
INFO 2026-06-08 08:29:55 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 2s. Last read position: chr22:24,644,787
INFO 2026-06-08 08:29:55 MarkDuplicates Tracking 47137 as yet unmatched pairs. 16423 records in RAM.
INFO 2026-06-08 08:29:57 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr22:29,742,453
INFO 2026-06-08 08:29:57 MarkDuplicates Tracking 44057 as yet unmatched pairs. 13328 records in RAM.
INFO 2026-06-08 08:29:58 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr22:36,506,359
INFO 2026-06-08 08:29:58 MarkDuplicates Tracking 41268 as yet unmatched pairs. 10539 records in RAM.
INFO 2026-06-08 08:30:00 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr22:39,488,029
INFO 2026-06-08 08:30:00 MarkDuplicates Tracking 38658 as yet unmatched pairs. 7929 records in RAM.
INFO 2026-06-08 08:30:01 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr22:42,212,957
INFO 2026-06-08 08:30:01 MarkDuplicates Tracking 36027 as yet unmatched pairs. 5298 records in RAM.
INFO 2026-06-08 08:30:02 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr22:50,255,784
INFO 2026-06-08 08:30:02 MarkDuplicates Tracking 33051 as yet unmatched pairs. 2322 records in RAM.
INFO 2026-06-08 08:30:04 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chrX:2,935,127
INFO 2026-06-08 08:30:04 MarkDuplicates Tracking 30007 as yet unmatched pairs. 20522 records in RAM.
INFO 2026-06-08 08:30:05 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chrX:40,710,004
INFO 2026-06-08 08:30:05 MarkDuplicates Tracking 27532 as yet unmatched pairs. 18042 records in RAM.
INFO 2026-06-08 08:30:07 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chrX:49,030,217
INFO 2026-06-08 08:30:07 MarkDuplicates Tracking 25817 as yet unmatched pairs. 16327 records in RAM.
INFO 2026-06-08 08:30:08 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chrX:53,409,491
INFO 2026-06-08 08:30:08 MarkDuplicates Tracking 22864 as yet unmatched pairs. 13374 records in RAM.
INFO 2026-06-08 08:30:10 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chrX:71,169,461
INFO 2026-06-08 08:30:10 MarkDuplicates Tracking 20681 as yet unmatched pairs. 11191 records in RAM.
INFO 2026-06-08 08:30:11 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chrX:100,665,255
INFO 2026-06-08 08:30:11 MarkDuplicates Tracking 18017 as yet unmatched pairs. 8525 records in RAM.
INFO 2026-06-08 08:30:12 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chrX:129,647,691
INFO 2026-06-08 08:30:12 MarkDuplicates Tracking 15645 as yet unmatched pairs. 6153 records in RAM.
INFO 2026-06-08 08:30:14 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chrX:153,804,554
INFO 2026-06-08 08:30:14 MarkDuplicates Tracking 13011 as yet unmatched pairs. 3517 records in RAM.
INFO 2026-06-08 08:30:16 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chrX:154,465,143
INFO 2026-06-08 08:30:16 MarkDuplicates Tracking 9984 as yet unmatched pairs. 490 records in RAM.
INFO 2026-06-08 08:30:17 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,736
INFO 2026-06-08 08:30:17 MarkDuplicates Tracking 6309 as yet unmatched pairs. 172 records in RAM.
INFO 2026-06-08 08:30:18 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: KI270733.1:130,996
INFO 2026-06-08 08:30:18 MarkDuplicates Tracking 5860 as yet unmatched pairs. 5849 records in RAM.
INFO 2026-06-08 08:30:19 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,391
INFO 2026-06-08 08:30:19 MarkDuplicates Tracking 65 as yet unmatched pairs. 54 records in RAM.
INFO 2026-06-08 08:30:20 MarkDuplicates Read 355342661 records. 0 pairs never matched.
INFO 2026-06-08 08:30:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 31823956736; totalMemory: 45432700928; maxMemory: 63585648640
INFO 2026-06-08 08:30:47 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:30:56 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:31:17 OpticalDuplicateFinder Large duplicate set. size = 1074
INFO 2026-06-08 08:31:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,921
INFO 2026-06-08 08:31:18 OpticalDuplicateFinder Large duplicate set. size = 1072
INFO 2026-06-08 08:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,626
INFO 2026-06-08 08:31:18 OpticalDuplicateFinder Large duplicate set. size = 1166
INFO 2026-06-08 08:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,022
INFO 2026-06-08 08:31:18 OpticalDuplicateFinder Large duplicate set. size = 1570
INFO 2026-06-08 08:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,642
INFO 2026-06-08 08:31:18 OpticalDuplicateFinder Large duplicate set. size = 1026
INFO 2026-06-08 08:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,340
INFO 2026-06-08 08:31:19 OpticalDuplicateFinder Large duplicate set. size = 1367
INFO 2026-06-08 08:31:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,687
INFO 2026-06-08 08:31:57 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:31:57 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:32:31 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:32:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 203984296; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:32:32 MarkDuplicates Marking 282505897 records as duplicates.
INFO 2026-06-08 08:32:32 MarkDuplicates Found 6718659 optical duplicate clusters.
INFO 2026-06-08 08:32:32 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:32:46 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:14s. Time for last 10,000,000: 14s. Last read position: chr1:44,776,709
INFO 2026-06-08 08:33:02 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:30s. Time for last 10,000,000: 16s. Last read position: chr1:154,251,244
INFO 2026-06-08 08:33:22 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 19s. Last read position: chr1:228,493,884
INFO 2026-06-08 08:33:38 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:06s. Time for last 10,000,000: 15s. Last read position: chr2:61,394,881
INFO 2026-06-08 08:33:55 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:22s. Time for last 10,000,000: 16s. Last read position: chr2:215,379,258
INFO 2026-06-08 08:34:10 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:37s. Time for last 10,000,000: 14s. Last read position: chr3:49,357,414
INFO 2026-06-08 08:34:25 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:52s. Time for last 10,000,000: 15s. Last read position: chr4:1,236,641
INFO 2026-06-08 08:34:39 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 14s. Last read position: chr5:14,487,679
INFO 2026-06-08 08:34:54 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:22s. Time for last 10,000,000: 15s. Last read position: chr5:141,864,855
INFO 2026-06-08 08:35:09 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:37s. Time for last 10,000,000: 14s. Last read position: chr6:31,829,476
INFO 2026-06-08 08:35:23 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:51s. Time for last 10,000,000: 14s. Last read position: chr6:169,668,628
INFO 2026-06-08 08:35:37 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:05s. Time for last 10,000,000: 14s. Last read position: chr7:44,079,574
INFO 2026-06-08 08:35:51 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:19s. Time for last 10,000,000: 14s. Last read position: chr7:55,165,386
INFO 2026-06-08 08:36:06 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:34s. Time for last 10,000,000: 14s. Last read position: chr7:98,281,875
INFO 2026-06-08 08:36:20 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:48s. Time for last 10,000,000: 14s. Last read position: chr7:127,701,164
INFO 2026-06-08 08:36:34 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:02s. Time for last 10,000,000: 14s. Last read position: chr8:70,128,892
INFO 2026-06-08 08:36:48 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:16s. Time for last 10,000,000: 13s. Last read position: chr9:121,328,942
INFO 2026-06-08 08:37:02 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:30s. Time for last 10,000,000: 13s. Last read position: chr10:95,414,632
INFO 2026-06-08 08:37:16 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:44s. Time for last 10,000,000: 13s. Last read position: chr11:64,767,619
INFO 2026-06-08 08:37:30 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:04:58s. Time for last 10,000,000: 14s. Last read position: chr12:6,587,775
INFO 2026-06-08 08:37:45 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:12s. Time for last 10,000,000: 14s. Last read position: chr12:71,636,846
INFO 2026-06-08 08:37:59 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:27s. Time for last 10,000,000: 14s. Last read position: chr13:112,690,405
INFO 2026-06-08 08:38:14 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:41s. Time for last 10,000,000: 14s. Last read position: chr15:29,762,351
INFO 2026-06-08 08:38:27 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:05:55s. Time for last 10,000,000: 13s. Last read position: chr16:1,445,503
INFO 2026-06-08 08:38:41 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:09s. Time for last 10,000,000: 13s. Last read position: chr16:27,740,690
INFO 2026-06-08 08:38:55 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:23s. Time for last 10,000,000: 14s. Last read position: chr16:89,560,956
INFO 2026-06-08 08:39:09 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:37s. Time for last 10,000,000: 13s. Last read position: chr17:40,404,200
INFO 2026-06-08 08:39:23 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:06:51s. Time for last 10,000,000: 13s. Last read position: chr17:75,923,265
INFO 2026-06-08 08:39:37 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:05s. Time for last 10,000,000: 13s. Last read position: chr19:2,041,160
INFO 2026-06-08 08:39:52 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:19s. Time for last 10,000,000: 14s. Last read position: chr19:16,523,193
INFO 2026-06-08 08:40:06 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:34s. Time for last 10,000,000: 14s. Last read position: chr19:42,323,948
INFO 2026-06-08 08:40:21 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:07:48s. Time for last 10,000,000: 14s. Last read position: chr19:58,563,271
INFO 2026-06-08 08:40:35 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:02s. Time for last 10,000,000: 14s. Last read position: chr20:63,566,861
INFO 2026-06-08 08:40:48 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:16s. Time for last 10,000,000: 13s. Last read position: chr22:36,506,359
INFO 2026-06-08 08:41:02 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:08:30s. Time for last 10,000,000: 14s. Last read position: chrX:129,647,691
INFO 2026-06-08 08:41:14 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:41:14 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:41:14 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:41:14 MarkDuplicates Before output close freeMemory: 203936464; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:41:14 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:41:14 MarkDuplicates After output close freeMemory: 104189488; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:41:14 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 21.87 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory