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 tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00586_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00586_B23MVV7LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:45:19.144 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 08:45:19 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00586_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00586_B23MVV7LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:45:19 GMT 2026] Executing as ?@nf-1a024336e116bc083ef08a44cd1b0a70-974b8-v245l 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 08:45:19	MarkDuplicates	Start of doWork freeMemory: 105828552; totalMemory: 134217728; maxMemory: 63585648640
INFO	2026-06-08 08:45:19	MarkDuplicates	Reading input file and constructing read end information.
INFO	2026-06-08 08:45:19	MarkDuplicates	Will retain up to 230382784 data points before spilling to disk.
INFO	2026-06-08 08:45:23	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:02s.  Time for last 1,000,000:    2s.  Last read position: chr1:1,642,664
INFO	2026-06-08 08:45:23	MarkDuplicates	Tracking 3674 as yet unmatched pairs. 435 records in RAM.
INFO	2026-06-08 08:45:26	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    3s.  Last read position: chr1:8,358,457
INFO	2026-06-08 08:45:26	MarkDuplicates	Tracking 7013 as yet unmatched pairs. 676 records in RAM.
INFO	2026-06-08 08:45:28	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    2s.  Last read position: chr1:11,925,543
INFO	2026-06-08 08:45:28	MarkDuplicates	Tracking 9415 as yet unmatched pairs. 237 records in RAM.
INFO	2026-06-08 08:45:30	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    1s.  Last read position: chr1:16,972,462
INFO	2026-06-08 08:45:30	MarkDuplicates	Tracking 12188 as yet unmatched pairs. 47 records in RAM.
INFO	2026-06-08 08:45:33	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    2s.  Last read position: chr1:20,747,637
INFO	2026-06-08 08:45:33	MarkDuplicates	Tracking 15593 as yet unmatched pairs. 680 records in RAM.
INFO	2026-06-08 08:45:36	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    2s.  Last read position: chr1:22,639,218
INFO	2026-06-08 08:45:36	MarkDuplicates	Tracking 22255 as yet unmatched pairs. 4285 records in RAM.
INFO	2026-06-08 08:45:38	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    2s.  Last read position: chr1:25,246,924
INFO	2026-06-08 08:45:38	MarkDuplicates	Tracking 21923 as yet unmatched pairs. 1140 records in RAM.
INFO	2026-06-08 08:45:40	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    1s.  Last read position: chr1:27,989,783
INFO	2026-06-08 08:45:40	MarkDuplicates	Tracking 23735 as yet unmatched pairs. 162 records in RAM.
INFO	2026-06-08 08:45:42	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    2s.  Last read position: chr1:32,334,710
INFO	2026-06-08 08:45:42	MarkDuplicates	Tracking 27269 as yet unmatched pairs. 851 records in RAM.
INFO	2026-06-08 08:45:44	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    1s.  Last read position: chr1:36,178,549
INFO	2026-06-08 08:45:44	MarkDuplicates	Tracking 30018 as yet unmatched pairs. 559 records in RAM.
INFO	2026-06-08 08:45:45	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    1s.  Last read position: chr1:40,064,238
INFO	2026-06-08 08:45:45	MarkDuplicates	Tracking 33742 as yet unmatched pairs. 1506 records in RAM.
INFO	2026-06-08 08:45:48	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    2s.  Last read position: chr1:43,667,925
INFO	2026-06-08 08:45:48	MarkDuplicates	Tracking 35357 as yet unmatched pairs. 282 records in RAM.
INFO	2026-06-08 08:45:50	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    1s.  Last read position: chr1:47,183,597
INFO	2026-06-08 08:45:50	MarkDuplicates	Tracking 38198 as yet unmatched pairs. 319 records in RAM.
INFO	2026-06-08 08:45:51	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    1s.  Last read position: chr1:59,832,193
INFO	2026-06-08 08:45:51	MarkDuplicates	Tracking 40874 as yet unmatched pairs. 172 records in RAM.
INFO	2026-06-08 08:45:54	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    2s.  Last read position: chr1:86,473,488
INFO	2026-06-08 08:45:54	MarkDuplicates	Tracking 46811 as yet unmatched pairs. 3678 records in RAM.
INFO	2026-06-08 08:45:56	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    2s.  Last read position: chr1:92,834,806
INFO	2026-06-08 08:45:56	MarkDuplicates	Tracking 45981 as yet unmatched pairs. 516 records in RAM.
INFO	2026-06-08 08:45:57	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    1s.  Last read position: chr1:109,910,744
INFO	2026-06-08 08:45:57	MarkDuplicates	Tracking 48025 as yet unmatched pairs. 55 records in RAM.
INFO	2026-06-08 08:45:59	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    1s.  Last read position: chr1:114,510,674
INFO	2026-06-08 08:45:59	MarkDuplicates	Tracking 52034 as yet unmatched pairs. 1329 records in RAM.
INFO	2026-06-08 08:46:01	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    1s.  Last read position: chr1:119,997,157
INFO	2026-06-08 08:46:01	MarkDuplicates	Tracking 54564 as yet unmatched pairs. 1264 records in RAM.
INFO	2026-06-08 08:46:03	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    2s.  Last read position: chr1:148,558,355
INFO	2026-06-08 08:46:03	MarkDuplicates	Tracking 54919 as yet unmatched pairs. 169 records in RAM.
INFO	2026-06-08 08:46:05	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    1s.  Last read position: chr1:149,886,335
INFO	2026-06-08 08:46:05	MarkDuplicates	Tracking 57549 as yet unmatched pairs. 1361 records in RAM.
INFO	2026-06-08 08:46:06	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    1s.  Last read position: chr1:151,316,219
INFO	2026-06-08 08:46:06	MarkDuplicates	Tracking 59534 as yet unmatched pairs. 656 records in RAM.
INFO	2026-06-08 08:46:08	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    1s.  Last read position: chr1:154,173,096
INFO	2026-06-08 08:46:08	MarkDuplicates	Tracking 67241 as yet unmatched pairs. 5708 records in RAM.
INFO	2026-06-08 08:46:10	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    1s.  Last read position: chr1:155,186,651
INFO	2026-06-08 08:46:10	MarkDuplicates	Tracking 66531 as yet unmatched pairs. 2166 records in RAM.
INFO	2026-06-08 08:46:12	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    2s.  Last read position: chr1:156,058,050
INFO	2026-06-08 08:46:12	MarkDuplicates	Tracking 66949 as yet unmatched pairs. 286 records in RAM.
INFO	2026-06-08 08:46:14	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    1s.  Last read position: chr1:160,205,454
INFO	2026-06-08 08:46:14	MarkDuplicates	Tracking 69886 as yet unmatched pairs. 314 records in RAM.
INFO	2026-06-08 08:46:15	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    1s.  Last read position: chr1:162,581,369
INFO	2026-06-08 08:46:15	MarkDuplicates	Tracking 72658 as yet unmatched pairs. 513 records in RAM.
INFO	2026-06-08 08:46:17	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    1s.  Last read position: chr1:171,589,576
INFO	2026-06-08 08:46:17	MarkDuplicates	Tracking 75292 as yet unmatched pairs. 522 records in RAM.
INFO	2026-06-08 08:46:19	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    2s.  Last read position: chr1:183,550,754
INFO	2026-06-08 08:46:19	MarkDuplicates	Tracking 77822 as yet unmatched pairs. 192 records in RAM.
INFO	2026-06-08 08:46:22	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    2s.  Last read position: chr1:201,649,267
INFO	2026-06-08 08:46:22	MarkDuplicates	Tracking 80507 as yet unmatched pairs. 278 records in RAM.
INFO	2026-06-08 08:46:23	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    1s.  Last read position: chr1:205,306,277
INFO	2026-06-08 08:46:23	MarkDuplicates	Tracking 83041 as yet unmatched pairs. 57 records in RAM.
INFO	2026-06-08 08:46:25	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    2s.  Last read position: chr1:206,932,505
INFO	2026-06-08 08:46:25	MarkDuplicates	Tracking 126688 as yet unmatched pairs. 41049 records in RAM.
INFO	2026-06-08 08:46:28	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    2s.  Last read position: chr1:206,935,533
INFO	2026-06-08 08:46:28	MarkDuplicates	Tracking 144917 as yet unmatched pairs. 55928 records in RAM.
INFO	2026-06-08 08:46:30	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    1s.  Last read position: chr1:206,937,582
INFO	2026-06-08 08:46:30	MarkDuplicates	Tracking 99653 as yet unmatched pairs. 7938 records in RAM.
INFO	2026-06-08 08:46:32	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    1s.  Last read position: chr1:208,045,844
INFO	2026-06-08 08:46:32	MarkDuplicates	Tracking 94277 as yet unmatched pairs. 11 records in RAM.
INFO	2026-06-08 08:46:34	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    2s.  Last read position: chr1:225,038,694
INFO	2026-06-08 08:46:34	MarkDuplicates	Tracking 96887 as yet unmatched pairs. 32 records in RAM.
INFO	2026-06-08 08:46:35	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    1s.  Last read position: chr1:230,067,397
INFO	2026-06-08 08:46:35	MarkDuplicates	Tracking 100160 as yet unmatched pairs. 61 records in RAM.
INFO	2026-06-08 08:46:37	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    1s.  Last read position: chr1:244,863,690
INFO	2026-06-08 08:46:37	MarkDuplicates	Tracking 105196 as yet unmatched pairs. 2243 records in RAM.
INFO	2026-06-08 08:46:39	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    2s.  Last read position: chr2:11,787,108
INFO	2026-06-08 08:46:39	MarkDuplicates	Tracking 106080 as yet unmatched pairs. 105359 records in RAM.
INFO	2026-06-08 08:46:41	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:    1s.  Last read position: chr2:27,040,070
INFO	2026-06-08 08:46:41	MarkDuplicates	Tracking 109532 as yet unmatched pairs. 108793 records in RAM.
INFO	2026-06-08 08:46:44	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    2s.  Last read position: chr2:31,386,419
INFO	2026-06-08 08:46:44	MarkDuplicates	Tracking 113161 as yet unmatched pairs. 112404 records in RAM.
INFO	2026-06-08 08:46:46	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    2s.  Last read position: chr2:32,916,264
INFO	2026-06-08 08:46:46	MarkDuplicates	Tracking 302466 as yet unmatched pairs. 97492 records in RAM.
INFO	2026-06-08 08:46:48	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    2s.  Last read position: chr2:32,916,399
INFO	2026-06-08 08:46:48	MarkDuplicates	Tracking 869638 as yet unmatched pairs. 55344 records in RAM.
INFO	2026-06-08 08:46:50	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    1s.  Last read position: chr2:32,916,406
INFO	2026-06-08 08:46:50	MarkDuplicates	Tracking 889547 as yet unmatched pairs. 53759 records in RAM.
INFO	2026-06-08 08:46:51	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:    1s.  Last read position: chr2:42,764,008
INFO	2026-06-08 08:46:51	MarkDuplicates	Tracking 946629 as yet unmatched pairs. 47718 records in RAM.
INFO	2026-06-08 08:46:53	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    1s.  Last read position: chr2:54,616,256
INFO	2026-06-08 08:46:53	MarkDuplicates	Tracking 944207 as yet unmatched pairs. 45270 records in RAM.
INFO	2026-06-08 08:46:55	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    1s.  Last read position: chr2:65,016,441
INFO	2026-06-08 08:46:55	MarkDuplicates	Tracking 941397 as yet unmatched pairs. 42437 records in RAM.
INFO	2026-06-08 08:46:57	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    1s.  Last read position: chr2:74,047,073
INFO	2026-06-08 08:46:57	MarkDuplicates	Tracking 939035 as yet unmatched pairs. 40056 records in RAM.
INFO	2026-06-08 08:46:58	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    1s.  Last read position: chr2:84,905,698
INFO	2026-06-08 08:46:58	MarkDuplicates	Tracking 937075 as yet unmatched pairs. 38090 records in RAM.
INFO	2026-06-08 08:47:00	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    1s.  Last read position: chr2:95,906,649
INFO	2026-06-08 08:47:00	MarkDuplicates	Tracking 933596 as yet unmatched pairs. 34591 records in RAM.
INFO	2026-06-08 08:47:01	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    1s.  Last read position: chr2:101,569,225
INFO	2026-06-08 08:47:01	MarkDuplicates	Tracking 930550 as yet unmatched pairs. 31512 records in RAM.
INFO	2026-06-08 08:47:03	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    1s.  Last read position: chr2:111,856,654
INFO	2026-06-08 08:47:03	MarkDuplicates	Tracking 928706 as yet unmatched pairs. 29644 records in RAM.
INFO	2026-06-08 08:47:05	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    1s.  Last read position: chr2:127,709,698
INFO	2026-06-08 08:47:05	MarkDuplicates	Tracking 926494 as yet unmatched pairs. 27410 records in RAM.
INFO	2026-06-08 08:47:07	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    1s.  Last read position: chr2:157,430,375
INFO	2026-06-08 08:47:07	MarkDuplicates	Tracking 923857 as yet unmatched pairs. 24749 records in RAM.
INFO	2026-06-08 08:47:09	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    2s.  Last read position: chr2:174,567,152
INFO	2026-06-08 08:47:09	MarkDuplicates	Tracking 922587 as yet unmatched pairs. 23451 records in RAM.
INFO	2026-06-08 08:47:12	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    2s.  Last read position: chr2:188,999,851
INFO	2026-06-08 08:47:12	MarkDuplicates	Tracking 920321 as yet unmatched pairs. 21177 records in RAM.
INFO	2026-06-08 08:47:14	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    1s.  Last read position: chr2:197,494,687
INFO	2026-06-08 08:47:14	MarkDuplicates	Tracking 917205 as yet unmatched pairs. 18041 records in RAM.
INFO	2026-06-08 08:47:15	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    1s.  Last read position: chr2:208,243,172
INFO	2026-06-08 08:47:15	MarkDuplicates	Tracking 913585 as yet unmatched pairs. 14402 records in RAM.
INFO	2026-06-08 08:47:17	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:    1s.  Last read position: chr2:216,415,083
INFO	2026-06-08 08:47:17	MarkDuplicates	Tracking 911134 as yet unmatched pairs. 11944 records in RAM.
INFO	2026-06-08 08:47:19	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    1s.  Last read position: chr2:219,539,789
INFO	2026-06-08 08:47:19	MarkDuplicates	Tracking 908660 as yet unmatched pairs. 9462 records in RAM.
INFO	2026-06-08 08:47:21	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    1s.  Last read position: chr2:231,075,530
INFO	2026-06-08 08:47:21	MarkDuplicates	Tracking 905534 as yet unmatched pairs. 6322 records in RAM.
INFO	2026-06-08 08:47:22	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    1s.  Last read position: chr2:237,376,803
INFO	2026-06-08 08:47:22	MarkDuplicates	Tracking 903264 as yet unmatched pairs. 4024 records in RAM.
INFO	2026-06-08 08:47:24	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    1s.  Last read position: chr2:241,633,817
INFO	2026-06-08 08:47:24	MarkDuplicates	Tracking 899886 as yet unmatched pairs. 632 records in RAM.
INFO	2026-06-08 08:47:26	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    1s.  Last read position: chr3:12,584,577
INFO	2026-06-08 08:47:26	MarkDuplicates	Tracking 897655 as yet unmatched pairs. 54746 records in RAM.
INFO	2026-06-08 08:47:28	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    1s.  Last read position: chr3:31,533,298
INFO	2026-06-08 08:47:28	MarkDuplicates	Tracking 894904 as yet unmatched pairs. 51972 records in RAM.
INFO	2026-06-08 08:47:30	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    1s.  Last read position: chr3:40,462,127
INFO	2026-06-08 08:47:30	MarkDuplicates	Tracking 891397 as yet unmatched pairs. 48450 records in RAM.
INFO	2026-06-08 08:47:31	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    1s.  Last read position: chr3:47,002,446
INFO	2026-06-08 08:47:31	MarkDuplicates	Tracking 888862 as yet unmatched pairs. 45877 records in RAM.
INFO	2026-06-08 08:47:33	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    2s.  Last read position: chr3:48,685,728
INFO	2026-06-08 08:47:33	MarkDuplicates	Tracking 885427 as yet unmatched pairs. 42428 records in RAM.
INFO	2026-06-08 08:47:35	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    1s.  Last read position: chr3:49,732,897
INFO	2026-06-08 08:47:35	MarkDuplicates	Tracking 882516 as yet unmatched pairs. 39508 records in RAM.
INFO	2026-06-08 08:47:36	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    1s.  Last read position: chr3:52,292,291
INFO	2026-06-08 08:47:36	MarkDuplicates	Tracking 879857 as yet unmatched pairs. 36819 records in RAM.
INFO	2026-06-08 08:47:38	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:    1s.  Last read position: chr3:57,757,603
INFO	2026-06-08 08:47:38	MarkDuplicates	Tracking 876741 as yet unmatched pairs. 33689 records in RAM.
INFO	2026-06-08 08:47:40	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    2s.  Last read position: chr3:88,055,377
INFO	2026-06-08 08:47:40	MarkDuplicates	Tracking 873903 as yet unmatched pairs. 30842 records in RAM.
INFO	2026-06-08 08:47:42	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:02:21s.  Time for last 1,000,000:    1s.  Last read position: chr3:119,216,243
INFO	2026-06-08 08:47:42	MarkDuplicates	Tracking 871521 as yet unmatched pairs. 28438 records in RAM.
INFO	2026-06-08 08:47:43	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    1s.  Last read position: chr3:124,910,430
INFO	2026-06-08 08:47:43	MarkDuplicates	Tracking 879216 as yet unmatched pairs. 36123 records in RAM.
INFO	2026-06-08 08:47:45	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    2s.  Last read position: chr3:129,315,457
INFO	2026-06-08 08:47:45	MarkDuplicates	Tracking 866210 as yet unmatched pairs. 23103 records in RAM.
INFO	2026-06-08 08:47:47	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    1s.  Last read position: chr3:142,694,416
INFO	2026-06-08 08:47:47	MarkDuplicates	Tracking 864173 as yet unmatched pairs. 21051 records in RAM.
INFO	2026-06-08 08:47:48	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    1s.  Last read position: chr3:169,966,825
INFO	2026-06-08 08:47:48	MarkDuplicates	Tracking 860750 as yet unmatched pairs. 17611 records in RAM.
INFO	2026-06-08 08:47:50	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    1s.  Last read position: chr3:184,317,330
INFO	2026-06-08 08:47:50	MarkDuplicates	Tracking 859759 as yet unmatched pairs. 16607 records in RAM.
INFO	2026-06-08 08:47:52	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    1s.  Last read position: chr3:194,672,064
INFO	2026-06-08 08:47:52	MarkDuplicates	Tracking 855558 as yet unmatched pairs. 12387 records in RAM.
INFO	2026-06-08 08:47:53	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    1s.  Last read position: chr3:195,778,936
INFO	2026-06-08 08:47:53	MarkDuplicates	Tracking 862502 as yet unmatched pairs. 19317 records in RAM.
INFO	2026-06-08 08:47:55	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    1s.  Last read position: chr3:195,780,555
INFO	2026-06-08 08:47:55	MarkDuplicates	Tracking 881541 as yet unmatched pairs. 38352 records in RAM.
INFO	2026-06-08 08:47:56	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    1s.  Last read position: chr3:195,781,765
INFO	2026-06-08 08:47:56	MarkDuplicates	Tracking 886199 as yet unmatched pairs. 43006 records in RAM.
INFO	2026-06-08 08:47:58	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:02:37s.  Time for last 1,000,000:    2s.  Last read position: chr3:195,783,183
INFO	2026-06-08 08:47:58	MarkDuplicates	Tracking 883070 as yet unmatched pairs. 39869 records in RAM.
INFO	2026-06-08 08:47:59	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    1s.  Last read position: chr3:195,784,770
INFO	2026-06-08 08:47:59	MarkDuplicates	Tracking 884842 as yet unmatched pairs. 41641 records in RAM.
INFO	2026-06-08 08:48:01	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    1s.  Last read position: chr3:195,786,129
INFO	2026-06-08 08:48:01	MarkDuplicates	Tracking 870272 as yet unmatched pairs. 27057 records in RAM.
INFO	2026-06-08 08:48:03	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:    1s.  Last read position: chr3:195,788,790
INFO	2026-06-08 08:48:03	MarkDuplicates	Tracking 851466 as yet unmatched pairs. 8242 records in RAM.
INFO	2026-06-08 08:48:05	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    2s.  Last read position: chr3:197,855,507
INFO	2026-06-08 08:48:05	MarkDuplicates	Tracking 843503 as yet unmatched pairs. 258 records in RAM.
INFO	2026-06-08 08:48:07	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    2s.  Last read position: chr4:2,261,737
INFO	2026-06-08 08:48:07	MarkDuplicates	Tracking 840844 as yet unmatched pairs. 23983 records in RAM.
INFO	2026-06-08 08:48:09	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    1s.  Last read position: chr4:10,097,749
INFO	2026-06-08 08:48:09	MarkDuplicates	Tracking 837933 as yet unmatched pairs. 21043 records in RAM.
INFO	2026-06-08 08:48:11	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:02:50s.  Time for last 1,000,000:    1s.  Last read position: chr4:39,458,210
INFO	2026-06-08 08:48:11	MarkDuplicates	Tracking 834874 as yet unmatched pairs. 17960 records in RAM.
INFO	2026-06-08 08:48:12	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    1s.  Last read position: chr4:56,931,172
INFO	2026-06-08 08:48:12	MarkDuplicates	Tracking 832380 as yet unmatched pairs. 15446 records in RAM.
INFO	2026-06-08 08:48:14	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    1s.  Last read position: chr4:75,657,568
INFO	2026-06-08 08:48:14	MarkDuplicates	Tracking 829666 as yet unmatched pairs. 12719 records in RAM.
INFO	2026-06-08 08:48:16	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    1s.  Last read position: chr4:87,115,081
INFO	2026-06-08 08:48:16	MarkDuplicates	Tracking 827210 as yet unmatched pairs. 10246 records in RAM.
INFO	2026-06-08 08:48:17	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    1s.  Last read position: chr4:112,587,828
INFO	2026-06-08 08:48:17	MarkDuplicates	Tracking 824096 as yet unmatched pairs. 7116 records in RAM.
INFO	2026-06-08 08:48:19	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    1s.  Last read position: chr4:145,119,972
INFO	2026-06-08 08:48:19	MarkDuplicates	Tracking 821817 as yet unmatched pairs. 4826 records in RAM.
INFO	2026-06-08 08:48:21	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    1s.  Last read position: chr4:168,894,667
INFO	2026-06-08 08:48:21	MarkDuplicates	Tracking 819394 as yet unmatched pairs. 2385 records in RAM.
INFO	2026-06-08 08:48:23	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    2s.  Last read position: chr5:1,002,167
INFO	2026-06-08 08:48:23	MarkDuplicates	Tracking 816102 as yet unmatched pairs. 41285 records in RAM.
INFO	2026-06-08 08:48:24	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    1s.  Last read position: chr5:14,487,548
INFO	2026-06-08 08:48:24	MarkDuplicates	Tracking 814056 as yet unmatched pairs. 39226 records in RAM.
INFO	2026-06-08 08:48:26	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    1s.  Last read position: chr5:42,728,286
INFO	2026-06-08 08:48:26	MarkDuplicates	Tracking 810623 as yet unmatched pairs. 35767 records in RAM.
INFO	2026-06-08 08:48:28	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    1s.  Last read position: chr5:69,894,594
INFO	2026-06-08 08:48:28	MarkDuplicates	Tracking 808224 as yet unmatched pairs. 33340 records in RAM.
INFO	2026-06-08 08:48:29	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    1s.  Last read position: chr5:82,276,489
INFO	2026-06-08 08:48:29	MarkDuplicates	Tracking 812452 as yet unmatched pairs. 37522 records in RAM.
INFO	2026-06-08 08:48:31	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:03:10s.  Time for last 1,000,000:    1s.  Last read position: chr5:113,001,402
INFO	2026-06-08 08:48:31	MarkDuplicates	Tracking 803832 as yet unmatched pairs. 28887 records in RAM.
INFO	2026-06-08 08:48:32	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    1s.  Last read position: chr5:132,618,241
INFO	2026-06-08 08:48:32	MarkDuplicates	Tracking 800940 as yet unmatched pairs. 25982 records in RAM.
INFO	2026-06-08 08:48:35	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    2s.  Last read position: chr5:138,557,876
INFO	2026-06-08 08:48:35	MarkDuplicates	Tracking 798765 as yet unmatched pairs. 23798 records in RAM.
INFO	2026-06-08 08:48:37	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    1s.  Last read position: chr5:141,580,872
INFO	2026-06-08 08:48:37	MarkDuplicates	Tracking 795744 as yet unmatched pairs. 20755 records in RAM.
INFO	2026-06-08 08:48:38	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,132,863
INFO	2026-06-08 08:48:38	MarkDuplicates	Tracking 793187 as yet unmatched pairs. 18175 records in RAM.
INFO	2026-06-08 08:48:40	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    2s.  Last read position: chr5:150,405,113
INFO	2026-06-08 08:48:40	MarkDuplicates	Tracking 833377 as yet unmatched pairs. 58360 records in RAM.
INFO	2026-06-08 08:48:43	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    2s.  Last read position: chr5:151,032,326
INFO	2026-06-08 08:48:43	MarkDuplicates	Tracking 787568 as yet unmatched pairs. 12537 records in RAM.
INFO	2026-06-08 08:48:45	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    2s.  Last read position: chr5:160,612,779
INFO	2026-06-08 08:48:45	MarkDuplicates	Tracking 785858 as yet unmatched pairs. 10805 records in RAM.
INFO	2026-06-08 08:48:47	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    1s.  Last read position: chr5:176,238,477
INFO	2026-06-08 08:48:47	MarkDuplicates	Tracking 781853 as yet unmatched pairs. 6783 records in RAM.
INFO	2026-06-08 08:48:49	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    1s.  Last read position: chr5:178,222,851
INFO	2026-06-08 08:48:49	MarkDuplicates	Tracking 779363 as yet unmatched pairs. 4281 records in RAM.
INFO	2026-06-08 08:48:51	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    1s.  Last read position: chr5:180,791,902
INFO	2026-06-08 08:48:51	MarkDuplicates	Tracking 776826 as yet unmatched pairs. 1723 records in RAM.
INFO	2026-06-08 08:48:53	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    2s.  Last read position: chr6:7,230,656
INFO	2026-06-08 08:48:53	MarkDuplicates	Tracking 774876 as yet unmatched pairs. 52485 records in RAM.
INFO	2026-06-08 08:48:54	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    1s.  Last read position: chr6:18,132,142
INFO	2026-06-08 08:48:54	MarkDuplicates	Tracking 770749 as yet unmatched pairs. 48350 records in RAM.
INFO	2026-06-08 08:48:56	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    1s.  Last read position: chr6:26,217,255
INFO	2026-06-08 08:48:56	MarkDuplicates	Tracking 768085 as yet unmatched pairs. 45673 records in RAM.
INFO	2026-06-08 08:48:58	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    1s.  Last read position: chr6:27,831,207
INFO	2026-06-08 08:48:58	MarkDuplicates	Tracking 768077 as yet unmatched pairs. 45651 records in RAM.
INFO	2026-06-08 08:49:00	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    1s.  Last read position: chr6:29,944,554
INFO	2026-06-08 08:49:00	MarkDuplicates	Tracking 779047 as yet unmatched pairs. 56616 records in RAM.
INFO	2026-06-08 08:49:01	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,156,787
INFO	2026-06-08 08:49:01	MarkDuplicates	Tracking 760579 as yet unmatched pairs. 38137 records in RAM.
INFO	2026-06-08 08:49:03	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,632,354
INFO	2026-06-08 08:49:03	MarkDuplicates	Tracking 758066 as yet unmatched pairs. 35608 records in RAM.
INFO	2026-06-08 08:49:04	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,874,956
INFO	2026-06-08 08:49:04	MarkDuplicates	Tracking 757913 as yet unmatched pairs. 35450 records in RAM.
INFO	2026-06-08 08:49:06	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    1s.  Last read position: chr6:32,521,974
INFO	2026-06-08 08:49:06	MarkDuplicates	Tracking 755888 as yet unmatched pairs. 33413 records in RAM.
INFO	2026-06-08 08:49:08	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    1s.  Last read position: chr6:33,069,221
INFO	2026-06-08 08:49:08	MarkDuplicates	Tracking 751832 as yet unmatched pairs. 29348 records in RAM.
INFO	2026-06-08 08:49:09	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    1s.  Last read position: chr6:33,678,773
INFO	2026-06-08 08:49:09	MarkDuplicates	Tracking 747608 as yet unmatched pairs. 25117 records in RAM.
INFO	2026-06-08 08:49:11	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    1s.  Last read position: chr6:37,819,980
INFO	2026-06-08 08:49:11	MarkDuplicates	Tracking 745093 as yet unmatched pairs. 22588 records in RAM.
INFO	2026-06-08 08:49:13	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    1s.  Last read position: chr6:43,770,967
INFO	2026-06-08 08:49:13	MarkDuplicates	Tracking 742399 as yet unmatched pairs. 19864 records in RAM.
INFO	2026-06-08 08:49:14	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    1s.  Last read position: chr6:63,211,763
INFO	2026-06-08 08:49:14	MarkDuplicates	Tracking 739055 as yet unmatched pairs. 16482 records in RAM.
INFO	2026-06-08 08:49:16	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    1s.  Last read position: chr6:89,265,690
INFO	2026-06-08 08:49:16	MarkDuplicates	Tracking 736245 as yet unmatched pairs. 13644 records in RAM.
INFO	2026-06-08 08:49:18	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:03:57s.  Time for last 1,000,000:    1s.  Last read position: chr6:109,452,596
INFO	2026-06-08 08:49:18	MarkDuplicates	Tracking 734175 as yet unmatched pairs. 11550 records in RAM.
INFO	2026-06-08 08:49:20	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    1s.  Last read position: chr6:130,956,395
INFO	2026-06-08 08:49:20	MarkDuplicates	Tracking 731248 as yet unmatched pairs. 8608 records in RAM.
INFO	2026-06-08 08:49:21	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    1s.  Last read position: chr6:144,447,670
INFO	2026-06-08 08:49:21	MarkDuplicates	Tracking 728863 as yet unmatched pairs. 6199 records in RAM.
INFO	2026-06-08 08:49:23	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    1s.  Last read position: chr6:158,767,115
INFO	2026-06-08 08:49:23	MarkDuplicates	Tracking 727237 as yet unmatched pairs. 4554 records in RAM.
INFO	2026-06-08 08:49:24	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    1s.  Last read position: chr6:170,282,717
INFO	2026-06-08 08:49:24	MarkDuplicates	Tracking 723096 as yet unmatched pairs. 403 records in RAM.
INFO	2026-06-08 08:49:27	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    2s.  Last read position: chr7:5,009,080
INFO	2026-06-08 08:49:27	MarkDuplicates	Tracking 719462 as yet unmatched pairs. 49228 records in RAM.
INFO	2026-06-08 08:49:28	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    1s.  Last read position: chr7:5,529,296
INFO	2026-06-08 08:49:28	MarkDuplicates	Tracking 732220 as yet unmatched pairs. 61977 records in RAM.
INFO	2026-06-08 08:49:30	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    1s.  Last read position: chr7:26,184,763
INFO	2026-06-08 08:49:30	MarkDuplicates	Tracking 714080 as yet unmatched pairs. 43804 records in RAM.
INFO	2026-06-08 08:49:31	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    1s.  Last read position: chr7:44,051,835
INFO	2026-06-08 08:49:31	MarkDuplicates	Tracking 711935 as yet unmatched pairs. 41621 records in RAM.
INFO	2026-06-08 08:49:33	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    1s.  Last read position: chr7:55,202,578
INFO	2026-06-08 08:49:33	MarkDuplicates	Tracking 708857 as yet unmatched pairs. 38528 records in RAM.
INFO	2026-06-08 08:49:35	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    1s.  Last read position: chr7:73,769,402
INFO	2026-06-08 08:49:35	MarkDuplicates	Tracking 709508 as yet unmatched pairs. 39168 records in RAM.
INFO	2026-06-08 08:49:36	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    1s.  Last read position: chr7:76,330,170
INFO	2026-06-08 08:49:36	MarkDuplicates	Tracking 705019 as yet unmatched pairs. 34649 records in RAM.
INFO	2026-06-08 08:49:38	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    1s.  Last read position: chr7:93,994,342
INFO	2026-06-08 08:49:38	MarkDuplicates	Tracking 701736 as yet unmatched pairs. 31345 records in RAM.
INFO	2026-06-08 08:49:40	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    1s.  Last read position: chr7:99,621,381
INFO	2026-06-08 08:49:40	MarkDuplicates	Tracking 698982 as yet unmatched pairs. 28565 records in RAM.
INFO	2026-06-08 08:49:41	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,884,477
INFO	2026-06-08 08:49:41	MarkDuplicates	Tracking 695799 as yet unmatched pairs. 25379 records in RAM.
INFO	2026-06-08 08:49:43	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,993,594
INFO	2026-06-08 08:49:43	MarkDuplicates	Tracking 697234 as yet unmatched pairs. 26811 records in RAM.
INFO	2026-06-08 08:49:44	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,995,085
INFO	2026-06-08 08:49:44	MarkDuplicates	Tracking 696066 as yet unmatched pairs. 25635 records in RAM.
INFO	2026-06-08 08:49:46	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,996,397
INFO	2026-06-08 08:49:46	MarkDuplicates	Tracking 715474 as yet unmatched pairs. 45043 records in RAM.
INFO	2026-06-08 08:49:47	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:04:26s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,997,150
INFO	2026-06-08 08:49:47	MarkDuplicates	Tracking 706330 as yet unmatched pairs. 35892 records in RAM.
INFO	2026-06-08 08:49:49	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,998,301
INFO	2026-06-08 08:49:49	MarkDuplicates	Tracking 695884 as yet unmatched pairs. 25445 records in RAM.
INFO	2026-06-08 08:49:50	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:04:30s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,999,070
INFO	2026-06-08 08:49:50	MarkDuplicates	Tracking 700009 as yet unmatched pairs. 29567 records in RAM.
INFO	2026-06-08 08:49:52	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    1s.  Last read position: chr7:101,000,176
INFO	2026-06-08 08:49:52	MarkDuplicates	Tracking 707157 as yet unmatched pairs. 36711 records in RAM.
INFO	2026-06-08 08:49:54	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    1s.  Last read position: chr7:101,001,187
INFO	2026-06-08 08:49:54	MarkDuplicates	Tracking 701039 as yet unmatched pairs. 30593 records in RAM.
INFO	2026-06-08 08:49:55	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:    1s.  Last read position: chr7:101,002,176
INFO	2026-06-08 08:49:55	MarkDuplicates	Tracking 691931 as yet unmatched pairs. 21485 records in RAM.
INFO	2026-06-08 08:49:56	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    1s.  Last read position: chr7:101,004,353
INFO	2026-06-08 08:49:56	MarkDuplicates	Tracking 687044 as yet unmatched pairs. 16598 records in RAM.
INFO	2026-06-08 08:49:58	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    1s.  Last read position: chr7:105,074,686
INFO	2026-06-08 08:49:58	MarkDuplicates	Tracking 685009 as yet unmatched pairs. 14546 records in RAM.
INFO	2026-06-08 08:49:59	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    1s.  Last read position: chr7:127,652,380
INFO	2026-06-08 08:49:59	MarkDuplicates	Tracking 687725 as yet unmatched pairs. 17241 records in RAM.
INFO	2026-06-08 08:50:01	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    1s.  Last read position: chr7:135,168,849
INFO	2026-06-08 08:50:01	MarkDuplicates	Tracking 680311 as yet unmatched pairs. 9820 records in RAM.
INFO	2026-06-08 08:50:03	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    1s.  Last read position: chr7:143,268,094
INFO	2026-06-08 08:50:03	MarkDuplicates	Tracking 677902 as yet unmatched pairs. 7392 records in RAM.
INFO	2026-06-08 08:50:04	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:04:44s.  Time for last 1,000,000:    1s.  Last read position: chr7:150,371,445
INFO	2026-06-08 08:50:04	MarkDuplicates	Tracking 675896 as yet unmatched pairs. 5382 records in RAM.
INFO	2026-06-08 08:50:06	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    1s.  Last read position: chr7:152,265,187
INFO	2026-06-08 08:50:06	MarkDuplicates	Tracking 672381 as yet unmatched pairs. 1862 records in RAM.
INFO	2026-06-08 08:50:08	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:04:47s.  Time for last 1,000,000:    1s.  Last read position: chr8:11,850,910
INFO	2026-06-08 08:50:08	MarkDuplicates	Tracking 670573 as yet unmatched pairs. 33826 records in RAM.
INFO	2026-06-08 08:50:10	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    1s.  Last read position: chr8:23,328,429
INFO	2026-06-08 08:50:10	MarkDuplicates	Tracking 666365 as yet unmatched pairs. 29609 records in RAM.
INFO	2026-06-08 08:50:11	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:04:51s.  Time for last 1,000,000:    1s.  Last read position: chr8:37,698,302
INFO	2026-06-08 08:50:11	MarkDuplicates	Tracking 663296 as yet unmatched pairs. 26525 records in RAM.
INFO	2026-06-08 08:50:13	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    1s.  Last read position: chr8:43,069,561
INFO	2026-06-08 08:50:13	MarkDuplicates	Tracking 660688 as yet unmatched pairs. 23911 records in RAM.
INFO	2026-06-08 08:50:15	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    1s.  Last read position: chr8:67,232,889
INFO	2026-06-08 08:50:15	MarkDuplicates	Tracking 657844 as yet unmatched pairs. 21046 records in RAM.
INFO	2026-06-08 08:50:16	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    1s.  Last read position: chr8:94,876,132
INFO	2026-06-08 08:50:16	MarkDuplicates	Tracking 655302 as yet unmatched pairs. 18470 records in RAM.
INFO	2026-06-08 08:50:18	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    1s.  Last read position: chr8:108,228,328
INFO	2026-06-08 08:50:18	MarkDuplicates	Tracking 653631 as yet unmatched pairs. 16778 records in RAM.
INFO	2026-06-08 08:50:20	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    1s.  Last read position: chr8:140,023,956
INFO	2026-06-08 08:50:20	MarkDuplicates	Tracking 650178 as yet unmatched pairs. 13301 records in RAM.
INFO	2026-06-08 08:50:22	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    2s.  Last read position: chr8:143,858,303
INFO	2026-06-08 08:50:22	MarkDuplicates	Tracking 646797 as yet unmatched pairs. 9898 records in RAM.
INFO	2026-06-08 08:50:23	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,862,547
INFO	2026-06-08 08:50:23	MarkDuplicates	Tracking 646627 as yet unmatched pairs. 9725 records in RAM.
INFO	2026-06-08 08:50:24	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,867,758
INFO	2026-06-08 08:50:24	MarkDuplicates	Tracking 645051 as yet unmatched pairs. 8144 records in RAM.
INFO	2026-06-08 08:50:26	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,984,662
INFO	2026-06-08 08:50:26	MarkDuplicates	Tracking 641933 as yet unmatched pairs. 5020 records in RAM.
INFO	2026-06-08 08:50:27	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:05:06s.  Time for last 1,000,000:    1s.  Last read position: chr8:144,614,426
INFO	2026-06-08 08:50:27	MarkDuplicates	Tracking 637278 as yet unmatched pairs. 338 records in RAM.
INFO	2026-06-08 08:50:29	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    2s.  Last read position: chr9:19,276,207
INFO	2026-06-08 08:50:29	MarkDuplicates	Tracking 635253 as yet unmatched pairs. 38274 records in RAM.
INFO	2026-06-08 08:50:31	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    1s.  Last read position: chr9:35,077,042
INFO	2026-06-08 08:50:31	MarkDuplicates	Tracking 632141 as yet unmatched pairs. 35155 records in RAM.
INFO	2026-06-08 08:50:33	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    1s.  Last read position: chr9:68,241,982
INFO	2026-06-08 08:50:33	MarkDuplicates	Tracking 629329 as yet unmatched pairs. 32292 records in RAM.
INFO	2026-06-08 08:50:35	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    1s.  Last read position: chr9:86,308,559
INFO	2026-06-08 08:50:35	MarkDuplicates	Tracking 627062 as yet unmatched pairs. 30024 records in RAM.
INFO	2026-06-08 08:50:36	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    1s.  Last read position: chr9:94,374,849
INFO	2026-06-08 08:50:36	MarkDuplicates	Tracking 624190 as yet unmatched pairs. 27134 records in RAM.
INFO	2026-06-08 08:50:38	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    1s.  Last read position: chr9:108,893,042
INFO	2026-06-08 08:50:38	MarkDuplicates	Tracking 621109 as yet unmatched pairs. 24028 records in RAM.
INFO	2026-06-08 08:50:40	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:05:19s.  Time for last 1,000,000:    2s.  Last read position: chr9:116,219,945
INFO	2026-06-08 08:50:40	MarkDuplicates	Tracking 618118 as yet unmatched pairs. 21027 records in RAM.
INFO	2026-06-08 08:50:42	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:05:21s.  Time for last 1,000,000:    1s.  Last read position: chr9:125,240,871
INFO	2026-06-08 08:50:42	MarkDuplicates	Tracking 619198 as yet unmatched pairs. 22085 records in RAM.
INFO	2026-06-08 08:50:44	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    2s.  Last read position: chr9:128,151,929
INFO	2026-06-08 08:50:44	MarkDuplicates	Tracking 623752 as yet unmatched pairs. 26611 records in RAM.
INFO	2026-06-08 08:50:46	MarkDuplicates	Read   181,000,000 records.  Elapsed time: 00:05:25s.  Time for last 1,000,000:    2s.  Last read position: chr9:129,008,712
INFO	2026-06-08 08:50:46	MarkDuplicates	Tracking 611629 as yet unmatched pairs. 14468 records in RAM.
INFO	2026-06-08 08:50:48	MarkDuplicates	Read   182,000,000 records.  Elapsed time: 00:05:27s.  Time for last 1,000,000:    1s.  Last read position: chr9:131,487,939
INFO	2026-06-08 08:50:48	MarkDuplicates	Tracking 607435 as yet unmatched pairs. 10268 records in RAM.
INFO	2026-06-08 08:50:50	MarkDuplicates	Read   183,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    1s.  Last read position: chr9:134,907,430
INFO	2026-06-08 08:50:50	MarkDuplicates	Tracking 604018 as yet unmatched pairs. 6828 records in RAM.
INFO	2026-06-08 08:50:51	MarkDuplicates	Read   184,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    1s.  Last read position: chr9:136,908,099
INFO	2026-06-08 08:50:51	MarkDuplicates	Tracking 601212 as yet unmatched pairs. 4006 records in RAM.
INFO	2026-06-08 08:50:53	MarkDuplicates	Read   185,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    1s.  Last read position: chr10:286,273
INFO	2026-06-08 08:50:53	MarkDuplicates	Tracking 597205 as yet unmatched pairs. 36890 records in RAM.
INFO	2026-06-08 08:50:55	MarkDuplicates	Read   186,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    1s.  Last read position: chr10:14,897,180
INFO	2026-06-08 08:50:55	MarkDuplicates	Tracking 594716 as yet unmatched pairs. 34390 records in RAM.
INFO	2026-06-08 08:50:57	MarkDuplicates	Read   187,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    1s.  Last read position: chr10:32,022,922
INFO	2026-06-08 08:50:57	MarkDuplicates	Tracking 593320 as yet unmatched pairs. 32984 records in RAM.
INFO	2026-06-08 08:50:58	MarkDuplicates	Read   188,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    1s.  Last read position: chr10:48,010,850
INFO	2026-06-08 08:50:58	MarkDuplicates	Tracking 589758 as yet unmatched pairs. 29417 records in RAM.
INFO	2026-06-08 08:51:00	MarkDuplicates	Read   189,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    1s.  Last read position: chr10:70,153,934
INFO	2026-06-08 08:51:00	MarkDuplicates	Tracking 587831 as yet unmatched pairs. 27474 records in RAM.
INFO	2026-06-08 08:51:01	MarkDuplicates	Read   190,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    1s.  Last read position: chr10:76,058,733
INFO	2026-06-08 08:51:01	MarkDuplicates	Tracking 584398 as yet unmatched pairs. 24030 records in RAM.
INFO	2026-06-08 08:51:03	MarkDuplicates	Read   191,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:    1s.  Last read position: chr10:89,414,733
INFO	2026-06-08 08:51:03	MarkDuplicates	Tracking 582083 as yet unmatched pairs. 21704 records in RAM.
INFO	2026-06-08 08:51:05	MarkDuplicates	Read   192,000,000 records.  Elapsed time: 00:05:44s.  Time for last 1,000,000:    1s.  Last read position: chr10:97,476,931
INFO	2026-06-08 08:51:05	MarkDuplicates	Tracking 579225 as yet unmatched pairs. 18836 records in RAM.
INFO	2026-06-08 08:51:07	MarkDuplicates	Read   193,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    1s.  Last read position: chr10:102,485,604
INFO	2026-06-08 08:51:07	MarkDuplicates	Tracking 576166 as yet unmatched pairs. 15765 records in RAM.
INFO	2026-06-08 08:51:08	MarkDuplicates	Read   194,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    1s.  Last read position: chr10:116,968,674
INFO	2026-06-08 08:51:08	MarkDuplicates	Tracking 574050 as yet unmatched pairs. 13639 records in RAM.
INFO	2026-06-08 08:51:10	MarkDuplicates	Read   195,000,000 records.  Elapsed time: 00:05:49s.  Time for last 1,000,000:    2s.  Last read position: chr10:122,579,659
INFO	2026-06-08 08:51:10	MarkDuplicates	Tracking 581945 as yet unmatched pairs. 21527 records in RAM.
INFO	2026-06-08 08:51:12	MarkDuplicates	Read   196,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    1s.  Last read position: chr10:122,588,989
INFO	2026-06-08 08:51:12	MarkDuplicates	Tracking 582434 as yet unmatched pairs. 22016 records in RAM.
INFO	2026-06-08 08:51:14	MarkDuplicates	Read   197,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    1s.  Last read position: chr10:122,598,859
INFO	2026-06-08 08:51:14	MarkDuplicates	Tracking 581326 as yet unmatched pairs. 20907 records in RAM.
INFO	2026-06-08 08:51:15	MarkDuplicates	Read   198,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    1s.  Last read position: chr10:122,605,987
INFO	2026-06-08 08:51:15	MarkDuplicates	Tracking 578610 as yet unmatched pairs. 18190 records in RAM.
INFO	2026-06-08 08:51:16	MarkDuplicates	Read   199,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    1s.  Last read position: chr10:122,614,188
INFO	2026-06-08 08:51:16	MarkDuplicates	Tracking 578852 as yet unmatched pairs. 18432 records in RAM.
INFO	2026-06-08 08:51:18	MarkDuplicates	Read   200,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:    1s.  Last read position: chr10:122,640,219
INFO	2026-06-08 08:51:18	MarkDuplicates	Tracking 567646 as yet unmatched pairs. 7219 records in RAM.
INFO	2026-06-08 08:51:19	MarkDuplicates	Read   201,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    1s.  Last read position: chr10:133,465,494
INFO	2026-06-08 08:51:19	MarkDuplicates	Tracking 560479 as yet unmatched pairs. 33 records in RAM.
INFO	2026-06-08 08:51:22	MarkDuplicates	Read   202,000,000 records.  Elapsed time: 00:06:01s.  Time for last 1,000,000:    2s.  Last read position: chr11:618,812
INFO	2026-06-08 08:51:22	MarkDuplicates	Tracking 557914 as yet unmatched pairs. 67138 records in RAM.
INFO	2026-06-08 08:51:23	MarkDuplicates	Read   203,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,082,383
INFO	2026-06-08 08:51:23	MarkDuplicates	Tracking 561719 as yet unmatched pairs. 70931 records in RAM.
INFO	2026-06-08 08:51:25	MarkDuplicates	Read   204,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,228,625
INFO	2026-06-08 08:51:25	MarkDuplicates	Tracking 553993 as yet unmatched pairs. 63191 records in RAM.
INFO	2026-06-08 08:51:27	MarkDuplicates	Read   205,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,244,538
INFO	2026-06-08 08:51:27	MarkDuplicates	Tracking 551277 as yet unmatched pairs. 60471 records in RAM.
INFO	2026-06-08 08:51:28	MarkDuplicates	Read   206,000,000 records.  Elapsed time: 00:06:07s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,248,195
INFO	2026-06-08 08:51:28	MarkDuplicates	Tracking 549441 as yet unmatched pairs. 58633 records in RAM.
INFO	2026-06-08 08:51:30	MarkDuplicates	Read   207,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    2s.  Last read position: chr11:1,261,490
INFO	2026-06-08 08:51:30	MarkDuplicates	Tracking 547305 as yet unmatched pairs. 56493 records in RAM.
INFO	2026-06-08 08:51:32	MarkDuplicates	Read   208,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    1s.  Last read position: chr11:6,223,795
INFO	2026-06-08 08:51:32	MarkDuplicates	Tracking 545174 as yet unmatched pairs. 54338 records in RAM.
INFO	2026-06-08 08:51:34	MarkDuplicates	Read   209,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    1s.  Last read position: chr11:11,896,394
INFO	2026-06-08 08:51:34	MarkDuplicates	Tracking 540343 as yet unmatched pairs. 49491 records in RAM.
INFO	2026-06-08 08:51:36	MarkDuplicates	Read   210,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    2s.  Last read position: chr11:32,934,941
INFO	2026-06-08 08:51:36	MarkDuplicates	Tracking 537800 as yet unmatched pairs. 46938 records in RAM.
INFO	2026-06-08 08:51:38	MarkDuplicates	Read   211,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    1s.  Last read position: chr11:46,316,356
INFO	2026-06-08 08:51:38	MarkDuplicates	Tracking 537685 as yet unmatched pairs. 46802 records in RAM.
INFO	2026-06-08 08:51:39	MarkDuplicates	Read   212,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    1s.  Last read position: chr11:57,309,175
INFO	2026-06-08 08:51:39	MarkDuplicates	Tracking 533110 as yet unmatched pairs. 42223 records in RAM.
INFO	2026-06-08 08:51:41	MarkDuplicates	Read   213,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    1s.  Last read position: chr11:60,951,114
INFO	2026-06-08 08:51:41	MarkDuplicates	Tracking 530037 as yet unmatched pairs. 39135 records in RAM.
INFO	2026-06-08 08:51:43	MarkDuplicates	Read   214,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    1s.  Last read position: chr11:62,572,582
INFO	2026-06-08 08:51:43	MarkDuplicates	Tracking 527910 as yet unmatched pairs. 37002 records in RAM.
INFO	2026-06-08 08:51:45	MarkDuplicates	Read   215,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    1s.  Last read position: chr11:64,226,634
INFO	2026-06-08 08:51:45	MarkDuplicates	Tracking 524368 as yet unmatched pairs. 33452 records in RAM.
INFO	2026-06-08 08:51:46	MarkDuplicates	Read   216,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    1s.  Last read position: chr11:64,913,274
INFO	2026-06-08 08:51:46	MarkDuplicates	Tracking 520680 as yet unmatched pairs. 29761 records in RAM.
INFO	2026-06-08 08:51:48	MarkDuplicates	Read   217,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    1s.  Last read position: chr11:65,641,335
INFO	2026-06-08 08:51:48	MarkDuplicates	Tracking 517913 as yet unmatched pairs. 26978 records in RAM.
INFO	2026-06-08 08:51:50	MarkDuplicates	Read   218,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    1s.  Last read position: chr11:66,643,489
INFO	2026-06-08 08:51:50	MarkDuplicates	Tracking 514370 as yet unmatched pairs. 23429 records in RAM.
INFO	2026-06-08 08:51:52	MarkDuplicates	Read   219,000,000 records.  Elapsed time: 00:06:31s.  Time for last 1,000,000:    1s.  Last read position: chr11:68,036,480
INFO	2026-06-08 08:51:52	MarkDuplicates	Tracking 510913 as yet unmatched pairs. 19966 records in RAM.
INFO	2026-06-08 08:51:54	MarkDuplicates	Read   220,000,000 records.  Elapsed time: 00:06:33s.  Time for last 1,000,000:    1s.  Last read position: chr11:72,013,724
INFO	2026-06-08 08:51:54	MarkDuplicates	Tracking 507802 as yet unmatched pairs. 16850 records in RAM.
INFO	2026-06-08 08:51:55	MarkDuplicates	Read   221,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    1s.  Last read position: chr11:75,404,174
INFO	2026-06-08 08:51:55	MarkDuplicates	Tracking 507267 as yet unmatched pairs. 16303 records in RAM.
INFO	2026-06-08 08:51:57	MarkDuplicates	Read   222,000,000 records.  Elapsed time: 00:06:36s.  Time for last 1,000,000:    1s.  Last read position: chr11:94,180,123
INFO	2026-06-08 08:51:57	MarkDuplicates	Tracking 501905 as yet unmatched pairs. 10931 records in RAM.
INFO	2026-06-08 08:51:59	MarkDuplicates	Read   223,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    1s.  Last read position: chr11:114,312,327
INFO	2026-06-08 08:51:59	MarkDuplicates	Tracking 499440 as yet unmatched pairs. 8461 records in RAM.
INFO	2026-06-08 08:52:00	MarkDuplicates	Read   224,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    1s.  Last read position: chr11:118,901,617
INFO	2026-06-08 08:52:00	MarkDuplicates	Tracking 497099 as yet unmatched pairs. 6115 records in RAM.
INFO	2026-06-08 08:52:03	MarkDuplicates	Read   225,000,000 records.  Elapsed time: 00:06:43s.  Time for last 1,000,000:    2s.  Last read position: chr11:124,751,463
INFO	2026-06-08 08:52:03	MarkDuplicates	Tracking 495030 as yet unmatched pairs. 4034 records in RAM.
INFO	2026-06-08 08:52:06	MarkDuplicates	Read   226,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    2s.  Last read position: chr11:134,202,832
INFO	2026-06-08 08:52:06	MarkDuplicates	Tracking 491345 as yet unmatched pairs. 346 records in RAM.
INFO	2026-06-08 08:52:08	MarkDuplicates	Read   227,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:    2s.  Last read position: chr12:6,200,468
INFO	2026-06-08 08:52:08	MarkDuplicates	Tracking 489757 as yet unmatched pairs. 48760 records in RAM.
INFO	2026-06-08 08:52:09	MarkDuplicates	Read   228,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    1s.  Last read position: chr12:6,940,869
INFO	2026-06-08 08:52:09	MarkDuplicates	Tracking 485783 as yet unmatched pairs. 44772 records in RAM.
INFO	2026-06-08 08:52:11	MarkDuplicates	Read   229,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:    1s.  Last read position: chr12:11,869,804
INFO	2026-06-08 08:52:11	MarkDuplicates	Tracking 484832 as yet unmatched pairs. 43808 records in RAM.
INFO	2026-06-08 08:52:13	MarkDuplicates	Read   230,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    1s.  Last read position: chr12:29,311,047
INFO	2026-06-08 08:52:13	MarkDuplicates	Tracking 480587 as yet unmatched pairs. 39559 records in RAM.
INFO	2026-06-08 08:52:15	MarkDuplicates	Read   231,000,000 records.  Elapsed time: 00:06:54s.  Time for last 1,000,000:    1s.  Last read position: chr12:48,836,132
INFO	2026-06-08 08:52:15	MarkDuplicates	Tracking 477957 as yet unmatched pairs. 36917 records in RAM.
INFO	2026-06-08 08:52:16	MarkDuplicates	Read   232,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    1s.  Last read position: chr12:49,759,239
INFO	2026-06-08 08:52:16	MarkDuplicates	Tracking 477484 as yet unmatched pairs. 36442 records in RAM.
INFO	2026-06-08 08:52:18	MarkDuplicates	Read   233,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    1s.  Last read position: chr12:53,295,552
INFO	2026-06-08 08:52:18	MarkDuplicates	Tracking 472345 as yet unmatched pairs. 31298 records in RAM.
INFO	2026-06-08 08:52:20	MarkDuplicates	Read   234,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    1s.  Last read position: chr12:55,938,971
INFO	2026-06-08 08:52:20	MarkDuplicates	Tracking 469932 as yet unmatched pairs. 28885 records in RAM.
INFO	2026-06-08 08:52:22	MarkDuplicates	Read   235,000,000 records.  Elapsed time: 00:07:01s.  Time for last 1,000,000:    1s.  Last read position: chr12:56,614,051
INFO	2026-06-08 08:52:22	MarkDuplicates	Tracking 468028 as yet unmatched pairs. 26966 records in RAM.
INFO	2026-06-08 08:52:23	MarkDuplicates	Read   236,000,000 records.  Elapsed time: 00:07:02s.  Time for last 1,000,000:    1s.  Last read position: chr12:57,196,095
INFO	2026-06-08 08:52:23	MarkDuplicates	Tracking 465516 as yet unmatched pairs. 24451 records in RAM.
INFO	2026-06-08 08:52:26	MarkDuplicates	Read   237,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:    3s.  Last read position: chr12:64,721,679
INFO	2026-06-08 08:52:26	MarkDuplicates	Tracking 462166 as yet unmatched pairs. 21095 records in RAM.
INFO	2026-06-08 08:52:28	MarkDuplicates	Read   238,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    1s.  Last read position: chr12:89,522,771
INFO	2026-06-08 08:52:28	MarkDuplicates	Tracking 459764 as yet unmatched pairs. 18674 records in RAM.
INFO	2026-06-08 08:52:30	MarkDuplicates	Read   239,000,000 records.  Elapsed time: 00:07:09s.  Time for last 1,000,000:    1s.  Last read position: chr12:103,946,686
INFO	2026-06-08 08:52:30	MarkDuplicates	Tracking 458959 as yet unmatched pairs. 17868 records in RAM.
INFO	2026-06-08 08:52:31	MarkDuplicates	Read   240,000,000 records.  Elapsed time: 00:07:11s.  Time for last 1,000,000:    1s.  Last read position: chr12:110,492,065
INFO	2026-06-08 08:52:31	MarkDuplicates	Tracking 454664 as yet unmatched pairs. 13561 records in RAM.
INFO	2026-06-08 08:52:33	MarkDuplicates	Read   241,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    1s.  Last read position: chr12:113,387,006
INFO	2026-06-08 08:52:33	MarkDuplicates	Tracking 451162 as yet unmatched pairs. 10053 records in RAM.
INFO	2026-06-08 08:52:35	MarkDuplicates	Read   242,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    1s.  Last read position: chr12:120,695,106
INFO	2026-06-08 08:52:35	MarkDuplicates	Tracking 448731 as yet unmatched pairs. 7614 records in RAM.
INFO	2026-06-08 08:52:36	MarkDuplicates	Read   243,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    1s.  Last read position: chr12:123,423,144
INFO	2026-06-08 08:52:36	MarkDuplicates	Tracking 445460 as yet unmatched pairs. 4324 records in RAM.
INFO	2026-06-08 08:52:38	MarkDuplicates	Read   244,000,000 records.  Elapsed time: 00:07:17s.  Time for last 1,000,000:    1s.  Last read position: chr12:132,571,504
INFO	2026-06-08 08:52:38	MarkDuplicates	Tracking 442901 as yet unmatched pairs. 1754 records in RAM.
INFO	2026-06-08 08:52:40	MarkDuplicates	Read   245,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    1s.  Last read position: chr13:27,116,487
INFO	2026-06-08 08:52:40	MarkDuplicates	Tracking 440119 as yet unmatched pairs. 15040 records in RAM.
INFO	2026-06-08 08:52:42	MarkDuplicates	Read   246,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    1s.  Last read position: chr13:44,434,803
INFO	2026-06-08 08:52:42	MarkDuplicates	Tracking 437811 as yet unmatched pairs. 12722 records in RAM.
INFO	2026-06-08 08:52:43	MarkDuplicates	Read   247,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    1s.  Last read position: chr13:53,028,951
INFO	2026-06-08 08:52:43	MarkDuplicates	Tracking 459603 as yet unmatched pairs. 34506 records in RAM.
INFO	2026-06-08 08:52:45	MarkDuplicates	Read   248,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    2s.  Last read position: chr13:71,675,342
INFO	2026-06-08 08:52:45	MarkDuplicates	Tracking 432178 as yet unmatched pairs. 7079 records in RAM.
INFO	2026-06-08 08:52:47	MarkDuplicates	Read   249,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    1s.  Last read position: chr13:100,668,603
INFO	2026-06-08 08:52:47	MarkDuplicates	Tracking 429672 as yet unmatched pairs. 4567 records in RAM.
INFO	2026-06-08 08:52:49	MarkDuplicates	Read   250,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:    1s.  Last read position: chr13:112,881,783
INFO	2026-06-08 08:52:49	MarkDuplicates	Tracking 426549 as yet unmatched pairs. 1432 records in RAM.
INFO	2026-06-08 08:52:51	MarkDuplicates	Read   251,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    2s.  Last read position: chr14:21,427,997
INFO	2026-06-08 08:52:51	MarkDuplicates	Tracking 423443 as yet unmatched pairs. 33743 records in RAM.
INFO	2026-06-08 08:52:53	MarkDuplicates	Read   252,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:    1s.  Last read position: chr14:24,138,483
INFO	2026-06-08 08:52:53	MarkDuplicates	Tracking 422278 as yet unmatched pairs. 32575 records in RAM.
INFO	2026-06-08 08:52:55	MarkDuplicates	Read   253,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    1s.  Last read position: chr14:34,435,262
INFO	2026-06-08 08:52:55	MarkDuplicates	Tracking 417809 as yet unmatched pairs. 28099 records in RAM.
INFO	2026-06-08 08:52:56	MarkDuplicates	Read   254,000,000 records.  Elapsed time: 00:07:36s.  Time for last 1,000,000:    1s.  Last read position: chr14:52,859,575
INFO	2026-06-08 08:52:56	MarkDuplicates	Tracking 415031 as yet unmatched pairs. 25290 records in RAM.
INFO	2026-06-08 08:52:59	MarkDuplicates	Read   255,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    2s.  Last read position: chr14:64,216,330
INFO	2026-06-08 08:52:59	MarkDuplicates	Tracking 412632 as yet unmatched pairs. 22880 records in RAM.
INFO	2026-06-08 08:53:01	MarkDuplicates	Read   256,000,000 records.  Elapsed time: 00:07:40s.  Time for last 1,000,000:    2s.  Last read position: chr14:71,108,655
INFO	2026-06-08 08:53:01	MarkDuplicates	Tracking 409928 as yet unmatched pairs. 20150 records in RAM.
INFO	2026-06-08 08:54:05	MarkDuplicates	Read   257,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:   64s.  Last read position: chr14:77,458,120
INFO	2026-06-08 08:54:05	MarkDuplicates	Tracking 407048 as yet unmatched pairs. 17268 records in RAM.
INFO	2026-06-08 08:54:08	MarkDuplicates	Read   258,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    2s.  Last read position: chr14:94,111,685
INFO	2026-06-08 08:54:08	MarkDuplicates	Tracking 407650 as yet unmatched pairs. 17858 records in RAM.
INFO	2026-06-08 08:54:10	MarkDuplicates	Read   259,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    1s.  Last read position: chr14:102,016,781
INFO	2026-06-08 08:54:10	MarkDuplicates	Tracking 401762 as yet unmatched pairs. 11956 records in RAM.
INFO	2026-06-08 08:54:12	MarkDuplicates	Read   260,000,000 records.  Elapsed time: 00:08:51s.  Time for last 1,000,000:    1s.  Last read position: chr14:104,883,931
INFO	2026-06-08 08:54:12	MarkDuplicates	Tracking 398573 as yet unmatched pairs. 8759 records in RAM.
INFO	2026-06-08 08:54:14	MarkDuplicates	Read   261,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    1s.  Last read position: chr14:105,587,812
INFO	2026-06-08 08:54:14	MarkDuplicates	Tracking 407840 as yet unmatched pairs. 18019 records in RAM.
INFO	2026-06-08 08:54:16	MarkDuplicates	Read   262,000,000 records.  Elapsed time: 00:08:55s.  Time for last 1,000,000:    2s.  Last read position: chr14:105,707,415
INFO	2026-06-08 08:54:16	MarkDuplicates	Tracking 405802 as yet unmatched pairs. 15979 records in RAM.
INFO	2026-06-08 08:54:18	MarkDuplicates	Read   263,000,000 records.  Elapsed time: 00:08:57s.  Time for last 1,000,000:    2s.  Last read position: chr14:105,855,794
INFO	2026-06-08 08:54:18	MarkDuplicates	Tracking 396161 as yet unmatched pairs. 6337 records in RAM.
INFO	2026-06-08 08:54:20	MarkDuplicates	Read   264,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:    2s.  Last read position: chr15:30,092,077
INFO	2026-06-08 08:54:20	MarkDuplicates	Tracking 388480 as yet unmatched pairs. 32846 records in RAM.
INFO	2026-06-08 08:54:22	MarkDuplicates	Read   265,000,000 records.  Elapsed time: 00:09:01s.  Time for last 1,000,000:    1s.  Last read position: chr15:40,001,043
INFO	2026-06-08 08:54:22	MarkDuplicates	Tracking 386212 as yet unmatched pairs. 30575 records in RAM.
INFO	2026-06-08 08:54:24	MarkDuplicates	Read   266,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    2s.  Last read position: chr15:42,694,075
INFO	2026-06-08 08:54:24	MarkDuplicates	Tracking 383416 as yet unmatched pairs. 27771 records in RAM.
INFO	2026-06-08 08:54:26	MarkDuplicates	Read   267,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:    1s.  Last read position: chr15:44,847,412
INFO	2026-06-08 08:54:26	MarkDuplicates	Tracking 380980 as yet unmatched pairs. 25329 records in RAM.
INFO	2026-06-08 08:54:28	MarkDuplicates	Read   268,000,000 records.  Elapsed time: 00:09:08s.  Time for last 1,000,000:    2s.  Last read position: chr15:45,106,279
INFO	2026-06-08 08:54:28	MarkDuplicates	Tracking 382643 as yet unmatched pairs. 26990 records in RAM.
INFO	2026-06-08 08:54:31	MarkDuplicates	Read   269,000,000 records.  Elapsed time: 00:09:10s.  Time for last 1,000,000:    2s.  Last read position: chr15:45,135,781
INFO	2026-06-08 08:54:31	MarkDuplicates	Tracking 377228 as yet unmatched pairs. 21573 records in RAM.
INFO	2026-06-08 08:54:34	MarkDuplicates	Read   270,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:    3s.  Last read position: chr15:58,888,524
INFO	2026-06-08 08:54:34	MarkDuplicates	Tracking 372581 as yet unmatched pairs. 16920 records in RAM.
INFO	2026-06-08 08:54:36	MarkDuplicates	Read   271,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    1s.  Last read position: chr15:64,162,114
INFO	2026-06-08 08:54:36	MarkDuplicates	Tracking 372702 as yet unmatched pairs. 17037 records in RAM.
INFO	2026-06-08 08:54:38	MarkDuplicates	Read   272,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:    1s.  Last read position: chr15:72,217,441
INFO	2026-06-08 08:54:38	MarkDuplicates	Tracking 368020 as yet unmatched pairs. 12345 records in RAM.
INFO	2026-06-08 08:54:39	MarkDuplicates	Read   273,000,000 records.  Elapsed time: 00:09:19s.  Time for last 1,000,000:    1s.  Last read position: chr15:75,211,053
INFO	2026-06-08 08:54:39	MarkDuplicates	Tracking 364054 as yet unmatched pairs. 8365 records in RAM.
INFO	2026-06-08 08:54:41	MarkDuplicates	Read   274,000,000 records.  Elapsed time: 00:09:21s.  Time for last 1,000,000:    1s.  Last read position: chr15:82,524,301
INFO	2026-06-08 08:54:41	MarkDuplicates	Tracking 360980 as yet unmatched pairs. 5283 records in RAM.
INFO	2026-06-08 08:54:43	MarkDuplicates	Read   275,000,000 records.  Elapsed time: 00:09:22s.  Time for last 1,000,000:    1s.  Last read position: chr15:90,230,379
INFO	2026-06-08 08:54:43	MarkDuplicates	Tracking 359401 as yet unmatched pairs. 3699 records in RAM.
INFO	2026-06-08 08:54:45	MarkDuplicates	Read   276,000,000 records.  Elapsed time: 00:09:25s.  Time for last 1,000,000:    2s.  Last read position: chr16:36,219
INFO	2026-06-08 08:54:45	MarkDuplicates	Tracking 355719 as yet unmatched pairs. 56118 records in RAM.
INFO	2026-06-08 08:54:47	MarkDuplicates	Read   277,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    1s.  Last read position: chr16:1,451,789
INFO	2026-06-08 08:54:47	MarkDuplicates	Tracking 352453 as yet unmatched pairs. 52844 records in RAM.
INFO	2026-06-08 08:54:49	MarkDuplicates	Read   278,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    1s.  Last read position: chr16:2,234,626
INFO	2026-06-08 08:54:49	MarkDuplicates	Tracking 348845 as yet unmatched pairs. 49231 records in RAM.
INFO	2026-06-08 08:54:51	MarkDuplicates	Read   279,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:    2s.  Last read position: chr16:2,972,939
INFO	2026-06-08 08:54:51	MarkDuplicates	Tracking 345926 as yet unmatched pairs. 46311 records in RAM.
INFO	2026-06-08 08:54:54	MarkDuplicates	Read   280,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    2s.  Last read position: chr16:5,025,594
INFO	2026-06-08 08:54:54	MarkDuplicates	Tracking 342832 as yet unmatched pairs. 43215 records in RAM.
INFO	2026-06-08 08:54:56	MarkDuplicates	Read   281,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    1s.  Last read position: chr16:14,857,286
INFO	2026-06-08 08:54:56	MarkDuplicates	Tracking 340134 as yet unmatched pairs. 40509 records in RAM.
INFO	2026-06-08 08:54:57	MarkDuplicates	Read   282,000,000 records.  Elapsed time: 00:09:36s.  Time for last 1,000,000:    1s.  Last read position: chr16:16,322,743
INFO	2026-06-08 08:54:57	MarkDuplicates	Tracking 338316 as yet unmatched pairs. 38689 records in RAM.
INFO	2026-06-08 08:54:59	MarkDuplicates	Read   283,000,000 records.  Elapsed time: 00:09:38s.  Time for last 1,000,000:    1s.  Last read position: chr16:18,868,208
INFO	2026-06-08 08:54:59	MarkDuplicates	Tracking 336530 as yet unmatched pairs. 36901 records in RAM.
INFO	2026-06-08 08:55:01	MarkDuplicates	Read   284,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    1s.  Last read position: chr16:21,834,940
INFO	2026-06-08 08:55:01	MarkDuplicates	Tracking 334747 as yet unmatched pairs. 35117 records in RAM.
INFO	2026-06-08 08:55:02	MarkDuplicates	Read   285,000,000 records.  Elapsed time: 00:09:41s.  Time for last 1,000,000:    1s.  Last read position: chr16:22,534,903
INFO	2026-06-08 08:55:02	MarkDuplicates	Tracking 334504 as yet unmatched pairs. 34872 records in RAM.
INFO	2026-06-08 08:55:04	MarkDuplicates	Read   286,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    1s.  Last read position: chr16:28,482,659
INFO	2026-06-08 08:55:04	MarkDuplicates	Tracking 332563 as yet unmatched pairs. 32927 records in RAM.
INFO	2026-06-08 08:55:06	MarkDuplicates	Read   287,000,000 records.  Elapsed time: 00:09:45s.  Time for last 1,000,000:    1s.  Last read position: chr16:29,449,208
INFO	2026-06-08 08:55:06	MarkDuplicates	Tracking 332008 as yet unmatched pairs. 32369 records in RAM.
INFO	2026-06-08 08:55:08	MarkDuplicates	Read   288,000,000 records.  Elapsed time: 00:09:47s.  Time for last 1,000,000:    1s.  Last read position: chr16:29,963,566
INFO	2026-06-08 08:55:08	MarkDuplicates	Tracking 328059 as yet unmatched pairs. 28412 records in RAM.
INFO	2026-06-08 08:55:10	MarkDuplicates	Read   289,000,000 records.  Elapsed time: 00:09:49s.  Time for last 1,000,000:    2s.  Last read position: chr16:30,343,149
INFO	2026-06-08 08:55:10	MarkDuplicates	Tracking 325555 as yet unmatched pairs. 25907 records in RAM.
INFO	2026-06-08 08:55:12	MarkDuplicates	Read   290,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:    2s.  Last read position: chr16:31,078,194
INFO	2026-06-08 08:55:12	MarkDuplicates	Tracking 322493 as yet unmatched pairs. 22842 records in RAM.
INFO	2026-06-08 08:55:14	MarkDuplicates	Read   291,000,000 records.  Elapsed time: 00:09:53s.  Time for last 1,000,000:    1s.  Last read position: chr16:51,646,497
INFO	2026-06-08 08:55:14	MarkDuplicates	Tracking 319570 as yet unmatched pairs. 19912 records in RAM.
INFO	2026-06-08 08:55:16	MarkDuplicates	Read   292,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    2s.  Last read position: chr16:57,755,119
INFO	2026-06-08 08:55:16	MarkDuplicates	Tracking 316934 as yet unmatched pairs. 17262 records in RAM.
INFO	2026-06-08 08:55:18	MarkDuplicates	Read   293,000,000 records.  Elapsed time: 00:09:57s.  Time for last 1,000,000:    2s.  Last read position: chr16:67,675,084
INFO	2026-06-08 08:55:18	MarkDuplicates	Tracking 313865 as yet unmatched pairs. 14181 records in RAM.
INFO	2026-06-08 08:55:20	MarkDuplicates	Read   294,000,000 records.  Elapsed time: 00:09:59s.  Time for last 1,000,000:    2s.  Last read position: chr16:70,254,030
INFO	2026-06-08 08:55:20	MarkDuplicates	Tracking 311734 as yet unmatched pairs. 12044 records in RAM.
INFO	2026-06-08 08:55:23	MarkDuplicates	Read   295,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    3s.  Last read position: chr16:75,648,237
INFO	2026-06-08 08:55:23	MarkDuplicates	Tracking 308328 as yet unmatched pairs. 8633 records in RAM.
INFO	2026-06-08 08:55:25	MarkDuplicates	Read   296,000,000 records.  Elapsed time: 00:10:04s.  Time for last 1,000,000:    1s.  Last read position: chr16:87,834,335
INFO	2026-06-08 08:55:25	MarkDuplicates	Tracking 305320 as yet unmatched pairs. 5613 records in RAM.
INFO	2026-06-08 08:55:27	MarkDuplicates	Read   297,000,000 records.  Elapsed time: 00:10:06s.  Time for last 1,000,000:    1s.  Last read position: chr16:89,300,647
INFO	2026-06-08 08:55:27	MarkDuplicates	Tracking 302060 as yet unmatched pairs. 2350 records in RAM.
INFO	2026-06-08 08:55:29	MarkDuplicates	Read   298,000,000 records.  Elapsed time: 00:10:08s.  Time for last 1,000,000:    2s.  Last read position: chr17:1,364,904
INFO	2026-06-08 08:55:29	MarkDuplicates	Tracking 304034 as yet unmatched pairs. 83434 records in RAM.
INFO	2026-06-08 08:55:31	MarkDuplicates	Read   299,000,000 records.  Elapsed time: 00:10:10s.  Time for last 1,000,000:    1s.  Last read position: chr17:3,663,724
INFO	2026-06-08 08:55:31	MarkDuplicates	Tracking 296692 as yet unmatched pairs. 76091 records in RAM.
INFO	2026-06-08 08:55:33	MarkDuplicates	Read   300,000,000 records.  Elapsed time: 00:10:12s.  Time for last 1,000,000:    1s.  Last read position: chr17:4,895,801
INFO	2026-06-08 08:55:33	MarkDuplicates	Tracking 293096 as yet unmatched pairs. 72488 records in RAM.
INFO	2026-06-08 08:55:35	MarkDuplicates	Read   301,000,000 records.  Elapsed time: 00:10:14s.  Time for last 1,000,000:    1s.  Last read position: chr17:7,259,574
INFO	2026-06-08 08:55:35	MarkDuplicates	Tracking 289801 as yet unmatched pairs. 69191 records in RAM.
INFO	2026-06-08 08:55:37	MarkDuplicates	Read   302,000,000 records.  Elapsed time: 00:10:17s.  Time for last 1,000,000:    2s.  Last read position: chr17:7,851,750
INFO	2026-06-08 08:55:37	MarkDuplicates	Tracking 287166 as yet unmatched pairs. 66551 records in RAM.
INFO	2026-06-08 08:55:39	MarkDuplicates	Read   303,000,000 records.  Elapsed time: 00:10:18s.  Time for last 1,000,000:    1s.  Last read position: chr17:16,381,152
INFO	2026-06-08 08:55:39	MarkDuplicates	Tracking 287271 as yet unmatched pairs. 66655 records in RAM.
INFO	2026-06-08 08:55:41	MarkDuplicates	Read   304,000,000 records.  Elapsed time: 00:10:20s.  Time for last 1,000,000:    1s.  Last read position: chr17:19,648,832
INFO	2026-06-08 08:55:41	MarkDuplicates	Tracking 281371 as yet unmatched pairs. 60752 records in RAM.
INFO	2026-06-08 08:55:43	MarkDuplicates	Read   305,000,000 records.  Elapsed time: 00:10:22s.  Time for last 1,000,000:    1s.  Last read position: chr17:28,357,293
INFO	2026-06-08 08:55:43	MarkDuplicates	Tracking 279532 as yet unmatched pairs. 58902 records in RAM.
INFO	2026-06-08 08:55:45	MarkDuplicates	Read   306,000,000 records.  Elapsed time: 00:10:24s.  Time for last 1,000,000:    2s.  Last read position: chr17:30,840,677
INFO	2026-06-08 08:55:45	MarkDuplicates	Tracking 275671 as yet unmatched pairs. 55039 records in RAM.
INFO	2026-06-08 08:55:47	MarkDuplicates	Read   307,000,000 records.  Elapsed time: 00:10:26s.  Time for last 1,000,000:    2s.  Last read position: chr17:36,527,515
INFO	2026-06-08 08:55:47	MarkDuplicates	Tracking 273380 as yet unmatched pairs. 52734 records in RAM.
INFO	2026-06-08 08:55:49	MarkDuplicates	Read   308,000,000 records.  Elapsed time: 00:10:29s.  Time for last 1,000,000:    2s.  Last read position: chr17:39,653,627
INFO	2026-06-08 08:55:49	MarkDuplicates	Tracking 271106 as yet unmatched pairs. 50458 records in RAM.
INFO	2026-06-08 08:55:51	MarkDuplicates	Read   309,000,000 records.  Elapsed time: 00:10:31s.  Time for last 1,000,000:    1s.  Last read position: chr17:40,880,102
INFO	2026-06-08 08:55:51	MarkDuplicates	Tracking 268182 as yet unmatched pairs. 47533 records in RAM.
INFO	2026-06-08 08:55:53	MarkDuplicates	Read   310,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:    1s.  Last read position: chr17:42,838,788
INFO	2026-06-08 08:55:53	MarkDuplicates	Tracking 265351 as yet unmatched pairs. 44702 records in RAM.
INFO	2026-06-08 08:55:55	MarkDuplicates	Read   311,000,000 records.  Elapsed time: 00:10:34s.  Time for last 1,000,000:    1s.  Last read position: chr17:45,245,098
INFO	2026-06-08 08:55:55	MarkDuplicates	Tracking 262599 as yet unmatched pairs. 41950 records in RAM.
INFO	2026-06-08 08:55:57	MarkDuplicates	Read   312,000,000 records.  Elapsed time: 00:10:36s.  Time for last 1,000,000:    1s.  Last read position: chr17:47,981,308
INFO	2026-06-08 08:55:57	MarkDuplicates	Tracking 260314 as yet unmatched pairs. 39658 records in RAM.
INFO	2026-06-08 08:55:59	MarkDuplicates	Read   313,000,000 records.  Elapsed time: 00:10:38s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,188,097
INFO	2026-06-08 08:55:59	MarkDuplicates	Tracking 279743 as yet unmatched pairs. 59079 records in RAM.
INFO	2026-06-08 08:56:01	MarkDuplicates	Read   314,000,000 records.  Elapsed time: 00:10:40s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,192,674
INFO	2026-06-08 08:56:01	MarkDuplicates	Tracking 275399 as yet unmatched pairs. 54734 records in RAM.
INFO	2026-06-08 08:56:03	MarkDuplicates	Read   315,000,000 records.  Elapsed time: 00:10:42s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,196,634
INFO	2026-06-08 08:56:03	MarkDuplicates	Tracking 269797 as yet unmatched pairs. 49128 records in RAM.
INFO	2026-06-08 08:56:05	MarkDuplicates	Read   316,000,000 records.  Elapsed time: 00:10:45s.  Time for last 1,000,000:    2s.  Last read position: chr17:55,403,804
INFO	2026-06-08 08:56:05	MarkDuplicates	Tracking 247620 as yet unmatched pairs. 26943 records in RAM.
INFO	2026-06-08 08:56:07	MarkDuplicates	Read   317,000,000 records.  Elapsed time: 00:10:46s.  Time for last 1,000,000:    1s.  Last read position: chr17:60,156,618
INFO	2026-06-08 08:56:07	MarkDuplicates	Tracking 245296 as yet unmatched pairs. 24607 records in RAM.
INFO	2026-06-08 08:56:09	MarkDuplicates	Read   318,000,000 records.  Elapsed time: 00:10:48s.  Time for last 1,000,000:    1s.  Last read position: chr17:65,014,598
INFO	2026-06-08 08:56:09	MarkDuplicates	Tracking 242377 as yet unmatched pairs. 21681 records in RAM.
INFO	2026-06-08 08:56:11	MarkDuplicates	Read   319,000,000 records.  Elapsed time: 00:10:50s.  Time for last 1,000,000:    1s.  Last read position: chr17:75,039,251
INFO	2026-06-08 08:56:11	MarkDuplicates	Tracking 239807 as yet unmatched pairs. 19111 records in RAM.
INFO	2026-06-08 08:56:13	MarkDuplicates	Read   320,000,000 records.  Elapsed time: 00:10:52s.  Time for last 1,000,000:    1s.  Last read position: chr17:75,778,661
INFO	2026-06-08 08:56:13	MarkDuplicates	Tracking 240429 as yet unmatched pairs. 19733 records in RAM.
INFO	2026-06-08 08:56:15	MarkDuplicates	Read   321,000,000 records.  Elapsed time: 00:10:54s.  Time for last 1,000,000:    2s.  Last read position: chr17:78,120,693
INFO	2026-06-08 08:56:15	MarkDuplicates	Tracking 234333 as yet unmatched pairs. 13636 records in RAM.
INFO	2026-06-08 08:56:17	MarkDuplicates	Read   322,000,000 records.  Elapsed time: 00:10:57s.  Time for last 1,000,000:    2s.  Last read position: chr17:80,288,723
INFO	2026-06-08 08:56:17	MarkDuplicates	Tracking 231146 as yet unmatched pairs. 10447 records in RAM.
INFO	2026-06-08 08:56:19	MarkDuplicates	Read   323,000,000 records.  Elapsed time: 00:10:59s.  Time for last 1,000,000:    2s.  Last read position: chr17:81,208,972
INFO	2026-06-08 08:56:19	MarkDuplicates	Tracking 227159 as yet unmatched pairs. 6453 records in RAM.
INFO	2026-06-08 08:56:21	MarkDuplicates	Read   324,000,000 records.  Elapsed time: 00:11:01s.  Time for last 1,000,000:    2s.  Last read position: chr17:81,905,072
INFO	2026-06-08 08:56:21	MarkDuplicates	Tracking 224018 as yet unmatched pairs. 3308 records in RAM.
INFO	2026-06-08 08:56:24	MarkDuplicates	Read   325,000,000 records.  Elapsed time: 00:11:03s.  Time for last 1,000,000:    2s.  Last read position: chr18:670,735
INFO	2026-06-08 08:56:24	MarkDuplicates	Tracking 221164 as yet unmatched pairs. 10601 records in RAM.
INFO	2026-06-08 08:56:26	MarkDuplicates	Read   326,000,000 records.  Elapsed time: 00:11:05s.  Time for last 1,000,000:    2s.  Last read position: chr18:23,898,974
INFO	2026-06-08 08:56:26	MarkDuplicates	Tracking 218127 as yet unmatched pairs. 7551 records in RAM.
INFO	2026-06-08 08:56:28	MarkDuplicates	Read   327,000,000 records.  Elapsed time: 00:11:07s.  Time for last 1,000,000:    1s.  Last read position: chr18:49,794,307
INFO	2026-06-08 08:56:28	MarkDuplicates	Tracking 215855 as yet unmatched pairs. 5275 records in RAM.
INFO	2026-06-08 08:56:30	MarkDuplicates	Read   328,000,000 records.  Elapsed time: 00:11:09s.  Time for last 1,000,000:    1s.  Last read position: chr18:62,860,478
INFO	2026-06-08 08:56:30	MarkDuplicates	Tracking 212252 as yet unmatched pairs. 1665 records in RAM.
INFO	2026-06-08 08:56:33	MarkDuplicates	Read   329,000,000 records.  Elapsed time: 00:11:12s.  Time for last 1,000,000:    2s.  Last read position: chr19:805,154
INFO	2026-06-08 08:56:33	MarkDuplicates	Tracking 210219 as yet unmatched pairs. 111759 records in RAM.
INFO	2026-06-08 08:56:35	MarkDuplicates	Read   330,000,000 records.  Elapsed time: 00:11:15s.  Time for last 1,000,000:    2s.  Last read position: chr19:1,300,590
INFO	2026-06-08 08:56:35	MarkDuplicates	Tracking 206082 as yet unmatched pairs. 107621 records in RAM.
INFO	2026-06-08 08:56:37	MarkDuplicates	Read   331,000,000 records.  Elapsed time: 00:11:17s.  Time for last 1,000,000:    1s.  Last read position: chr19:2,246,751
INFO	2026-06-08 08:56:37	MarkDuplicates	Tracking 202719 as yet unmatched pairs. 104258 records in RAM.
INFO	2026-06-08 08:56:39	MarkDuplicates	Read   332,000,000 records.  Elapsed time: 00:11:18s.  Time for last 1,000,000:    1s.  Last read position: chr19:4,094,488
INFO	2026-06-08 08:56:39	MarkDuplicates	Tracking 199743 as yet unmatched pairs. 101282 records in RAM.
INFO	2026-06-08 08:56:41	MarkDuplicates	Read   333,000,000 records.  Elapsed time: 00:11:20s.  Time for last 1,000,000:    1s.  Last read position: chr19:5,831,616
INFO	2026-06-08 08:56:41	MarkDuplicates	Tracking 196660 as yet unmatched pairs. 98199 records in RAM.
INFO	2026-06-08 08:56:43	MarkDuplicates	Read   334,000,000 records.  Elapsed time: 00:11:22s.  Time for last 1,000,000:    1s.  Last read position: chr19:7,555,269
INFO	2026-06-08 08:56:43	MarkDuplicates	Tracking 192710 as yet unmatched pairs. 94247 records in RAM.
INFO	2026-06-08 08:56:45	MarkDuplicates	Read   335,000,000 records.  Elapsed time: 00:11:24s.  Time for last 1,000,000:    1s.  Last read position: chr19:10,175,606
INFO	2026-06-08 08:56:45	MarkDuplicates	Tracking 189773 as yet unmatched pairs. 91308 records in RAM.
INFO	2026-06-08 08:56:47	MarkDuplicates	Read   336,000,000 records.  Elapsed time: 00:11:26s.  Time for last 1,000,000:    2s.  Last read position: chr19:11,058,838
INFO	2026-06-08 08:56:47	MarkDuplicates	Tracking 186902 as yet unmatched pairs. 88436 records in RAM.
INFO	2026-06-08 08:56:49	MarkDuplicates	Read   337,000,000 records.  Elapsed time: 00:11:28s.  Time for last 1,000,000:    2s.  Last read position: chr19:12,940,091
INFO	2026-06-08 08:56:49	MarkDuplicates	Tracking 186131 as yet unmatched pairs. 87665 records in RAM.
INFO	2026-06-08 08:56:51	MarkDuplicates	Read   338,000,000 records.  Elapsed time: 00:11:30s.  Time for last 1,000,000:    1s.  Last read position: chr19:14,516,690
INFO	2026-06-08 08:56:51	MarkDuplicates	Tracking 183468 as yet unmatched pairs. 84996 records in RAM.
INFO	2026-06-08 08:56:52	MarkDuplicates	Read   339,000,000 records.  Elapsed time: 00:11:32s.  Time for last 1,000,000:    1s.  Last read position: chr19:16,519,230
INFO	2026-06-08 08:56:52	MarkDuplicates	Tracking 177585 as yet unmatched pairs. 79113 records in RAM.
INFO	2026-06-08 08:56:54	MarkDuplicates	Read   340,000,000 records.  Elapsed time: 00:11:34s.  Time for last 1,000,000:    1s.  Last read position: chr19:18,083,464
INFO	2026-06-08 08:56:54	MarkDuplicates	Tracking 174458 as yet unmatched pairs. 75985 records in RAM.
INFO	2026-06-08 08:56:56	MarkDuplicates	Read   341,000,000 records.  Elapsed time: 00:11:35s.  Time for last 1,000,000:    1s.  Last read position: chr19:19,527,309
INFO	2026-06-08 08:56:56	MarkDuplicates	Tracking 172022 as yet unmatched pairs. 73549 records in RAM.
INFO	2026-06-08 08:56:58	MarkDuplicates	Read   342,000,000 records.  Elapsed time: 00:11:37s.  Time for last 1,000,000:    1s.  Last read position: chr19:35,267,175
INFO	2026-06-08 08:56:58	MarkDuplicates	Tracking 171107 as yet unmatched pairs. 72632 records in RAM.
INFO	2026-06-08 08:57:00	MarkDuplicates	Read   343,000,000 records.  Elapsed time: 00:11:39s.  Time for last 1,000,000:    1s.  Last read position: chr19:38,327,182
INFO	2026-06-08 08:57:00	MarkDuplicates	Tracking 164634 as yet unmatched pairs. 66158 records in RAM.
INFO	2026-06-08 08:57:02	MarkDuplicates	Read   344,000,000 records.  Elapsed time: 00:11:41s.  Time for last 1,000,000:    2s.  Last read position: chr19:39,422,939
INFO	2026-06-08 08:57:02	MarkDuplicates	Tracking 161596 as yet unmatched pairs. 63111 records in RAM.
INFO	2026-06-08 08:57:04	MarkDuplicates	Read   345,000,000 records.  Elapsed time: 00:11:43s.  Time for last 1,000,000:    2s.  Last read position: chr19:39,873,420
INFO	2026-06-08 08:57:04	MarkDuplicates	Tracking 171299 as yet unmatched pairs. 72814 records in RAM.
INFO	2026-06-08 08:57:06	MarkDuplicates	Read   346,000,000 records.  Elapsed time: 00:11:45s.  Time for last 1,000,000:    2s.  Last read position: chr19:39,876,857
INFO	2026-06-08 08:57:06	MarkDuplicates	Tracking 156867 as yet unmatched pairs. 58382 records in RAM.
INFO	2026-06-08 08:57:07	MarkDuplicates	Read   347,000,000 records.  Elapsed time: 00:11:46s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,877,984
INFO	2026-06-08 08:57:07	MarkDuplicates	Tracking 176127 as yet unmatched pairs. 77642 records in RAM.
INFO	2026-06-08 08:57:09	MarkDuplicates	Read   348,000,000 records.  Elapsed time: 00:11:48s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,885,751
INFO	2026-06-08 08:57:09	MarkDuplicates	Tracking 200207 as yet unmatched pairs. 101722 records in RAM.
INFO	2026-06-08 08:57:11	MarkDuplicates	Read   349,000,000 records.  Elapsed time: 00:11:50s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,889,532
INFO	2026-06-08 08:57:11	MarkDuplicates	Tracking 178804 as yet unmatched pairs. 80319 records in RAM.
INFO	2026-06-08 08:57:12	MarkDuplicates	Read   350,000,000 records.  Elapsed time: 00:11:51s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,891,744
INFO	2026-06-08 08:57:12	MarkDuplicates	Tracking 216852 as yet unmatched pairs. 118367 records in RAM.
INFO	2026-06-08 08:57:14	MarkDuplicates	Read   351,000,000 records.  Elapsed time: 00:11:53s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,892,971
INFO	2026-06-08 08:57:14	MarkDuplicates	Tracking 190660 as yet unmatched pairs. 92174 records in RAM.
INFO	2026-06-08 08:57:16	MarkDuplicates	Read   352,000,000 records.  Elapsed time: 00:11:55s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,894,069
INFO	2026-06-08 08:57:16	MarkDuplicates	Tracking 172144 as yet unmatched pairs. 73656 records in RAM.
INFO	2026-06-08 08:57:17	MarkDuplicates	Read   353,000,000 records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,901,997
INFO	2026-06-08 08:57:17	MarkDuplicates	Tracking 163283 as yet unmatched pairs. 64794 records in RAM.
INFO	2026-06-08 08:57:19	MarkDuplicates	Read   354,000,000 records.  Elapsed time: 00:11:58s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,905,992
INFO	2026-06-08 08:57:19	MarkDuplicates	Tracking 172714 as yet unmatched pairs. 74224 records in RAM.
INFO	2026-06-08 08:57:21	MarkDuplicates	Read   355,000,000 records.  Elapsed time: 00:12:00s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,918,312
INFO	2026-06-08 08:57:21	MarkDuplicates	Tracking 153177 as yet unmatched pairs. 54683 records in RAM.
INFO	2026-06-08 08:57:23	MarkDuplicates	Read   356,000,000 records.  Elapsed time: 00:12:03s.  Time for last 1,000,000:    2s.  Last read position: chr19:40,235,954
INFO	2026-06-08 08:57:23	MarkDuplicates	Tracking 132048 as yet unmatched pairs. 33554 records in RAM.
INFO	2026-06-08 08:57:25	MarkDuplicates	Read   357,000,000 records.  Elapsed time: 00:12:04s.  Time for last 1,000,000:    1s.  Last read position: chr19:41,709,715
INFO	2026-06-08 08:57:25	MarkDuplicates	Tracking 144935 as yet unmatched pairs. 46439 records in RAM.
INFO	2026-06-08 08:57:27	MarkDuplicates	Read   358,000,000 records.  Elapsed time: 00:12:06s.  Time for last 1,000,000:    1s.  Last read position: chr19:41,720,926
INFO	2026-06-08 08:57:27	MarkDuplicates	Tracking 132875 as yet unmatched pairs. 34379 records in RAM.
INFO	2026-06-08 08:57:29	MarkDuplicates	Read   359,000,000 records.  Elapsed time: 00:12:08s.  Time for last 1,000,000:    1s.  Last read position: chr19:42,287,694
INFO	2026-06-08 08:57:29	MarkDuplicates	Tracking 123773 as yet unmatched pairs. 25267 records in RAM.
INFO	2026-06-08 08:57:30	MarkDuplicates	Read   360,000,000 records.  Elapsed time: 00:12:10s.  Time for last 1,000,000:    1s.  Last read position: chr19:45,040,270
INFO	2026-06-08 08:57:30	MarkDuplicates	Tracking 120342 as yet unmatched pairs. 21828 records in RAM.
INFO	2026-06-08 08:57:32	MarkDuplicates	Read   361,000,000 records.  Elapsed time: 00:12:11s.  Time for last 1,000,000:    1s.  Last read position: chr19:46,921,006
INFO	2026-06-08 08:57:32	MarkDuplicates	Tracking 116458 as yet unmatched pairs. 17942 records in RAM.
INFO	2026-06-08 08:57:34	MarkDuplicates	Read   362,000,000 records.  Elapsed time: 00:12:13s.  Time for last 1,000,000:    1s.  Last read position: chr19:48,987,362
INFO	2026-06-08 08:57:34	MarkDuplicates	Tracking 113238 as yet unmatched pairs. 14712 records in RAM.
INFO	2026-06-08 08:57:36	MarkDuplicates	Read   363,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:    1s.  Last read position: chr19:49,664,680
INFO	2026-06-08 08:57:36	MarkDuplicates	Tracking 110641 as yet unmatched pairs. 12115 records in RAM.
INFO	2026-06-08 08:57:38	MarkDuplicates	Read   364,000,000 records.  Elapsed time: 00:12:17s.  Time for last 1,000,000:    1s.  Last read position: chr19:51,346,915
INFO	2026-06-08 08:57:38	MarkDuplicates	Tracking 107036 as yet unmatched pairs. 8510 records in RAM.
INFO	2026-06-08 08:57:39	MarkDuplicates	Read   365,000,000 records.  Elapsed time: 00:12:18s.  Time for last 1,000,000:    1s.  Last read position: chr19:54,458,692
INFO	2026-06-08 08:57:39	MarkDuplicates	Tracking 105013 as yet unmatched pairs. 6487 records in RAM.
INFO	2026-06-08 08:57:41	MarkDuplicates	Read   366,000,000 records.  Elapsed time: 00:12:20s.  Time for last 1,000,000:    1s.  Last read position: chr19:56,088,072
INFO	2026-06-08 08:57:41	MarkDuplicates	Tracking 100548 as yet unmatched pairs. 2022 records in RAM.
INFO	2026-06-08 08:57:43	MarkDuplicates	Read   367,000,000 records.  Elapsed time: 00:12:22s.  Time for last 1,000,000:    2s.  Last read position: chr20:1,464,342
INFO	2026-06-08 08:57:43	MarkDuplicates	Tracking 97675 as yet unmatched pairs. 24674 records in RAM.
INFO	2026-06-08 08:57:45	MarkDuplicates	Read   368,000,000 records.  Elapsed time: 00:12:24s.  Time for last 1,000,000:    1s.  Last read position: chr20:10,622,720
INFO	2026-06-08 08:57:45	MarkDuplicates	Tracking 94436 as yet unmatched pairs. 21435 records in RAM.
INFO	2026-06-08 08:57:48	MarkDuplicates	Read   369,000,000 records.  Elapsed time: 00:12:27s.  Time for last 1,000,000:    2s.  Last read position: chr20:24,970,270
INFO	2026-06-08 08:57:48	MarkDuplicates	Tracking 92109 as yet unmatched pairs. 19108 records in RAM.
INFO	2026-06-08 08:57:49	MarkDuplicates	Read   370,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:    1s.  Last read position: chr20:34,750,500
INFO	2026-06-08 08:57:49	MarkDuplicates	Tracking 88938 as yet unmatched pairs. 15934 records in RAM.
INFO	2026-06-08 08:57:51	MarkDuplicates	Read   371,000,000 records.  Elapsed time: 00:12:30s.  Time for last 1,000,000:    1s.  Last read position: chr20:38,138,252
INFO	2026-06-08 08:57:51	MarkDuplicates	Tracking 86251 as yet unmatched pairs. 13245 records in RAM.
INFO	2026-06-08 08:57:53	MarkDuplicates	Read   372,000,000 records.  Elapsed time: 00:12:32s.  Time for last 1,000,000:    1s.  Last read position: chr20:45,803,340
INFO	2026-06-08 08:57:53	MarkDuplicates	Tracking 83349 as yet unmatched pairs. 10342 records in RAM.
INFO	2026-06-08 08:57:54	MarkDuplicates	Read   373,000,000 records.  Elapsed time: 00:12:34s.  Time for last 1,000,000:    1s.  Last read position: chr20:50,579,807
INFO	2026-06-08 08:57:54	MarkDuplicates	Tracking 80555 as yet unmatched pairs. 7548 records in RAM.
INFO	2026-06-08 08:57:56	MarkDuplicates	Read   374,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:    1s.  Last read position: chr20:62,283,999
INFO	2026-06-08 08:57:56	MarkDuplicates	Tracking 77532 as yet unmatched pairs. 4512 records in RAM.
INFO	2026-06-08 08:57:58	MarkDuplicates	Read   375,000,000 records.  Elapsed time: 00:12:37s.  Time for last 1,000,000:    1s.  Last read position: chr20:63,701,848
INFO	2026-06-08 08:57:58	MarkDuplicates	Tracking 74479 as yet unmatched pairs. 1459 records in RAM.
INFO	2026-06-08 08:58:00	MarkDuplicates	Read   376,000,000 records.  Elapsed time: 00:12:39s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,258,917
INFO	2026-06-08 08:58:00	MarkDuplicates	Tracking 71888 as yet unmatched pairs. 14004 records in RAM.
INFO	2026-06-08 08:58:02	MarkDuplicates	Read   377,000,000 records.  Elapsed time: 00:12:41s.  Time for last 1,000,000:    1s.  Last read position: chr21:9,325,130
INFO	2026-06-08 08:58:02	MarkDuplicates	Tracking 70320 as yet unmatched pairs. 12433 records in RAM.
INFO	2026-06-08 08:58:03	MarkDuplicates	Read   378,000,000 records.  Elapsed time: 00:12:43s.  Time for last 1,000,000:    1s.  Last read position: chr21:33,554,297
INFO	2026-06-08 08:58:03	MarkDuplicates	Tracking 67953 as yet unmatched pairs. 10065 records in RAM.
INFO	2026-06-08 08:58:05	MarkDuplicates	Read   379,000,000 records.  Elapsed time: 00:12:44s.  Time for last 1,000,000:    1s.  Last read position: chr21:41,471,815
INFO	2026-06-08 08:58:05	MarkDuplicates	Tracking 66928 as yet unmatched pairs. 9035 records in RAM.
INFO	2026-06-08 08:58:07	MarkDuplicates	Read   380,000,000 records.  Elapsed time: 00:12:46s.  Time for last 1,000,000:    1s.  Last read position: chr21:44,313,011
INFO	2026-06-08 08:58:07	MarkDuplicates	Tracking 62586 as yet unmatched pairs. 4692 records in RAM.
INFO	2026-06-08 08:58:09	MarkDuplicates	Read   381,000,000 records.  Elapsed time: 00:12:48s.  Time for last 1,000,000:    1s.  Last read position: chr21:46,260,820
INFO	2026-06-08 08:58:09	MarkDuplicates	Tracking 58943 as yet unmatched pairs. 1049 records in RAM.
INFO	2026-06-08 08:58:12	MarkDuplicates	Read   382,000,000 records.  Elapsed time: 00:12:51s.  Time for last 1,000,000:    3s.  Last read position: chr22:20,585,212
INFO	2026-06-08 08:58:12	MarkDuplicates	Tracking 56670 as yet unmatched pairs. 28982 records in RAM.
INFO	2026-06-08 08:58:14	MarkDuplicates	Read   383,000,000 records.  Elapsed time: 00:12:53s.  Time for last 1,000,000:    2s.  Last read position: chr22:24,056,233
INFO	2026-06-08 08:58:14	MarkDuplicates	Tracking 52643 as yet unmatched pairs. 24953 records in RAM.
INFO	2026-06-08 08:58:16	MarkDuplicates	Read   384,000,000 records.  Elapsed time: 00:12:55s.  Time for last 1,000,000:    1s.  Last read position: chr22:29,298,881
INFO	2026-06-08 08:58:16	MarkDuplicates	Tracking 53271 as yet unmatched pairs. 25581 records in RAM.
INFO	2026-06-08 08:58:18	MarkDuplicates	Read   385,000,000 records.  Elapsed time: 00:12:57s.  Time for last 1,000,000:    1s.  Last read position: chr22:32,110,016
INFO	2026-06-08 08:58:18	MarkDuplicates	Tracking 47161 as yet unmatched pairs. 19469 records in RAM.
INFO	2026-06-08 08:58:20	MarkDuplicates	Read   386,000,000 records.  Elapsed time: 00:12:59s.  Time for last 1,000,000:    1s.  Last read position: chr22:36,526,001
INFO	2026-06-08 08:58:20	MarkDuplicates	Tracking 44584 as yet unmatched pairs. 16892 records in RAM.
INFO	2026-06-08 08:58:21	MarkDuplicates	Read   387,000,000 records.  Elapsed time: 00:13:01s.  Time for last 1,000,000:    1s.  Last read position: chr22:38,485,992
INFO	2026-06-08 08:58:21	MarkDuplicates	Tracking 42502 as yet unmatched pairs. 14810 records in RAM.
INFO	2026-06-08 08:58:23	MarkDuplicates	Read   388,000,000 records.  Elapsed time: 00:13:02s.  Time for last 1,000,000:    1s.  Last read position: chr22:41,160,705
INFO	2026-06-08 08:58:23	MarkDuplicates	Tracking 38343 as yet unmatched pairs. 10651 records in RAM.
INFO	2026-06-08 08:58:25	MarkDuplicates	Read   389,000,000 records.  Elapsed time: 00:13:04s.  Time for last 1,000,000:    1s.  Last read position: chr22:44,189,186
INFO	2026-06-08 08:58:25	MarkDuplicates	Tracking 35482 as yet unmatched pairs. 7790 records in RAM.
INFO	2026-06-08 08:58:27	MarkDuplicates	Read   390,000,000 records.  Elapsed time: 00:13:06s.  Time for last 1,000,000:    2s.  Last read position: chr22:50,284,573
INFO	2026-06-08 08:58:27	MarkDuplicates	Tracking 33008 as yet unmatched pairs. 5316 records in RAM.
INFO	2026-06-08 08:58:29	MarkDuplicates	Read   391,000,000 records.  Elapsed time: 00:13:09s.  Time for last 1,000,000:    2s.  Last read position: chr22:50,627,276
INFO	2026-06-08 08:58:29	MarkDuplicates	Tracking 28811 as yet unmatched pairs. 1119 records in RAM.
INFO	2026-06-08 08:58:32	MarkDuplicates	Read   392,000,000 records.  Elapsed time: 00:13:11s.  Time for last 1,000,000:    2s.  Last read position: chrX:19,746,317
INFO	2026-06-08 08:58:32	MarkDuplicates	Tracking 25369 as yet unmatched pairs. 19969 records in RAM.
INFO	2026-06-08 08:58:34	MarkDuplicates	Read   393,000,000 records.  Elapsed time: 00:13:13s.  Time for last 1,000,000:    2s.  Last read position: chrX:47,142,621
INFO	2026-06-08 08:58:34	MarkDuplicates	Tracking 23866 as yet unmatched pairs. 18466 records in RAM.
INFO	2026-06-08 08:58:36	MarkDuplicates	Read   394,000,000 records.  Elapsed time: 00:13:15s.  Time for last 1,000,000:    2s.  Last read position: chrX:49,250,150
INFO	2026-06-08 08:58:36	MarkDuplicates	Tracking 19747 as yet unmatched pairs. 14347 records in RAM.
INFO	2026-06-08 08:58:38	MarkDuplicates	Read   395,000,000 records.  Elapsed time: 00:13:17s.  Time for last 1,000,000:    2s.  Last read position: chrX:65,737,228
INFO	2026-06-08 08:58:38	MarkDuplicates	Tracking 18230 as yet unmatched pairs. 12830 records in RAM.
INFO	2026-06-08 08:58:40	MarkDuplicates	Read   396,000,000 records.  Elapsed time: 00:13:19s.  Time for last 1,000,000:    1s.  Last read position: chrX:77,857,481
INFO	2026-06-08 08:58:40	MarkDuplicates	Tracking 14817 as yet unmatched pairs. 9417 records in RAM.
INFO	2026-06-08 08:58:42	MarkDuplicates	Read   397,000,000 records.  Elapsed time: 00:13:21s.  Time for last 1,000,000:    2s.  Last read position: chrX:119,637,142
INFO	2026-06-08 08:58:42	MarkDuplicates	Tracking 12323 as yet unmatched pairs. 6923 records in RAM.
INFO	2026-06-08 08:58:44	MarkDuplicates	Read   398,000,000 records.  Elapsed time: 00:13:23s.  Time for last 1,000,000:    2s.  Last read position: chrX:153,797,547
INFO	2026-06-08 08:58:44	MarkDuplicates	Tracking 10487 as yet unmatched pairs. 5087 records in RAM.
INFO	2026-06-08 08:58:47	MarkDuplicates	Read   399,000,000 records.  Elapsed time: 00:13:26s.  Time for last 1,000,000:    2s.  Last read position: chrX:154,450,425
INFO	2026-06-08 08:58:47	MarkDuplicates	Tracking 6394 as yet unmatched pairs. 994 records in RAM.
INFO	2026-06-08 08:58:48	MarkDuplicates	Read   400,000,000 records.  Elapsed time: 00:13:28s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:158,119
INFO	2026-06-08 08:58:48	MarkDuplicates	Tracking 3414 as yet unmatched pairs. 61 records in RAM.
INFO	2026-06-08 08:58:50	MarkDuplicates	Read   401,000,000 records.  Elapsed time: 00:13:29s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:176,090
INFO	2026-06-08 08:58:50	MarkDuplicates	Tracking 57 as yet unmatched pairs. 47 records in RAM.
INFO	2026-06-08 08:58:50	MarkDuplicates	Read 401307024 records. 0 pairs never matched.
INFO	2026-06-08 08:59:36	MarkDuplicates	After buildSortedReadEndLists freeMemory: 34871453064; totalMemory: 49794777088; maxMemory: 63585648640
INFO	2026-06-08 08:59:36	MarkDuplicates	Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO	2026-06-08 09:00:01	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2026-06-08 09:00:21	OpticalDuplicateFinder	Large duplicate set. size = 1104
INFO	2026-06-08 09:00:21	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-31,577
INFO	2026-06-08 09:00:24	OpticalDuplicateFinder	Large duplicate set. size = 1045
INFO	2026-06-08 09:00:24	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:1,607
INFO	2026-06-08 09:00:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
WARNING	2026-06-08 09:00:45	SortingCollection	There is not enough memory per file for buffering. Reading will be unbuffered.
INFO	2026-06-08 09:01:40	MarkDuplicates	Sorting list of duplicate records.
INFO	2026-06-08 09:01:47	MarkDuplicates	After generateDuplicateIndexes freeMemory: 33711072072; totalMemory: 49660559360; maxMemory: 63585648640
INFO	2026-06-08 09:01:47	MarkDuplicates	Marking 163274816 records as duplicates.
INFO	2026-06-08 09:01:47	MarkDuplicates	Found 20403574 optical duplicate clusters.
INFO	2026-06-08 09:01:47	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2026-06-08 09:02:08	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:00:20s.  Time for last 10,000,000:   20s.  Last read position: chr1:36,178,549
INFO	2026-06-08 09:02:30	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:00:43s.  Time for last 10,000,000:   22s.  Last read position: chr1:148,558,355
INFO	2026-06-08 09:02:50	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:01:03s.  Time for last 10,000,000:   20s.  Last read position: chr1:201,649,267
INFO	2026-06-08 09:03:12	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:01:25s.  Time for last 10,000,000:   21s.  Last read position: chr2:27,040,070
INFO	2026-06-08 09:03:33	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:01:46s.  Time for last 10,000,000:   21s.  Last read position: chr2:95,906,649
INFO	2026-06-08 09:03:53	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:02:05s.  Time for last 10,000,000:   19s.  Last read position: chr2:219,539,789
INFO	2026-06-08 09:04:13	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:02:25s.  Time for last 10,000,000:   20s.  Last read position: chr3:52,292,291
INFO	2026-06-08 09:04:33	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:02:45s.  Time for last 10,000,000:   19s.  Last read position: chr3:195,778,936
INFO	2026-06-08 09:04:52	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:03:05s.  Time for last 10,000,000:   19s.  Last read position: chr4:39,458,210
INFO	2026-06-08 09:05:15	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:03:28s.  Time for last 10,000,000:   22s.  Last read position: chr5:69,894,594
INFO	2026-06-08 09:05:34	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:03:47s.  Time for last 10,000,000:   18s.  Last read position: chr5:176,238,477
INFO	2026-06-08 09:05:53	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:04:05s.  Time for last 10,000,000:   18s.  Last read position: chr6:31,874,956
INFO	2026-06-08 09:06:11	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:04:24s.  Time for last 10,000,000:   18s.  Last read position: chr6:144,447,670
INFO	2026-06-08 09:06:30	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:04:42s.  Time for last 10,000,000:   18s.  Last read position: chr7:93,994,342
INFO	2026-06-08 09:06:49	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:05:02s.  Time for last 10,000,000:   19s.  Last read position: chr7:101,001,187
INFO	2026-06-08 09:07:10	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:05:23s.  Time for last 10,000,000:   20s.  Last read position: chr8:23,328,429
INFO	2026-06-08 09:07:30	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:05:42s.  Time for last 10,000,000:   19s.  Last read position: chr8:143,984,662
INFO	2026-06-08 09:07:50	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:06:02s.  Time for last 10,000,000:   20s.  Last read position: chr9:128,151,929
INFO	2026-06-08 09:08:12	MarkDuplicates	Written   190,000,000 records.  Elapsed time: 00:06:24s.  Time for last 10,000,000:   21s.  Last read position: chr10:76,058,733
INFO	2026-06-08 09:08:29	MarkDuplicates	Written   200,000,000 records.  Elapsed time: 00:06:41s.  Time for last 10,000,000:   17s.  Last read position: chr10:122,640,219
INFO	2026-06-08 09:08:50	MarkDuplicates	Written   210,000,000 records.  Elapsed time: 00:07:02s.  Time for last 10,000,000:   21s.  Last read position: chr11:32,934,941
INFO	2026-06-08 09:09:14	MarkDuplicates	Written   220,000,000 records.  Elapsed time: 00:07:26s.  Time for last 10,000,000:   23s.  Last read position: chr11:72,013,724
INFO	2026-06-08 09:09:37	MarkDuplicates	Written   230,000,000 records.  Elapsed time: 00:07:49s.  Time for last 10,000,000:   22s.  Last read position: chr12:29,311,047
INFO	2026-06-08 09:09:58	MarkDuplicates	Written   240,000,000 records.  Elapsed time: 00:08:10s.  Time for last 10,000,000:   21s.  Last read position: chr12:110,492,065
INFO	2026-06-08 09:10:19	MarkDuplicates	Written   250,000,000 records.  Elapsed time: 00:08:32s.  Time for last 10,000,000:   21s.  Last read position: chr13:112,881,783
INFO	2026-06-08 09:10:40	MarkDuplicates	Written   260,000,000 records.  Elapsed time: 00:08:52s.  Time for last 10,000,000:   20s.  Last read position: chr14:104,883,931
INFO	2026-06-08 09:11:00	MarkDuplicates	Written   270,000,000 records.  Elapsed time: 00:09:12s.  Time for last 10,000,000:   20s.  Last read position: chr15:58,888,524
INFO	2026-06-08 09:11:20	MarkDuplicates	Written   280,000,000 records.  Elapsed time: 00:09:32s.  Time for last 10,000,000:   19s.  Last read position: chr16:5,025,594
INFO	2026-06-08 09:11:38	MarkDuplicates	Written   290,000,000 records.  Elapsed time: 00:09:50s.  Time for last 10,000,000:   18s.  Last read position: chr16:31,078,194
INFO	2026-06-08 09:11:56	MarkDuplicates	Written   300,000,000 records.  Elapsed time: 00:10:08s.  Time for last 10,000,000:   17s.  Last read position: chr17:4,895,801
INFO	2026-06-08 09:12:14	MarkDuplicates	Written   310,000,000 records.  Elapsed time: 00:10:26s.  Time for last 10,000,000:   17s.  Last read position: chr17:42,838,788
INFO	2026-06-08 09:12:34	MarkDuplicates	Written   320,000,000 records.  Elapsed time: 00:10:46s.  Time for last 10,000,000:   20s.  Last read position: chr17:75,778,661
INFO	2026-06-08 09:12:53	MarkDuplicates	Written   330,000,000 records.  Elapsed time: 00:11:06s.  Time for last 10,000,000:   19s.  Last read position: chr19:1,300,590
INFO	2026-06-08 09:13:23	MarkDuplicates	Written   340,000,000 records.  Elapsed time: 00:11:35s.  Time for last 10,000,000:   29s.  Last read position: chr19:18,083,464
INFO	2026-06-08 09:13:51	MarkDuplicates	Written   350,000,000 records.  Elapsed time: 00:12:03s.  Time for last 10,000,000:   28s.  Last read position: chr19:39,891,744
INFO	2026-06-08 09:14:17	MarkDuplicates	Written   360,000,000 records.  Elapsed time: 00:12:30s.  Time for last 10,000,000:   26s.  Last read position: chr19:45,040,270
INFO	2026-06-08 09:14:39	MarkDuplicates	Written   370,000,000 records.  Elapsed time: 00:12:51s.  Time for last 10,000,000:   21s.  Last read position: chr20:34,750,500
INFO	2026-06-08 09:15:02	MarkDuplicates	Written   380,000,000 records.  Elapsed time: 00:13:14s.  Time for last 10,000,000:   22s.  Last read position: chr21:44,313,011
INFO	2026-06-08 09:15:21	MarkDuplicates	Written   390,000,000 records.  Elapsed time: 00:13:33s.  Time for last 10,000,000:   18s.  Last read position: chr22:50,284,573
INFO	2026-06-08 09:15:38	MarkDuplicates	Written   400,000,000 records.  Elapsed time: 00:13:51s.  Time for last 10,000,000:   17s.  Last read position: GL000220.1:158,119
INFO	2026-06-08 09:15:50	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2026-06-08 09:15:50	MarkDuplicates	Duplicate Index cleanup.
INFO	2026-06-08 09:15:50	MarkDuplicates	Getting Memory Stats.
INFO	2026-06-08 09:15:50	MarkDuplicates	Before output close freeMemory: 202555880; totalMemory: 234881024; maxMemory: 63585648640
INFO	2026-06-08 09:15:50	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2026-06-08 09:15:50	MarkDuplicates	After output close freeMemory: 104866920; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 09:15:50 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 30.53 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory