Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/03fea4fe27076ec7b933be0363b6bd/aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/81ccc52351481089ad85a333cc6b5a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/81ccc52351481089ad85a333cc6b5a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)

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 -Xmx121241M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
09:40:07.277 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 09:40:07 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 09:40:07 GMT 2026] Executing as ?@nf-b181ccc52351481089ad85a333cc6b5a-11f5a-nh9xb 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 09:40:07	MarkDuplicates	Start of doWork freeMemory: 105132952; totalMemory: 134217728; maxMemory: 127137742848
INFO	2026-06-08 09:40:07	MarkDuplicates	Reading input file and constructing read end information.
INFO	2026-06-08 09:40:07	MarkDuplicates	Will retain up to 460643995 data points before spilling to disk.
INFO	2026-06-08 09:40:12	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:02s.  Time for last 1,000,000:    2s.  Last read position: chr1:1,310,974
INFO	2026-06-08 09:40:12	MarkDuplicates	Tracking 2005 as yet unmatched pairs. 146 records in RAM.
INFO	2026-06-08 09:40:15	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    2s.  Last read position: chr1:1,804,499
INFO	2026-06-08 09:40:15	MarkDuplicates	Tracking 5318 as yet unmatched pairs. 1422 records in RAM.
INFO	2026-06-08 09:40:17	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    2s.  Last read position: chr1:7,970,959
INFO	2026-06-08 09:40:17	MarkDuplicates	Tracking 6128 as yet unmatched pairs. 273 records in RAM.
INFO	2026-06-08 09:40:19	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    2s.  Last read position: chr1:11,144,694
INFO	2026-06-08 09:40:19	MarkDuplicates	Tracking 7664 as yet unmatched pairs. 184 records in RAM.
INFO	2026-06-08 09:40:22	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    2s.  Last read position: chr1:15,935,341
INFO	2026-06-08 09:40:22	MarkDuplicates	Tracking 9532 as yet unmatched pairs. 478 records in RAM.
INFO	2026-06-08 09:40:24	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    1s.  Last read position: chr1:19,151,707
INFO	2026-06-08 09:40:24	MarkDuplicates	Tracking 10850 as yet unmatched pairs. 240 records in RAM.
INFO	2026-06-08 09:40:26	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    2s.  Last read position: chr1:21,839,072
INFO	2026-06-08 09:40:26	MarkDuplicates	Tracking 12815 as yet unmatched pairs. 521 records in RAM.
INFO	2026-06-08 09:40:29	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    2s.  Last read position: chr1:23,310,777
INFO	2026-06-08 09:40:29	MarkDuplicates	Tracking 14149 as yet unmatched pairs. 248 records in RAM.
INFO	2026-06-08 09:40:31	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    2s.  Last read position: chr1:26,546,873
INFO	2026-06-08 09:40:31	MarkDuplicates	Tracking 15841 as yet unmatched pairs. 369 records in RAM.
INFO	2026-06-08 09:40:33	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    2s.  Last read position: chr1:28,743,707
INFO	2026-06-08 09:40:33	MarkDuplicates	Tracking 17574 as yet unmatched pairs. 486 records in RAM.
INFO	2026-06-08 09:40:35	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    2s.  Last read position: chr1:32,226,505
INFO	2026-06-08 09:40:35	MarkDuplicates	Tracking 19372 as yet unmatched pairs. 645 records in RAM.
INFO	2026-06-08 09:40:38	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    2s.  Last read position: chr1:35,389,952
INFO	2026-06-08 09:40:38	MarkDuplicates	Tracking 20662 as yet unmatched pairs. 229 records in RAM.
INFO	2026-06-08 09:40:40	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    2s.  Last read position: chr1:39,318,588
INFO	2026-06-08 09:40:40	MarkDuplicates	Tracking 23011 as yet unmatched pairs. 880 records in RAM.
INFO	2026-06-08 09:40:42	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    2s.  Last read position: chr1:41,581,236
INFO	2026-06-08 09:40:42	MarkDuplicates	Tracking 23882 as yet unmatched pairs. 219 records in RAM.
INFO	2026-06-08 09:40:45	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    2s.  Last read position: chr1:43,621,114
INFO	2026-06-08 09:40:45	MarkDuplicates	Tracking 26896 as yet unmatched pairs. 1580 records in RAM.
INFO	2026-06-08 09:40:47	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    2s.  Last read position: chr1:46,194,363
INFO	2026-06-08 09:40:47	MarkDuplicates	Tracking 27262 as yet unmatched pairs. 295 records in RAM.
INFO	2026-06-08 09:40:50	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    2s.  Last read position: chr1:54,043,424
INFO	2026-06-08 09:40:50	MarkDuplicates	Tracking 29857 as yet unmatched pairs. 1221 records in RAM.
INFO	2026-06-08 09:40:52	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    2s.  Last read position: chr1:64,867,180
INFO	2026-06-08 09:40:52	MarkDuplicates	Tracking 30517 as yet unmatched pairs. 383 records in RAM.
INFO	2026-06-08 09:40:54	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    2s.  Last read position: chr1:87,339,555
INFO	2026-06-08 09:40:54	MarkDuplicates	Tracking 31854 as yet unmatched pairs. 231 records in RAM.
INFO	2026-06-08 09:40:56	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    1s.  Last read position: chr1:102,962,738
INFO	2026-06-08 09:40:56	MarkDuplicates	Tracking 33902 as yet unmatched pairs. 869 records in RAM.
INFO	2026-06-08 09:40:58	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    2s.  Last read position: chr1:110,340,009
INFO	2026-06-08 09:40:58	MarkDuplicates	Tracking 35185 as yet unmatched pairs. 582 records in RAM.
INFO	2026-06-08 09:41:00	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    2s.  Last read position: chr1:114,464,338
INFO	2026-06-08 09:41:00	MarkDuplicates	Tracking 36813 as yet unmatched pairs. 724 records in RAM.
INFO	2026-06-08 09:41:02	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    2s.  Last read position: chr1:117,402,326
INFO	2026-06-08 09:41:02	MarkDuplicates	Tracking 38551 as yet unmatched pairs. 333 records in RAM.
INFO	2026-06-08 09:41:05	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    2s.  Last read position: chr1:120,439,613
INFO	2026-06-08 09:41:05	MarkDuplicates	Tracking 39830 as yet unmatched pairs. 86 records in RAM.
INFO	2026-06-08 09:41:07	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    2s.  Last read position: chr1:145,393,883
INFO	2026-06-08 09:41:07	MarkDuplicates	Tracking 40721 as yet unmatched pairs. 292 records in RAM.
INFO	2026-06-08 09:41:09	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    1s.  Last read position: chr1:146,139,964
INFO	2026-06-08 09:41:09	MarkDuplicates	Tracking 42611 as yet unmatched pairs. 1318 records in RAM.
INFO	2026-06-08 09:41:10	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    1s.  Last read position: chr1:148,110,495
INFO	2026-06-08 09:41:10	MarkDuplicates	Tracking 42723 as yet unmatched pairs. 494 records in RAM.
INFO	2026-06-08 09:41:12	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    1s.  Last read position: chr1:148,586,152
INFO	2026-06-08 09:41:12	MarkDuplicates	Tracking 43434 as yet unmatched pairs. 833 records in RAM.
INFO	2026-06-08 09:41:14	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    1s.  Last read position: chr1:149,455,539
INFO	2026-06-08 09:41:14	MarkDuplicates	Tracking 44781 as yet unmatched pairs. 1419 records in RAM.
INFO	2026-06-08 09:41:16	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    1s.  Last read position: chr1:149,887,155
INFO	2026-06-08 09:41:16	MarkDuplicates	Tracking 45115 as yet unmatched pairs. 1035 records in RAM.
INFO	2026-06-08 09:41:18	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    1s.  Last read position: chr1:150,579,310
INFO	2026-06-08 09:41:18	MarkDuplicates	Tracking 47234 as yet unmatched pairs. 1565 records in RAM.
INFO	2026-06-08 09:41:20	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    2s.  Last read position: chr1:151,103,560
INFO	2026-06-08 09:41:20	MarkDuplicates	Tracking 47351 as yet unmatched pairs. 211 records in RAM.
INFO	2026-06-08 09:41:22	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    2s.  Last read position: chr1:151,440,974
INFO	2026-06-08 09:41:22	MarkDuplicates	Tracking 49705 as yet unmatched pairs. 902 records in RAM.
INFO	2026-06-08 09:41:24	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    2s.  Last read position: chr1:153,817,522
INFO	2026-06-08 09:41:24	MarkDuplicates	Tracking 50932 as yet unmatched pairs. 516 records in RAM.
INFO	2026-06-08 09:41:26	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    1s.  Last read position: chr1:154,172,094
INFO	2026-06-08 09:41:26	MarkDuplicates	Tracking 56209 as yet unmatched pairs. 4266 records in RAM.
INFO	2026-06-08 09:41:29	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:01:18s.  Time for last 1,000,000:    2s.  Last read position: chr1:154,601,361
INFO	2026-06-08 09:41:29	MarkDuplicates	Tracking 55056 as yet unmatched pairs. 1689 records in RAM.
INFO	2026-06-08 09:41:31	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    2s.  Last read position: chr1:155,057,348
INFO	2026-06-08 09:41:31	MarkDuplicates	Tracking 59162 as yet unmatched pairs. 4190 records in RAM.
INFO	2026-06-08 09:41:33	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    2s.  Last read position: chr1:155,190,768
INFO	2026-06-08 09:41:33	MarkDuplicates	Tracking 56840 as yet unmatched pairs. 366 records in RAM.
INFO	2026-06-08 09:41:35	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    1s.  Last read position: chr1:155,481,798
INFO	2026-06-08 09:41:35	MarkDuplicates	Tracking 58602 as yet unmatched pairs. 712 records in RAM.
INFO	2026-06-08 09:41:37	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    2s.  Last read position: chr1:156,050,479
INFO	2026-06-08 09:41:37	MarkDuplicates	Tracking 59658 as yet unmatched pairs. 365 records in RAM.
INFO	2026-06-08 09:41:39	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    2s.  Last read position: chr1:156,246,215
INFO	2026-06-08 09:41:39	MarkDuplicates	Tracking 62711 as yet unmatched pairs. 1533 records in RAM.
INFO	2026-06-08 09:41:41	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    2s.  Last read position: chr1:156,700,571
INFO	2026-06-08 09:41:41	MarkDuplicates	Tracking 66519 as yet unmatched pairs. 3698 records in RAM.
INFO	2026-06-08 09:41:43	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    1s.  Last read position: chr1:160,211,613
INFO	2026-06-08 09:41:43	MarkDuplicates	Tracking 65361 as yet unmatched pairs. 901 records in RAM.
INFO	2026-06-08 09:41:45	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:    2s.  Last read position: chr1:161,049,322
INFO	2026-06-08 09:41:45	MarkDuplicates	Tracking 66477 as yet unmatched pairs. 399 records in RAM.
INFO	2026-06-08 09:41:47	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    2s.  Last read position: chr1:161,802,177
INFO	2026-06-08 09:41:47	MarkDuplicates	Tracking 68532 as yet unmatched pairs. 827 records in RAM.
INFO	2026-06-08 09:41:49	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    2s.  Last read position: chr1:169,106,747
INFO	2026-06-08 09:41:49	MarkDuplicates	Tracking 71724 as yet unmatched pairs. 2428 records in RAM.
INFO	2026-06-08 09:41:51	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    2s.  Last read position: chr1:171,566,653
INFO	2026-06-08 09:41:51	MarkDuplicates	Tracking 71371 as yet unmatched pairs. 648 records in RAM.
INFO	2026-06-08 09:41:53	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    1s.  Last read position: chr1:179,107,777
INFO	2026-06-08 09:41:53	MarkDuplicates	Tracking 72457 as yet unmatched pairs. 263 records in RAM.
INFO	2026-06-08 09:41:55	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    2s.  Last read position: chr1:183,590,164
INFO	2026-06-08 09:41:55	MarkDuplicates	Tracking 73897 as yet unmatched pairs. 203 records in RAM.
INFO	2026-06-08 09:41:57	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    2s.  Last read position: chr1:186,346,247
INFO	2026-06-08 09:41:57	MarkDuplicates	Tracking 77003 as yet unmatched pairs. 1998 records in RAM.
INFO	2026-06-08 09:41:59	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    1s.  Last read position: chr1:200,911,696
INFO	2026-06-08 09:41:59	MarkDuplicates	Tracking 76697 as yet unmatched pairs. 268 records in RAM.
INFO	2026-06-08 09:42:02	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    2s.  Last read position: chr1:202,896,885
INFO	2026-06-08 09:42:02	MarkDuplicates	Tracking 78267 as yet unmatched pairs. 227 records in RAM.
INFO	2026-06-08 09:42:04	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    2s.  Last read position: chr1:204,410,841
INFO	2026-06-08 09:42:04	MarkDuplicates	Tracking 79867 as yet unmatched pairs. 395 records in RAM.
INFO	2026-06-08 09:42:06	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:    1s.  Last read position: chr1:207,757,145
INFO	2026-06-08 09:42:06	MarkDuplicates	Tracking 83261 as yet unmatched pairs. 2212 records in RAM.
INFO	2026-06-08 09:42:08	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    2s.  Last read position: chr1:215,567,720
INFO	2026-06-08 09:42:08	MarkDuplicates	Tracking 82855 as yet unmatched pairs. 273 records in RAM.
INFO	2026-06-08 09:42:11	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    2s.  Last read position: chr1:223,553,865
INFO	2026-06-08 09:42:11	MarkDuplicates	Tracking 85524 as yet unmatched pairs. 1561 records in RAM.
INFO	2026-06-08 09:42:12	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    1s.  Last read position: chr1:225,517,296
INFO	2026-06-08 09:42:12	MarkDuplicates	Tracking 86079 as yet unmatched pairs. 584 records in RAM.
INFO	2026-06-08 09:42:14	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    1s.  Last read position: chr1:227,029,158
INFO	2026-06-08 09:42:14	MarkDuplicates	Tracking 87309 as yet unmatched pairs. 368 records in RAM.
INFO	2026-06-08 09:42:17	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    2s.  Last read position: chr1:228,401,173
INFO	2026-06-08 09:42:17	MarkDuplicates	Tracking 89161 as yet unmatched pairs. 347 records in RAM.
INFO	2026-06-08 09:42:19	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    2s.  Last read position: chr1:234,430,051
INFO	2026-06-08 09:42:19	MarkDuplicates	Tracking 91348 as yet unmatched pairs. 787 records in RAM.
INFO	2026-06-08 09:42:21	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    1s.  Last read position: chr1:236,795,727
INFO	2026-06-08 09:42:21	MarkDuplicates	Tracking 92610 as yet unmatched pairs. 366 records in RAM.
INFO	2026-06-08 09:42:23	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    1s.  Last read position: chr1:244,864,157
INFO	2026-06-08 09:42:23	MarkDuplicates	Tracking 97244 as yet unmatched pairs. 3543 records in RAM.
INFO	2026-06-08 09:42:26	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    3s.  Last read position: chr2:1,665,043
INFO	2026-06-08 09:42:26	MarkDuplicates	Tracking 95632 as yet unmatched pairs. 93778 records in RAM.
INFO	2026-06-08 09:42:28	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    2s.  Last read position: chr2:10,793,134
INFO	2026-06-08 09:42:28	MarkDuplicates	Tracking 97482 as yet unmatched pairs. 95609 records in RAM.
INFO	2026-06-08 09:42:30	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    2s.  Last read position: chr2:20,203,881
INFO	2026-06-08 09:42:30	MarkDuplicates	Tracking 103467 as yet unmatched pairs. 101575 records in RAM.
INFO	2026-06-08 09:42:32	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    2s.  Last read position: chr2:24,726,589
INFO	2026-06-08 09:42:32	MarkDuplicates	Tracking 100746 as yet unmatched pairs. 98825 records in RAM.
INFO	2026-06-08 09:42:35	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    2s.  Last read position: chr2:27,039,777
INFO	2026-06-08 09:42:35	MarkDuplicates	Tracking 102549 as yet unmatched pairs. 100622 records in RAM.
INFO	2026-06-08 09:42:37	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    2s.  Last read position: chr2:27,439,792
INFO	2026-06-08 09:42:37	MarkDuplicates	Tracking 103987 as yet unmatched pairs. 102039 records in RAM.
INFO	2026-06-08 09:42:39	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    2s.  Last read position: chr2:31,943,312
INFO	2026-06-08 09:42:39	MarkDuplicates	Tracking 105736 as yet unmatched pairs. 103770 records in RAM.
INFO	2026-06-08 09:42:41	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    2s.  Last read position: chr2:32,916,260
INFO	2026-06-08 09:42:41	MarkDuplicates	Tracking 143954 as yet unmatched pairs. 102030 records in RAM.
INFO	2026-06-08 09:42:44	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    2s.  Last read position: chr2:32,916,264
INFO	2026-06-08 09:42:44	MarkDuplicates	Tracking 736970 as yet unmatched pairs. 70955 records in RAM.
INFO	2026-06-08 09:42:45	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    1s.  Last read position: chr2:32,916,406
INFO	2026-06-08 09:42:45	MarkDuplicates	Tracking 830147 as yet unmatched pairs. 66301 records in RAM.
INFO	2026-06-08 09:42:48	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:    2s.  Last read position: chr2:37,138,292
INFO	2026-06-08 09:42:48	MarkDuplicates	Tracking 879187 as yet unmatched pairs. 63630 records in RAM.
INFO	2026-06-08 09:42:51	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    2s.  Last read position: chr2:43,225,155
INFO	2026-06-08 09:42:51	MarkDuplicates	Tracking 877294 as yet unmatched pairs. 61718 records in RAM.
INFO	2026-06-08 09:42:53	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:    2s.  Last read position: chr2:46,759,226
INFO	2026-06-08 09:42:53	MarkDuplicates	Tracking 875690 as yet unmatched pairs. 60098 records in RAM.
INFO	2026-06-08 09:42:55	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:    2s.  Last read position: chr2:54,612,217
INFO	2026-06-08 09:42:55	MarkDuplicates	Tracking 874706 as yet unmatched pairs. 59088 records in RAM.
INFO	2026-06-08 09:42:58	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    2s.  Last read position: chr2:61,188,692
INFO	2026-06-08 09:42:58	MarkDuplicates	Tracking 872694 as yet unmatched pairs. 57057 records in RAM.
INFO	2026-06-08 09:43:00	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    2s.  Last read position: chr2:65,239,874
INFO	2026-06-08 09:43:00	MarkDuplicates	Tracking 872910 as yet unmatched pairs. 57261 records in RAM.
INFO	2026-06-08 09:43:02	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    2s.  Last read position: chr2:71,349,353
INFO	2026-06-08 09:43:02	MarkDuplicates	Tracking 870202 as yet unmatched pairs. 54535 records in RAM.
INFO	2026-06-08 09:43:04	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    2s.  Last read position: chr2:74,369,152
INFO	2026-06-08 09:43:04	MarkDuplicates	Tracking 868567 as yet unmatched pairs. 52886 records in RAM.
INFO	2026-06-08 09:43:06	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    2s.  Last read position: chr2:85,326,527
INFO	2026-06-08 09:43:06	MarkDuplicates	Tracking 867462 as yet unmatched pairs. 51765 records in RAM.
INFO	2026-06-08 09:43:08	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    2s.  Last read position: chr2:86,604,593
INFO	2026-06-08 09:43:08	MarkDuplicates	Tracking 865351 as yet unmatched pairs. 49621 records in RAM.
INFO	2026-06-08 09:43:10	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    1s.  Last read position: chr2:95,279,117
INFO	2026-06-08 09:43:10	MarkDuplicates	Tracking 865671 as yet unmatched pairs. 49926 records in RAM.
INFO	2026-06-08 09:43:12	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    2s.  Last read position: chr2:96,848,297
INFO	2026-06-08 09:43:12	MarkDuplicates	Tracking 862798 as yet unmatched pairs. 47037 records in RAM.
INFO	2026-06-08 09:43:15	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    2s.  Last read position: chr2:100,571,670
INFO	2026-06-08 09:43:15	MarkDuplicates	Tracking 861050 as yet unmatched pairs. 45270 records in RAM.
INFO	2026-06-08 09:43:17	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    1s.  Last read position: chr2:108,452,210
INFO	2026-06-08 09:43:17	MarkDuplicates	Tracking 860160 as yet unmatched pairs. 44374 records in RAM.
INFO	2026-06-08 09:43:19	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    1s.  Last read position: chr2:108,772,896
INFO	2026-06-08 09:43:19	MarkDuplicates	Tracking 859671 as yet unmatched pairs. 43877 records in RAM.
INFO	2026-06-08 09:43:21	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    1s.  Last read position: chr2:110,546,844
INFO	2026-06-08 09:43:21	MarkDuplicates	Tracking 858977 as yet unmatched pairs. 43177 records in RAM.
INFO	2026-06-08 09:43:23	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    1s.  Last read position: chr2:113,184,984
INFO	2026-06-08 09:43:23	MarkDuplicates	Tracking 857593 as yet unmatched pairs. 41787 records in RAM.
INFO	2026-06-08 09:43:25	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    1s.  Last read position: chr2:127,651,667
INFO	2026-06-08 09:43:25	MarkDuplicates	Tracking 855896 as yet unmatched pairs. 40045 records in RAM.
INFO	2026-06-08 09:43:27	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    2s.  Last read position: chr2:130,656,864
INFO	2026-06-08 09:43:27	MarkDuplicates	Tracking 854307 as yet unmatched pairs. 38431 records in RAM.
INFO	2026-06-08 09:43:29	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:    1s.  Last read position: chr2:134,338,349
INFO	2026-06-08 09:43:29	MarkDuplicates	Tracking 852996 as yet unmatched pairs. 37082 records in RAM.
INFO	2026-06-08 09:43:31	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    2s.  Last read position: chr2:142,877,687
INFO	2026-06-08 09:43:31	MarkDuplicates	Tracking 851554 as yet unmatched pairs. 35507 records in RAM.
INFO	2026-06-08 09:43:33	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    2s.  Last read position: chr2:159,170,692
INFO	2026-06-08 09:43:33	MarkDuplicates	Tracking 850940 as yet unmatched pairs. 34848 records in RAM.
INFO	2026-06-08 09:43:35	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    2s.  Last read position: chr2:169,812,482
INFO	2026-06-08 09:43:35	MarkDuplicates	Tracking 849371 as yet unmatched pairs. 33255 records in RAM.
INFO	2026-06-08 09:43:37	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    1s.  Last read position: chr2:177,216,864
INFO	2026-06-08 09:43:37	MarkDuplicates	Tracking 847428 as yet unmatched pairs. 31292 records in RAM.
INFO	2026-06-08 09:43:40	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    2s.  Last read position: chr2:182,758,847
INFO	2026-06-08 09:43:40	MarkDuplicates	Tracking 846532 as yet unmatched pairs. 30356 records in RAM.
INFO	2026-06-08 09:43:42	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    2s.  Last read position: chr2:189,043,212
INFO	2026-06-08 09:43:42	MarkDuplicates	Tracking 844866 as yet unmatched pairs. 28670 records in RAM.
INFO	2026-06-08 09:43:44	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    1s.  Last read position: chr2:197,408,408
INFO	2026-06-08 09:43:44	MarkDuplicates	Tracking 844266 as yet unmatched pairs. 28055 records in RAM.
INFO	2026-06-08 09:43:47	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    2s.  Last read position: chr2:203,391,075
INFO	2026-06-08 09:43:47	MarkDuplicates	Tracking 841679 as yet unmatched pairs. 25432 records in RAM.
INFO	2026-06-08 09:43:49	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    2s.  Last read position: chr2:214,942,929
INFO	2026-06-08 09:43:49	MarkDuplicates	Tracking 840632 as yet unmatched pairs. 24345 records in RAM.
INFO	2026-06-08 09:43:51	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,365,564
INFO	2026-06-08 09:43:51	MarkDuplicates	Tracking 852670 as yet unmatched pairs. 36374 records in RAM.
INFO	2026-06-08 09:43:54	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,372,200
INFO	2026-06-08 09:43:54	MarkDuplicates	Tracking 858825 as yet unmatched pairs. 42515 records in RAM.
INFO	2026-06-08 09:43:56	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,376,541
INFO	2026-06-08 09:43:56	MarkDuplicates	Tracking 855620 as yet unmatched pairs. 39307 records in RAM.
INFO	2026-06-08 09:43:58	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,383,367
INFO	2026-06-08 09:43:58	MarkDuplicates	Tracking 845637 as yet unmatched pairs. 29317 records in RAM.
INFO	2026-06-08 09:44:00	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    1s.  Last read position: chr2:215,391,801
INFO	2026-06-08 09:44:00	MarkDuplicates	Tracking 843463 as yet unmatched pairs. 27142 records in RAM.
INFO	2026-06-08 09:44:02	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,406,245
INFO	2026-06-08 09:44:02	MarkDuplicates	Tracking 845013 as yet unmatched pairs. 28687 records in RAM.
INFO	2026-06-08 09:44:04	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,409,714
INFO	2026-06-08 09:44:04	MarkDuplicates	Tracking 838267 as yet unmatched pairs. 21928 records in RAM.
INFO	2026-06-08 09:44:06	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    1s.  Last read position: chr2:215,423,475
INFO	2026-06-08 09:44:06	MarkDuplicates	Tracking 842683 as yet unmatched pairs. 26342 records in RAM.
INFO	2026-06-08 09:44:09	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,433,337
INFO	2026-06-08 09:44:09	MarkDuplicates	Tracking 841934 as yet unmatched pairs. 25572 records in RAM.
INFO	2026-06-08 09:44:11	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    1s.  Last read position: chr2:217,812,373
INFO	2026-06-08 09:44:11	MarkDuplicates	Tracking 827358 as yet unmatched pairs. 10984 records in RAM.
INFO	2026-06-08 09:44:13	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    2s.  Last read position: chr2:219,381,425
INFO	2026-06-08 09:44:13	MarkDuplicates	Tracking 825746 as yet unmatched pairs. 9357 records in RAM.
INFO	2026-06-08 09:44:16	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    2s.  Last read position: chr2:229,792,034
INFO	2026-06-08 09:44:16	MarkDuplicates	Tracking 823954 as yet unmatched pairs. 7529 records in RAM.
INFO	2026-06-08 09:44:18	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    2s.  Last read position: chr2:233,251,808
INFO	2026-06-08 09:44:18	MarkDuplicates	Tracking 822652 as yet unmatched pairs. 6207 records in RAM.
INFO	2026-06-08 09:44:20	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    1s.  Last read position: chr2:237,374,699
INFO	2026-06-08 09:44:20	MarkDuplicates	Tracking 821416 as yet unmatched pairs. 4950 records in RAM.
INFO	2026-06-08 09:44:22	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    2s.  Last read position: chr2:239,990,135
INFO	2026-06-08 09:44:22	MarkDuplicates	Tracking 819552 as yet unmatched pairs. 3064 records in RAM.
INFO	2026-06-08 09:44:24	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    2s.  Last read position: chr2:241,316,472
INFO	2026-06-08 09:44:24	MarkDuplicates	Tracking 818073 as yet unmatched pairs. 1543 records in RAM.
INFO	2026-06-08 09:44:27	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    2s.  Last read position: chr3:9,678,025
INFO	2026-06-08 09:44:27	MarkDuplicates	Tracking 815998 as yet unmatched pairs. 45937 records in RAM.
INFO	2026-06-08 09:44:29	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    1s.  Last read position: chr3:12,590,948
INFO	2026-06-08 09:44:29	MarkDuplicates	Tracking 814845 as yet unmatched pairs. 44751 records in RAM.
INFO	2026-06-08 09:44:31	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    2s.  Last read position: chr3:16,270,978
INFO	2026-06-08 09:44:31	MarkDuplicates	Tracking 812556 as yet unmatched pairs. 42446 records in RAM.
INFO	2026-06-08 09:44:33	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    2s.  Last read position: chr3:33,072,689
INFO	2026-06-08 09:44:33	MarkDuplicates	Tracking 811020 as yet unmatched pairs. 40884 records in RAM.
INFO	2026-06-08 09:44:35	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    1s.  Last read position: chr3:39,408,625
INFO	2026-06-08 09:44:35	MarkDuplicates	Tracking 811898 as yet unmatched pairs. 41751 records in RAM.
INFO	2026-06-08 09:44:38	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    2s.  Last read position: chr3:43,348,125
INFO	2026-06-08 09:44:38	MarkDuplicates	Tracking 808156 as yet unmatched pairs. 37992 records in RAM.
INFO	2026-06-08 09:44:40	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:04:30s.  Time for last 1,000,000:    2s.  Last read position: chr3:47,008,561
INFO	2026-06-08 09:44:40	MarkDuplicates	Tracking 807178 as yet unmatched pairs. 36987 records in RAM.
INFO	2026-06-08 09:44:42	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    1s.  Last read position: chr3:47,918,724
INFO	2026-06-08 09:44:42	MarkDuplicates	Tracking 806404 as yet unmatched pairs. 36200 records in RAM.
INFO	2026-06-08 09:44:45	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:    2s.  Last read position: chr3:48,694,926
INFO	2026-06-08 09:44:45	MarkDuplicates	Tracking 805084 as yet unmatched pairs. 34855 records in RAM.
INFO	2026-06-08 09:44:47	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    2s.  Last read position: chr3:49,122,710
INFO	2026-06-08 09:44:47	MarkDuplicates	Tracking 802135 as yet unmatched pairs. 31890 records in RAM.
INFO	2026-06-08 09:44:49	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    2s.  Last read position: chr3:49,685,615
INFO	2026-06-08 09:44:49	MarkDuplicates	Tracking 799777 as yet unmatched pairs. 29525 records in RAM.
INFO	2026-06-08 09:44:51	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    1s.  Last read position: chr3:50,607,982
INFO	2026-06-08 09:44:51	MarkDuplicates	Tracking 798153 as yet unmatched pairs. 27888 records in RAM.
INFO	2026-06-08 09:44:53	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    2s.  Last read position: chr3:52,522,041
INFO	2026-06-08 09:44:53	MarkDuplicates	Tracking 796577 as yet unmatched pairs. 26293 records in RAM.
INFO	2026-06-08 09:44:56	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    2s.  Last read position: chr3:57,577,361
INFO	2026-06-08 09:44:56	MarkDuplicates	Tracking 795292 as yet unmatched pairs. 24985 records in RAM.
INFO	2026-06-08 09:44:57	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:04:47s.  Time for last 1,000,000:    1s.  Last read position: chr3:69,047,359
INFO	2026-06-08 09:44:57	MarkDuplicates	Tracking 793537 as yet unmatched pairs. 23195 records in RAM.
INFO	2026-06-08 09:45:00	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    2s.  Last read position: chr3:100,386,974
INFO	2026-06-08 09:45:00	MarkDuplicates	Tracking 791916 as yet unmatched pairs. 21548 records in RAM.
INFO	2026-06-08 09:45:02	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    2s.  Last read position: chr3:107,791,289
INFO	2026-06-08 09:45:02	MarkDuplicates	Tracking 790341 as yet unmatched pairs. 19965 records in RAM.
INFO	2026-06-08 09:45:04	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    1s.  Last read position: chr3:120,404,879
INFO	2026-06-08 09:45:04	MarkDuplicates	Tracking 789045 as yet unmatched pairs. 18616 records in RAM.
INFO	2026-06-08 09:45:07	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    2s.  Last read position: chr3:123,931,501
INFO	2026-06-08 09:45:07	MarkDuplicates	Tracking 788186 as yet unmatched pairs. 17733 records in RAM.
INFO	2026-06-08 09:45:09	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    2s.  Last read position: chr3:128,067,502
INFO	2026-06-08 09:45:09	MarkDuplicates	Tracking 788595 as yet unmatched pairs. 18119 records in RAM.
INFO	2026-06-08 09:45:11	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    2s.  Last read position: chr3:129,556,335
INFO	2026-06-08 09:45:11	MarkDuplicates	Tracking 784431 as yet unmatched pairs. 13937 records in RAM.
INFO	2026-06-08 09:45:13	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    1s.  Last read position: chr3:136,283,874
INFO	2026-06-08 09:45:13	MarkDuplicates	Tracking 783024 as yet unmatched pairs. 12515 records in RAM.
INFO	2026-06-08 09:45:15	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    2s.  Last read position: chr3:149,129,922
INFO	2026-06-08 09:45:15	MarkDuplicates	Tracking 781722 as yet unmatched pairs. 11203 records in RAM.
INFO	2026-06-08 09:45:17	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    1s.  Last read position: chr3:158,823,444
INFO	2026-06-08 09:45:17	MarkDuplicates	Tracking 780739 as yet unmatched pairs. 10195 records in RAM.
INFO	2026-06-08 09:45:19	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    2s.  Last read position: chr3:172,397,288
INFO	2026-06-08 09:45:19	MarkDuplicates	Tracking 778454 as yet unmatched pairs. 7888 records in RAM.
INFO	2026-06-08 09:45:22	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    2s.  Last read position: chr3:183,961,586
INFO	2026-06-08 09:45:22	MarkDuplicates	Tracking 777271 as yet unmatched pairs. 6671 records in RAM.
INFO	2026-06-08 09:45:24	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    2s.  Last read position: chr3:184,323,576
INFO	2026-06-08 09:45:24	MarkDuplicates	Tracking 776041 as yet unmatched pairs. 5433 records in RAM.
INFO	2026-06-08 09:45:26	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    1s.  Last read position: chr3:188,524,776
INFO	2026-06-08 09:45:26	MarkDuplicates	Tracking 776210 as yet unmatched pairs. 5583 records in RAM.
INFO	2026-06-08 09:45:28	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    2s.  Last read position: chr3:195,867,365
INFO	2026-06-08 09:45:28	MarkDuplicates	Tracking 773565 as yet unmatched pairs. 2912 records in RAM.
INFO	2026-06-08 09:45:30	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    2s.  Last read position: chr4:442,834
INFO	2026-06-08 09:45:30	MarkDuplicates	Tracking 770814 as yet unmatched pairs. 23047 records in RAM.
INFO	2026-06-08 09:45:32	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    1s.  Last read position: chr4:1,349,758
INFO	2026-06-08 09:45:32	MarkDuplicates	Tracking 769052 as yet unmatched pairs. 21254 records in RAM.
INFO	2026-06-08 09:45:35	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:05:25s.  Time for last 1,000,000:    2s.  Last read position: chr4:2,928,363
INFO	2026-06-08 09:45:35	MarkDuplicates	Tracking 767695 as yet unmatched pairs. 19869 records in RAM.
INFO	2026-06-08 09:45:37	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:05:27s.  Time for last 1,000,000:    2s.  Last read position: chr4:6,863,505
INFO	2026-06-08 09:45:37	MarkDuplicates	Tracking 765638 as yet unmatched pairs. 17799 records in RAM.
INFO	2026-06-08 09:45:40	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    2s.  Last read position: chr4:17,588,959
INFO	2026-06-08 09:45:40	MarkDuplicates	Tracking 763852 as yet unmatched pairs. 15997 records in RAM.
INFO	2026-06-08 09:45:41	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:05:31s.  Time for last 1,000,000:    1s.  Last read position: chr4:40,816,112
INFO	2026-06-08 09:45:41	MarkDuplicates	Tracking 763827 as yet unmatched pairs. 15954 records in RAM.
INFO	2026-06-08 09:45:44	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    2s.  Last read position: chr4:48,505,587
INFO	2026-06-08 09:45:44	MarkDuplicates	Tracking 761056 as yet unmatched pairs. 13135 records in RAM.
INFO	2026-06-08 09:45:46	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    1s.  Last read position: chr4:57,032,445
INFO	2026-06-08 09:45:46	MarkDuplicates	Tracking 760738 as yet unmatched pairs. 12801 records in RAM.
INFO	2026-06-08 09:45:48	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    2s.  Last read position: chr4:76,754,779
INFO	2026-06-08 09:45:48	MarkDuplicates	Tracking 758117 as yet unmatched pairs. 10153 records in RAM.
INFO	2026-06-08 09:45:50	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:05:40s.  Time for last 1,000,000:    2s.  Last read position: chr4:86,015,208
INFO	2026-06-08 09:45:50	MarkDuplicates	Tracking 756402 as yet unmatched pairs. 8405 records in RAM.
INFO	2026-06-08 09:45:52	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:    1s.  Last read position: chr4:100,187,848
INFO	2026-06-08 09:45:52	MarkDuplicates	Tracking 754945 as yet unmatched pairs. 6908 records in RAM.
INFO	2026-06-08 09:45:54	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:05:44s.  Time for last 1,000,000:    2s.  Last read position: chr4:112,356,103
INFO	2026-06-08 09:45:54	MarkDuplicates	Tracking 753459 as yet unmatched pairs. 5415 records in RAM.
INFO	2026-06-08 09:45:56	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    2s.  Last read position: chr4:128,257,517
INFO	2026-06-08 09:45:56	MarkDuplicates	Tracking 752110 as yet unmatched pairs. 4039 records in RAM.
INFO	2026-06-08 09:45:58	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:05:48s.  Time for last 1,000,000:    1s.  Last read position: chr4:150,607,879
INFO	2026-06-08 09:45:58	MarkDuplicates	Tracking 751192 as yet unmatched pairs. 3084 records in RAM.
INFO	2026-06-08 09:46:00	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    2s.  Last read position: chr4:168,924,939
INFO	2026-06-08 09:46:00	MarkDuplicates	Tracking 749900 as yet unmatched pairs. 1768 records in RAM.
INFO	2026-06-08 09:46:03	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    2s.  Last read position: chr5:878,431
INFO	2026-06-08 09:46:03	MarkDuplicates	Tracking 748098 as yet unmatched pairs. 49285 records in RAM.
INFO	2026-06-08 09:46:05	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    1s.  Last read position: chr5:13,913,790
INFO	2026-06-08 09:46:05	MarkDuplicates	Tracking 746174 as yet unmatched pairs. 47328 records in RAM.
INFO	2026-06-08 09:46:08	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    2s.  Last read position: chr5:14,498,605
INFO	2026-06-08 09:46:08	MarkDuplicates	Tracking 746493 as yet unmatched pairs. 47618 records in RAM.
INFO	2026-06-08 09:46:10	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    2s.  Last read position: chr5:34,452,578
INFO	2026-06-08 09:46:10	MarkDuplicates	Tracking 742910 as yet unmatched pairs. 43999 records in RAM.
INFO	2026-06-08 09:46:12	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    1s.  Last read position: chr5:44,813,162
INFO	2026-06-08 09:46:12	MarkDuplicates	Tracking 741986 as yet unmatched pairs. 43065 records in RAM.
INFO	2026-06-08 09:46:14	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    2s.  Last read position: chr5:60,893,137
INFO	2026-06-08 09:46:14	MarkDuplicates	Tracking 740312 as yet unmatched pairs. 41370 records in RAM.
INFO	2026-06-08 09:46:16	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    1s.  Last read position: chr5:69,365,659
INFO	2026-06-08 09:46:16	MarkDuplicates	Tracking 739753 as yet unmatched pairs. 40790 records in RAM.
INFO	2026-06-08 09:46:18	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    1s.  Last read position: chr5:71,003,790
INFO	2026-06-08 09:46:18	MarkDuplicates	Tracking 738383 as yet unmatched pairs. 39402 records in RAM.
INFO	2026-06-08 09:46:20	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:    2s.  Last read position: chr5:73,752,970
INFO	2026-06-08 09:46:20	MarkDuplicates	Tracking 737240 as yet unmatched pairs. 38235 records in RAM.
INFO	2026-06-08 09:46:22	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    1s.  Last read position: chr5:80,068,001
INFO	2026-06-08 09:46:22	MarkDuplicates	Tracking 735617 as yet unmatched pairs. 36593 records in RAM.
INFO	2026-06-08 09:46:24	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:06:14s.  Time for last 1,000,000:    2s.  Last read position: chr5:90,647,656
INFO	2026-06-08 09:46:24	MarkDuplicates	Tracking 734455 as yet unmatched pairs. 35413 records in RAM.
INFO	2026-06-08 09:46:26	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    1s.  Last read position: chr5:96,892,336
INFO	2026-06-08 09:46:26	MarkDuplicates	Tracking 732867 as yet unmatched pairs. 33810 records in RAM.
INFO	2026-06-08 09:46:29	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:06:18s.  Time for last 1,000,000:    2s.  Last read position: chr5:114,463,064
INFO	2026-06-08 09:46:29	MarkDuplicates	Tracking 731474 as yet unmatched pairs. 32402 records in RAM.
INFO	2026-06-08 09:46:31	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    2s.  Last read position: chr5:128,134,203
INFO	2026-06-08 09:46:31	MarkDuplicates	Tracking 731205 as yet unmatched pairs. 32127 records in RAM.
INFO	2026-06-08 09:46:33	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    2s.  Last read position: chr5:132,934,427
INFO	2026-06-08 09:46:33	MarkDuplicates	Tracking 729140 as yet unmatched pairs. 30045 records in RAM.
INFO	2026-06-08 09:46:35	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:    2s.  Last read position: chr5:135,578,492
INFO	2026-06-08 09:46:35	MarkDuplicates	Tracking 727971 as yet unmatched pairs. 28866 records in RAM.
INFO	2026-06-08 09:46:37	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    2s.  Last read position: chr5:138,917,769
INFO	2026-06-08 09:46:37	MarkDuplicates	Tracking 726604 as yet unmatched pairs. 27461 records in RAM.
INFO	2026-06-08 09:46:39	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    1s.  Last read position: chr5:140,527,897
INFO	2026-06-08 09:46:39	MarkDuplicates	Tracking 724239 as yet unmatched pairs. 25063 records in RAM.
INFO	2026-06-08 09:46:41	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:06:31s.  Time for last 1,000,000:    2s.  Last read position: chr5:141,189,277
INFO	2026-06-08 09:46:41	MarkDuplicates	Tracking 722790 as yet unmatched pairs. 23580 records in RAM.
INFO	2026-06-08 09:46:43	MarkDuplicates	Read   181,000,000 records.  Elapsed time: 00:06:33s.  Time for last 1,000,000:    2s.  Last read position: chr5:141,404,914
INFO	2026-06-08 09:46:43	MarkDuplicates	Tracking 721671 as yet unmatched pairs. 22451 records in RAM.
INFO	2026-06-08 09:46:45	MarkDuplicates	Read   182,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    1s.  Last read position: chr5:141,869,354
INFO	2026-06-08 09:46:45	MarkDuplicates	Tracking 720022 as yet unmatched pairs. 20790 records in RAM.
INFO	2026-06-08 09:46:48	MarkDuplicates	Read   183,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    2s.  Last read position: chr5:150,006,586
INFO	2026-06-08 09:46:48	MarkDuplicates	Tracking 717706 as yet unmatched pairs. 18446 records in RAM.
INFO	2026-06-08 09:46:50	MarkDuplicates	Read   184,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    2s.  Last read position: chr5:150,402,240
INFO	2026-06-08 09:46:50	MarkDuplicates	Tracking 747520 as yet unmatched pairs. 48250 records in RAM.
INFO	2026-06-08 09:46:52	MarkDuplicates	Read   185,000,000 records.  Elapsed time: 00:06:42s.  Time for last 1,000,000:    2s.  Last read position: chr5:150,407,158
INFO	2026-06-08 09:46:52	MarkDuplicates	Tracking 725716 as yet unmatched pairs. 26430 records in RAM.
INFO	2026-06-08 09:46:55	MarkDuplicates	Read   186,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:    2s.  Last read position: chr5:151,797,376
INFO	2026-06-08 09:46:55	MarkDuplicates	Tracking 713572 as yet unmatched pairs. 14268 records in RAM.
INFO	2026-06-08 09:46:57	MarkDuplicates	Read   187,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:    2s.  Last read position: chr5:163,442,383
INFO	2026-06-08 09:46:57	MarkDuplicates	Tracking 711570 as yet unmatched pairs. 12242 records in RAM.
INFO	2026-06-08 09:46:59	MarkDuplicates	Read   188,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    2s.  Last read position: chr5:171,392,947
INFO	2026-06-08 09:46:59	MarkDuplicates	Tracking 716167 as yet unmatched pairs. 16832 records in RAM.
INFO	2026-06-08 09:47:01	MarkDuplicates	Read   189,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:    1s.  Last read position: chr5:176,347,795
INFO	2026-06-08 09:47:01	MarkDuplicates	Tracking 708805 as yet unmatched pairs. 9427 records in RAM.
INFO	2026-06-08 09:47:03	MarkDuplicates	Read   190,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    2s.  Last read position: chr5:177,460,485
INFO	2026-06-08 09:47:03	MarkDuplicates	Tracking 707645 as yet unmatched pairs. 8247 records in RAM.
INFO	2026-06-08 09:47:05	MarkDuplicates	Read   191,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    1s.  Last read position: chr5:179,615,555
INFO	2026-06-08 09:47:05	MarkDuplicates	Tracking 706670 as yet unmatched pairs. 7257 records in RAM.
INFO	2026-06-08 09:47:07	MarkDuplicates	Read   192,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    2s.  Last read position: chr5:179,820,919
INFO	2026-06-08 09:47:07	MarkDuplicates	Tracking 706197 as yet unmatched pairs. 6768 records in RAM.
INFO	2026-06-08 09:47:09	MarkDuplicates	Read   193,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    2s.  Last read position: chr5:179,833,118
INFO	2026-06-08 09:47:09	MarkDuplicates	Tracking 711502 as yet unmatched pairs. 12062 records in RAM.
INFO	2026-06-08 09:47:12	MarkDuplicates	Read   194,000,000 records.  Elapsed time: 00:07:01s.  Time for last 1,000,000:    2s.  Last read position: chr5:180,630,013
INFO	2026-06-08 09:47:12	MarkDuplicates	Tracking 700391 as yet unmatched pairs. 919 records in RAM.
INFO	2026-06-08 09:47:14	MarkDuplicates	Read   195,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    2s.  Last read position: chr6:3,323,873
INFO	2026-06-08 09:47:14	MarkDuplicates	Tracking 699997 as yet unmatched pairs. 51622 records in RAM.
INFO	2026-06-08 09:47:16	MarkDuplicates	Read   196,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    2s.  Last read position: chr6:7,565,424
INFO	2026-06-08 09:47:16	MarkDuplicates	Tracking 698365 as yet unmatched pairs. 49985 records in RAM.
INFO	2026-06-08 09:47:18	MarkDuplicates	Read   197,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    2s.  Last read position: chr6:12,120,023
INFO	2026-06-08 09:47:18	MarkDuplicates	Tracking 695815 as yet unmatched pairs. 47421 records in RAM.
INFO	2026-06-08 09:47:20	MarkDuplicates	Read   198,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    1s.  Last read position: chr6:24,718,557
INFO	2026-06-08 09:47:20	MarkDuplicates	Tracking 694454 as yet unmatched pairs. 46036 records in RAM.
INFO	2026-06-08 09:47:22	MarkDuplicates	Read   199,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    2s.  Last read position: chr6:27,867,008
INFO	2026-06-08 09:47:22	MarkDuplicates	Tracking 692923 as yet unmatched pairs. 44493 records in RAM.
INFO	2026-06-08 09:47:25	MarkDuplicates	Read   200,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    2s.  Last read position: chr6:30,660,118
INFO	2026-06-08 09:47:25	MarkDuplicates	Tracking 691482 as yet unmatched pairs. 43036 records in RAM.
INFO	2026-06-08 09:47:27	MarkDuplicates	Read   201,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,271,091
INFO	2026-06-08 09:47:27	MarkDuplicates	Tracking 693259 as yet unmatched pairs. 44794 records in RAM.
INFO	2026-06-08 09:47:29	MarkDuplicates	Read   202,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    2s.  Last read position: chr6:31,636,897
INFO	2026-06-08 09:47:29	MarkDuplicates	Tracking 689203 as yet unmatched pairs. 40728 records in RAM.
INFO	2026-06-08 09:47:31	MarkDuplicates	Read   203,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    2s.  Last read position: chr6:31,816,466
INFO	2026-06-08 09:47:31	MarkDuplicates	Tracking 686729 as yet unmatched pairs. 38244 records in RAM.
INFO	2026-06-08 09:47:33	MarkDuplicates	Read   204,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,869,178
INFO	2026-06-08 09:47:33	MarkDuplicates	Tracking 686958 as yet unmatched pairs. 38456 records in RAM.
INFO	2026-06-08 09:47:35	MarkDuplicates	Read   205,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    2s.  Last read position: chr6:31,994,509
INFO	2026-06-08 09:47:35	MarkDuplicates	Tracking 687975 as yet unmatched pairs. 39465 records in RAM.
INFO	2026-06-08 09:47:37	MarkDuplicates	Read   206,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    1s.  Last read position: chr6:32,119,070
INFO	2026-06-08 09:47:37	MarkDuplicates	Tracking 683465 as yet unmatched pairs. 34946 records in RAM.
INFO	2026-06-08 09:47:39	MarkDuplicates	Read   207,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:    2s.  Last read position: chr6:32,978,374
INFO	2026-06-08 09:47:39	MarkDuplicates	Tracking 682316 as yet unmatched pairs. 33770 records in RAM.
INFO	2026-06-08 09:47:41	MarkDuplicates	Read   208,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:    2s.  Last read position: chr6:33,305,201
INFO	2026-06-08 09:47:41	MarkDuplicates	Tracking 681204 as yet unmatched pairs. 32653 records in RAM.
INFO	2026-06-08 09:47:43	MarkDuplicates	Read   209,000,000 records.  Elapsed time: 00:07:33s.  Time for last 1,000,000:    1s.  Last read position: chr6:34,424,744
INFO	2026-06-08 09:47:43	MarkDuplicates	Tracking 679382 as yet unmatched pairs. 30819 records in RAM.
INFO	2026-06-08 09:47:46	MarkDuplicates	Read   210,000,000 records.  Elapsed time: 00:07:36s.  Time for last 1,000,000:    2s.  Last read position: chr6:36,978,078
INFO	2026-06-08 09:47:46	MarkDuplicates	Tracking 677272 as yet unmatched pairs. 28673 records in RAM.
INFO	2026-06-08 09:47:48	MarkDuplicates	Read   211,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    2s.  Last read position: chr6:42,880,911
INFO	2026-06-08 09:47:48	MarkDuplicates	Tracking 675037 as yet unmatched pairs. 26414 records in RAM.
INFO	2026-06-08 09:47:50	MarkDuplicates	Read   212,000,000 records.  Elapsed time: 00:07:40s.  Time for last 1,000,000:    1s.  Last read position: chr6:43,551,315
INFO	2026-06-08 09:47:50	MarkDuplicates	Tracking 673591 as yet unmatched pairs. 24952 records in RAM.
INFO	2026-06-08 09:47:52	MarkDuplicates	Read   213,000,000 records.  Elapsed time: 00:07:42s.  Time for last 1,000,000:    2s.  Last read position: chr6:47,284,341
INFO	2026-06-08 09:47:52	MarkDuplicates	Tracking 672218 as yet unmatched pairs. 23562 records in RAM.
INFO	2026-06-08 09:47:54	MarkDuplicates	Read   214,000,000 records.  Elapsed time: 00:07:44s.  Time for last 1,000,000:    2s.  Last read position: chr6:57,318,571
INFO	2026-06-08 09:47:54	MarkDuplicates	Tracking 670529 as yet unmatched pairs. 21828 records in RAM.
INFO	2026-06-08 09:47:56	MarkDuplicates	Read   215,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:    2s.  Last read position: chr6:75,670,589
INFO	2026-06-08 09:47:56	MarkDuplicates	Tracking 669717 as yet unmatched pairs. 20981 records in RAM.
INFO	2026-06-08 09:47:58	MarkDuplicates	Read   216,000,000 records.  Elapsed time: 00:07:48s.  Time for last 1,000,000:    1s.  Last read position: chr6:85,614,966
INFO	2026-06-08 09:47:58	MarkDuplicates	Tracking 667905 as yet unmatched pairs. 19144 records in RAM.
INFO	2026-06-08 09:48:01	MarkDuplicates	Read   217,000,000 records.  Elapsed time: 00:07:51s.  Time for last 1,000,000:    2s.  Last read position: chr6:99,551,879
INFO	2026-06-08 09:48:01	MarkDuplicates	Tracking 666398 as yet unmatched pairs. 17614 records in RAM.
INFO	2026-06-08 09:48:03	MarkDuplicates	Read   218,000,000 records.  Elapsed time: 00:07:53s.  Time for last 1,000,000:    2s.  Last read position: chr6:110,213,120
INFO	2026-06-08 09:48:03	MarkDuplicates	Tracking 664669 as yet unmatched pairs. 15861 records in RAM.
INFO	2026-06-08 09:48:05	MarkDuplicates	Read   219,000,000 records.  Elapsed time: 00:07:55s.  Time for last 1,000,000:    1s.  Last read position: chr6:122,717,904
INFO	2026-06-08 09:48:05	MarkDuplicates	Tracking 663205 as yet unmatched pairs. 14365 records in RAM.
INFO	2026-06-08 09:48:07	MarkDuplicates	Read   220,000,000 records.  Elapsed time: 00:07:57s.  Time for last 1,000,000:    2s.  Last read position: chr6:136,275,555
INFO	2026-06-08 09:48:07	MarkDuplicates	Tracking 662183 as yet unmatched pairs. 13301 records in RAM.
INFO	2026-06-08 09:48:09	MarkDuplicates	Read   221,000,000 records.  Elapsed time: 00:07:59s.  Time for last 1,000,000:    2s.  Last read position: chr6:142,770,816
INFO	2026-06-08 09:48:09	MarkDuplicates	Tracking 660123 as yet unmatched pairs. 11222 records in RAM.
INFO	2026-06-08 09:48:11	MarkDuplicates	Read   222,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    1s.  Last read position: chr6:149,820,630
INFO	2026-06-08 09:48:11	MarkDuplicates	Tracking 658772 as yet unmatched pairs. 9840 records in RAM.
INFO	2026-06-08 09:48:13	MarkDuplicates	Read   223,000,000 records.  Elapsed time: 00:08:03s.  Time for last 1,000,000:    2s.  Last read position: chr6:151,842,393
INFO	2026-06-08 09:48:13	MarkDuplicates	Tracking 669970 as yet unmatched pairs. 21013 records in RAM.
INFO	2026-06-08 09:48:15	MarkDuplicates	Read   224,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:    2s.  Last read position: chr6:152,098,990
INFO	2026-06-08 09:48:15	MarkDuplicates	Tracking 656188 as yet unmatched pairs. 7209 records in RAM.
INFO	2026-06-08 09:48:17	MarkDuplicates	Read   225,000,000 records.  Elapsed time: 00:08:07s.  Time for last 1,000,000:    1s.  Last read position: chr6:158,766,840
INFO	2026-06-08 09:48:17	MarkDuplicates	Tracking 659384 as yet unmatched pairs. 10387 records in RAM.
INFO	2026-06-08 09:48:20	MarkDuplicates	Read   226,000,000 records.  Elapsed time: 00:08:09s.  Time for last 1,000,000:    2s.  Last read position: chr6:158,785,550
INFO	2026-06-08 09:48:20	MarkDuplicates	Tracking 664510 as yet unmatched pairs. 15507 records in RAM.
INFO	2026-06-08 09:48:22	MarkDuplicates	Read   227,000,000 records.  Elapsed time: 00:08:12s.  Time for last 1,000,000:    2s.  Last read position: chr6:166,929,713
INFO	2026-06-08 09:48:22	MarkDuplicates	Tracking 651408 as yet unmatched pairs. 2386 records in RAM.
INFO	2026-06-08 09:48:24	MarkDuplicates	Read   228,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:    2s.  Last read position: chr7:832,527
INFO	2026-06-08 09:48:24	MarkDuplicates	Tracking 650316 as yet unmatched pairs. 50460 records in RAM.
INFO	2026-06-08 09:48:26	MarkDuplicates	Read   229,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    2s.  Last read position: chr7:2,377,003
INFO	2026-06-08 09:48:26	MarkDuplicates	Tracking 647440 as yet unmatched pairs. 47562 records in RAM.
INFO	2026-06-08 09:48:29	MarkDuplicates	Read   230,000,000 records.  Elapsed time: 00:08:18s.  Time for last 1,000,000:    2s.  Last read position: chr7:5,361,593
INFO	2026-06-08 09:48:29	MarkDuplicates	Tracking 645433 as yet unmatched pairs. 45526 records in RAM.
INFO	2026-06-08 09:48:31	MarkDuplicates	Read   231,000,000 records.  Elapsed time: 00:08:21s.  Time for last 1,000,000:    2s.  Last read position: chr7:5,528,042
INFO	2026-06-08 09:48:31	MarkDuplicates	Tracking 665010 as yet unmatched pairs. 65095 records in RAM.
INFO	2026-06-08 09:48:33	MarkDuplicates	Read   232,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    1s.  Last read position: chr7:5,529,534
INFO	2026-06-08 09:48:33	MarkDuplicates	Tracking 648726 as yet unmatched pairs. 48804 records in RAM.
INFO	2026-06-08 09:48:35	MarkDuplicates	Read   233,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    2s.  Last read position: chr7:8,235,930
INFO	2026-06-08 09:48:35	MarkDuplicates	Tracking 640208 as yet unmatched pairs. 40272 records in RAM.
INFO	2026-06-08 09:48:37	MarkDuplicates	Read   234,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:    2s.  Last read position: chr7:23,266,568
INFO	2026-06-08 09:48:37	MarkDuplicates	Tracking 639417 as yet unmatched pairs. 39438 records in RAM.
INFO	2026-06-08 09:48:39	MarkDuplicates	Read   235,000,000 records.  Elapsed time: 00:08:29s.  Time for last 1,000,000:    1s.  Last read position: chr7:29,955,353
INFO	2026-06-08 09:48:39	MarkDuplicates	Tracking 640205 as yet unmatched pairs. 40209 records in RAM.
INFO	2026-06-08 09:48:41	MarkDuplicates	Read   236,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    2s.  Last read position: chr7:31,643,265
INFO	2026-06-08 09:48:41	MarkDuplicates	Tracking 635519 as yet unmatched pairs. 35502 records in RAM.
INFO	2026-06-08 09:48:44	MarkDuplicates	Read   237,000,000 records.  Elapsed time: 00:08:33s.  Time for last 1,000,000:    2s.  Last read position: chr7:38,754,715
INFO	2026-06-08 09:48:44	MarkDuplicates	Tracking 635496 as yet unmatched pairs. 35445 records in RAM.
INFO	2026-06-08 09:48:45	MarkDuplicates	Read   238,000,000 records.  Elapsed time: 00:08:35s.  Time for last 1,000,000:    1s.  Last read position: chr7:44,007,362
INFO	2026-06-08 09:48:45	MarkDuplicates	Tracking 633212 as yet unmatched pairs. 33140 records in RAM.
INFO	2026-06-08 09:48:48	MarkDuplicates	Read   239,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:    2s.  Last read position: chr7:44,247,170
INFO	2026-06-08 09:48:48	MarkDuplicates	Tracking 631028 as yet unmatched pairs. 30950 records in RAM.
INFO	2026-06-08 09:48:50	MarkDuplicates	Read   240,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:    2s.  Last read position: chr7:44,885,025
INFO	2026-06-08 09:48:50	MarkDuplicates	Tracking 629616 as yet unmatched pairs. 29525 records in RAM.
INFO	2026-06-08 09:48:52	MarkDuplicates	Read   241,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    1s.  Last read position: chr7:64,992,895
INFO	2026-06-08 09:48:52	MarkDuplicates	Tracking 628045 as yet unmatched pairs. 27942 records in RAM.
INFO	2026-06-08 09:48:54	MarkDuplicates	Read   242,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    2s.  Last read position: chr7:73,183,133
INFO	2026-06-08 09:48:54	MarkDuplicates	Tracking 626884 as yet unmatched pairs. 26766 records in RAM.
INFO	2026-06-08 09:48:56	MarkDuplicates	Read   243,000,000 records.  Elapsed time: 00:08:46s.  Time for last 1,000,000:    2s.  Last read position: chr7:74,698,998
INFO	2026-06-08 09:48:56	MarkDuplicates	Tracking 625847 as yet unmatched pairs. 25718 records in RAM.
INFO	2026-06-08 09:48:58	MarkDuplicates	Read   244,000,000 records.  Elapsed time: 00:08:48s.  Time for last 1,000,000:    1s.  Last read position: chr7:75,888,587
INFO	2026-06-08 09:48:58	MarkDuplicates	Tracking 624435 as yet unmatched pairs. 24294 records in RAM.
INFO	2026-06-08 09:49:00	MarkDuplicates	Read   245,000,000 records.  Elapsed time: 00:08:50s.  Time for last 1,000,000:    2s.  Last read position: chr7:76,492,082
INFO	2026-06-08 09:49:00	MarkDuplicates	Tracking 622976 as yet unmatched pairs. 22813 records in RAM.
INFO	2026-06-08 09:49:02	MarkDuplicates	Read   246,000,000 records.  Elapsed time: 00:08:52s.  Time for last 1,000,000:    1s.  Last read position: chr7:91,992,937
INFO	2026-06-08 09:49:02	MarkDuplicates	Tracking 622166 as yet unmatched pairs. 21977 records in RAM.
INFO	2026-06-08 09:49:04	MarkDuplicates	Read   247,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    2s.  Last read position: chr7:94,400,204
INFO	2026-06-08 09:49:04	MarkDuplicates	Tracking 622165 as yet unmatched pairs. 21971 records in RAM.
INFO	2026-06-08 09:49:06	MarkDuplicates	Read   248,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:    2s.  Last read position: chr7:98,217,986
INFO	2026-06-08 09:49:06	MarkDuplicates	Tracking 618759 as yet unmatched pairs. 18550 records in RAM.
INFO	2026-06-08 09:49:08	MarkDuplicates	Read   249,000,000 records.  Elapsed time: 00:08:58s.  Time for last 1,000,000:    1s.  Last read position: chr7:99,968,187
INFO	2026-06-08 09:49:08	MarkDuplicates	Tracking 621463 as yet unmatched pairs. 21240 records in RAM.
INFO	2026-06-08 09:49:10	MarkDuplicates	Read   250,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    2s.  Last read position: chr7:100,374,353
INFO	2026-06-08 09:49:10	MarkDuplicates	Tracking 615723 as yet unmatched pairs. 15489 records in RAM.
INFO	2026-06-08 09:49:13	MarkDuplicates	Read   251,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    2s.  Last read position: chr7:101,212,912
INFO	2026-06-08 09:49:13	MarkDuplicates	Tracking 614017 as yet unmatched pairs. 13775 records in RAM.
INFO	2026-06-08 09:49:14	MarkDuplicates	Read   252,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    1s.  Last read position: chr7:102,594,084
INFO	2026-06-08 09:49:14	MarkDuplicates	Tracking 614220 as yet unmatched pairs. 13958 records in RAM.
INFO	2026-06-08 09:49:17	MarkDuplicates	Read   253,000,000 records.  Elapsed time: 00:09:07s.  Time for last 1,000,000:    2s.  Last read position: chr7:107,580,260
INFO	2026-06-08 09:49:17	MarkDuplicates	Tracking 611792 as yet unmatched pairs. 11517 records in RAM.
INFO	2026-06-08 09:49:19	MarkDuplicates	Read   254,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    1s.  Last read position: chr7:127,698,938
INFO	2026-06-08 09:49:19	MarkDuplicates	Tracking 613201 as yet unmatched pairs. 12908 records in RAM.
INFO	2026-06-08 09:49:21	MarkDuplicates	Read   255,000,000 records.  Elapsed time: 00:09:11s.  Time for last 1,000,000:    2s.  Last read position: chr7:129,762,638
INFO	2026-06-08 09:49:21	MarkDuplicates	Tracking 608837 as yet unmatched pairs. 8538 records in RAM.
INFO	2026-06-08 09:49:23	MarkDuplicates	Read   256,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:    2s.  Last read position: chr7:138,871,282
INFO	2026-06-08 09:49:23	MarkDuplicates	Tracking 607913 as yet unmatched pairs. 7604 records in RAM.
INFO	2026-06-08 09:49:25	MarkDuplicates	Read   257,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    1s.  Last read position: chr7:143,139,149
INFO	2026-06-08 09:49:25	MarkDuplicates	Tracking 607385 as yet unmatched pairs. 7058 records in RAM.
INFO	2026-06-08 09:49:27	MarkDuplicates	Read   258,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:    2s.  Last read position: chr7:149,012,243
INFO	2026-06-08 09:49:27	MarkDuplicates	Tracking 605127 as yet unmatched pairs. 4794 records in RAM.
INFO	2026-06-08 09:49:29	MarkDuplicates	Read   259,000,000 records.  Elapsed time: 00:09:19s.  Time for last 1,000,000:    2s.  Last read position: chr7:151,071,694
INFO	2026-06-08 09:49:29	MarkDuplicates	Tracking 603672 as yet unmatched pairs. 3322 records in RAM.
INFO	2026-06-08 09:49:31	MarkDuplicates	Read   260,000,000 records.  Elapsed time: 00:09:21s.  Time for last 1,000,000:    1s.  Last read position: chr7:152,816,575
INFO	2026-06-08 09:49:31	MarkDuplicates	Tracking 601432 as yet unmatched pairs. 1054 records in RAM.
INFO	2026-06-08 09:49:34	MarkDuplicates	Read   261,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    2s.  Last read position: chr8:11,284,920
INFO	2026-06-08 09:49:34	MarkDuplicates	Tracking 599752 as yet unmatched pairs. 30520 records in RAM.
INFO	2026-06-08 09:49:36	MarkDuplicates	Read   262,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    2s.  Last read position: chr8:17,935,642
INFO	2026-06-08 09:49:36	MarkDuplicates	Tracking 598952 as yet unmatched pairs. 29705 records in RAM.
INFO	2026-06-08 09:49:38	MarkDuplicates	Read   263,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    1s.  Last read position: chr8:22,614,490
INFO	2026-06-08 09:49:38	MarkDuplicates	Tracking 598357 as yet unmatched pairs. 29096 records in RAM.
INFO	2026-06-08 09:49:40	MarkDuplicates	Read   264,000,000 records.  Elapsed time: 00:09:30s.  Time for last 1,000,000:    2s.  Last read position: chr8:29,070,433
INFO	2026-06-08 09:49:40	MarkDuplicates	Tracking 595597 as yet unmatched pairs. 26308 records in RAM.
INFO	2026-06-08 09:49:43	MarkDuplicates	Read   265,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    2s.  Last read position: chr8:37,697,469
INFO	2026-06-08 09:49:43	MarkDuplicates	Tracking 594818 as yet unmatched pairs. 25511 records in RAM.
INFO	2026-06-08 09:49:45	MarkDuplicates	Read   266,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    2s.  Last read position: chr8:38,936,037
INFO	2026-06-08 09:49:45	MarkDuplicates	Tracking 591900 as yet unmatched pairs. 22585 records in RAM.
INFO	2026-06-08 09:49:47	MarkDuplicates	Read   267,000,000 records.  Elapsed time: 00:09:37s.  Time for last 1,000,000:    2s.  Last read position: chr8:47,860,959
INFO	2026-06-08 09:49:47	MarkDuplicates	Tracking 591323 as yet unmatched pairs. 21983 records in RAM.
INFO	2026-06-08 09:49:49	MarkDuplicates	Read   268,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    2s.  Last read position: chr8:61,637,947
INFO	2026-06-08 09:49:49	MarkDuplicates	Tracking 589778 as yet unmatched pairs. 20414 records in RAM.
INFO	2026-06-08 09:49:52	MarkDuplicates	Read   269,000,000 records.  Elapsed time: 00:09:41s.  Time for last 1,000,000:    2s.  Last read position: chr8:70,162,816
INFO	2026-06-08 09:49:52	MarkDuplicates	Tracking 588604 as yet unmatched pairs. 19218 records in RAM.
INFO	2026-06-08 09:49:53	MarkDuplicates	Read   270,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    1s.  Last read position: chr8:89,786,612
INFO	2026-06-08 09:49:53	MarkDuplicates	Tracking 586405 as yet unmatched pairs. 16988 records in RAM.
INFO	2026-06-08 09:49:56	MarkDuplicates	Read   271,000,000 records.  Elapsed time: 00:09:46s.  Time for last 1,000,000:    2s.  Last read position: chr8:98,041,792
INFO	2026-06-08 09:49:56	MarkDuplicates	Tracking 589460 as yet unmatched pairs. 20030 records in RAM.
INFO	2026-06-08 09:49:58	MarkDuplicates	Read   272,000,000 records.  Elapsed time: 00:09:48s.  Time for last 1,000,000:    2s.  Last read position: chr8:100,920,668
INFO	2026-06-08 09:49:58	MarkDuplicates	Tracking 584769 as yet unmatched pairs. 15328 records in RAM.
INFO	2026-06-08 09:50:00	MarkDuplicates	Read   273,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:    1s.  Last read position: chr8:115,414,005
INFO	2026-06-08 09:50:00	MarkDuplicates	Tracking 582708 as yet unmatched pairs. 13248 records in RAM.
INFO	2026-06-08 09:50:02	MarkDuplicates	Read   274,000,000 records.  Elapsed time: 00:09:52s.  Time for last 1,000,000:    2s.  Last read position: chr8:117,152,962
INFO	2026-06-08 09:50:02	MarkDuplicates	Tracking 581562 as yet unmatched pairs. 12083 records in RAM.
INFO	2026-06-08 09:50:05	MarkDuplicates	Read   275,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    2s.  Last read position: chr8:127,738,800
INFO	2026-06-08 09:50:05	MarkDuplicates	Tracking 579700 as yet unmatched pairs. 10198 records in RAM.
INFO	2026-06-08 09:50:07	MarkDuplicates	Read   276,000,000 records.  Elapsed time: 00:09:56s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,579,818
INFO	2026-06-08 09:50:07	MarkDuplicates	Tracking 577429 as yet unmatched pairs. 7898 records in RAM.
INFO	2026-06-08 09:50:09	MarkDuplicates	Read   277,000,000 records.  Elapsed time: 00:09:58s.  Time for last 1,000,000:    2s.  Last read position: chr8:143,859,888
INFO	2026-06-08 09:50:09	MarkDuplicates	Tracking 576319 as yet unmatched pairs. 6781 records in RAM.
INFO	2026-06-08 09:50:10	MarkDuplicates	Read   278,000,000 records.  Elapsed time: 00:10:00s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,865,464
INFO	2026-06-08 09:50:10	MarkDuplicates	Tracking 575066 as yet unmatched pairs. 5523 records in RAM.
INFO	2026-06-08 09:50:12	MarkDuplicates	Read   279,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,922,539
INFO	2026-06-08 09:50:12	MarkDuplicates	Tracking 574074 as yet unmatched pairs. 4524 records in RAM.
INFO	2026-06-08 09:50:14	MarkDuplicates	Read   280,000,000 records.  Elapsed time: 00:10:04s.  Time for last 1,000,000:    1s.  Last read position: chr8:144,243,377
INFO	2026-06-08 09:50:14	MarkDuplicates	Tracking 571573 as yet unmatched pairs. 2014 records in RAM.
INFO	2026-06-08 09:50:16	MarkDuplicates	Read   281,000,000 records.  Elapsed time: 00:10:06s.  Time for last 1,000,000:    2s.  Last read position: chr9:711,404
INFO	2026-06-08 09:50:16	MarkDuplicates	Tracking 569580 as yet unmatched pairs. 31318 records in RAM.
INFO	2026-06-08 09:50:18	MarkDuplicates	Read   282,000,000 records.  Elapsed time: 00:10:08s.  Time for last 1,000,000:    1s.  Last read position: chr9:33,026,881
INFO	2026-06-08 09:50:18	MarkDuplicates	Tracking 568146 as yet unmatched pairs. 29838 records in RAM.
INFO	2026-06-08 09:50:21	MarkDuplicates	Read   283,000,000 records.  Elapsed time: 00:10:10s.  Time for last 1,000,000:    2s.  Last read position: chr9:35,698,898
INFO	2026-06-08 09:50:21	MarkDuplicates	Tracking 566753 as yet unmatched pairs. 28425 records in RAM.
INFO	2026-06-08 09:50:23	MarkDuplicates	Read   284,000,000 records.  Elapsed time: 00:10:13s.  Time for last 1,000,000:    2s.  Last read position: chr9:69,221,296
INFO	2026-06-08 09:50:23	MarkDuplicates	Tracking 565615 as yet unmatched pairs. 27271 records in RAM.
INFO	2026-06-08 09:50:25	MarkDuplicates	Read   285,000,000 records.  Elapsed time: 00:10:15s.  Time for last 1,000,000:    1s.  Last read position: chr9:86,027,805
INFO	2026-06-08 09:50:25	MarkDuplicates	Tracking 564541 as yet unmatched pairs. 26159 records in RAM.
INFO	2026-06-08 09:50:27	MarkDuplicates	Read   286,000,000 records.  Elapsed time: 00:10:17s.  Time for last 1,000,000:    2s.  Last read position: chr9:93,234,848
INFO	2026-06-08 09:50:27	MarkDuplicates	Tracking 562300 as yet unmatched pairs. 23900 records in RAM.
INFO	2026-06-08 09:50:29	MarkDuplicates	Read   287,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:    2s.  Last read position: chr9:98,109,927
INFO	2026-06-08 09:50:29	MarkDuplicates	Tracking 560588 as yet unmatched pairs. 22174 records in RAM.
INFO	2026-06-08 09:50:31	MarkDuplicates	Read   288,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:    1s.  Last read position: chr9:110,244,131
INFO	2026-06-08 09:50:31	MarkDuplicates	Tracking 560159 as yet unmatched pairs. 21743 records in RAM.
INFO	2026-06-08 09:50:33	MarkDuplicates	Read   289,000,000 records.  Elapsed time: 00:10:23s.  Time for last 1,000,000:    2s.  Last read position: chr9:114,611,478
INFO	2026-06-08 09:50:33	MarkDuplicates	Tracking 557032 as yet unmatched pairs. 18613 records in RAM.
INFO	2026-06-08 09:50:35	MarkDuplicates	Read   290,000,000 records.  Elapsed time: 00:10:25s.  Time for last 1,000,000:    2s.  Last read position: chr9:124,321,461
INFO	2026-06-08 09:50:35	MarkDuplicates	Tracking 555781 as yet unmatched pairs. 17341 records in RAM.
INFO	2026-06-08 09:50:37	MarkDuplicates	Read   291,000,000 records.  Elapsed time: 00:10:27s.  Time for last 1,000,000:    1s.  Last read position: chr9:127,809,788
INFO	2026-06-08 09:50:37	MarkDuplicates	Tracking 554568 as yet unmatched pairs. 16113 records in RAM.
INFO	2026-06-08 09:50:40	MarkDuplicates	Read   292,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    2s.  Last read position: chr9:128,607,633
INFO	2026-06-08 09:50:40	MarkDuplicates	Tracking 552436 as yet unmatched pairs. 13974 records in RAM.
INFO	2026-06-08 09:50:42	MarkDuplicates	Read   293,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:    2s.  Last read position: chr9:130,092,283
INFO	2026-06-08 09:50:42	MarkDuplicates	Tracking 550851 as yet unmatched pairs. 12366 records in RAM.
INFO	2026-06-08 09:50:44	MarkDuplicates	Read   294,000,000 records.  Elapsed time: 00:10:34s.  Time for last 1,000,000:    1s.  Last read position: chr9:131,589,953
INFO	2026-06-08 09:50:44	MarkDuplicates	Tracking 549204 as yet unmatched pairs. 10714 records in RAM.
INFO	2026-06-08 09:50:46	MarkDuplicates	Read   295,000,000 records.  Elapsed time: 00:10:36s.  Time for last 1,000,000:    2s.  Last read position: chr9:134,048,301
INFO	2026-06-08 09:50:46	MarkDuplicates	Tracking 548778 as yet unmatched pairs. 10275 records in RAM.
INFO	2026-06-08 09:50:49	MarkDuplicates	Read   296,000,000 records.  Elapsed time: 00:10:38s.  Time for last 1,000,000:    2s.  Last read position: chr9:136,443,851
INFO	2026-06-08 09:50:49	MarkDuplicates	Tracking 547740 as yet unmatched pairs. 9233 records in RAM.
INFO	2026-06-08 09:50:50	MarkDuplicates	Read   297,000,000 records.  Elapsed time: 00:10:40s.  Time for last 1,000,000:    1s.  Last read position: chr9:136,839,256
INFO	2026-06-08 09:50:50	MarkDuplicates	Tracking 544699 as yet unmatched pairs. 6180 records in RAM.
INFO	2026-06-08 09:50:53	MarkDuplicates	Read   298,000,000 records.  Elapsed time: 00:10:43s.  Time for last 1,000,000:    2s.  Last read position: chr9:137,162,179
INFO	2026-06-08 09:50:53	MarkDuplicates	Tracking 542579 as yet unmatched pairs. 4055 records in RAM.
INFO	2026-06-08 09:50:55	MarkDuplicates	Read   299,000,000 records.  Elapsed time: 00:10:45s.  Time for last 1,000,000:    2s.  Last read position: chr9:137,452,768
INFO	2026-06-08 09:50:55	MarkDuplicates	Tracking 540000 as yet unmatched pairs. 1460 records in RAM.
INFO	2026-06-08 09:50:57	MarkDuplicates	Read   300,000,000 records.  Elapsed time: 00:10:47s.  Time for last 1,000,000:    2s.  Last read position: chr10:3,149,673
INFO	2026-06-08 09:50:57	MarkDuplicates	Tracking 538731 as yet unmatched pairs. 32863 records in RAM.
INFO	2026-06-08 09:50:59	MarkDuplicates	Read   301,000,000 records.  Elapsed time: 00:10:49s.  Time for last 1,000,000:    2s.  Last read position: chr10:5,925,412
INFO	2026-06-08 09:50:59	MarkDuplicates	Tracking 536619 as yet unmatched pairs. 30743 records in RAM.
INFO	2026-06-08 09:51:01	MarkDuplicates	Read   302,000,000 records.  Elapsed time: 00:10:51s.  Time for last 1,000,000:    2s.  Last read position: chr10:12,177,752
INFO	2026-06-08 09:51:01	MarkDuplicates	Tracking 535226 as yet unmatched pairs. 29329 records in RAM.
INFO	2026-06-08 09:51:03	MarkDuplicates	Read   303,000,000 records.  Elapsed time: 00:10:53s.  Time for last 1,000,000:    1s.  Last read position: chr10:24,495,148
INFO	2026-06-08 09:51:03	MarkDuplicates	Tracking 533615 as yet unmatched pairs. 27710 records in RAM.
INFO	2026-06-08 09:51:06	MarkDuplicates	Read   304,000,000 records.  Elapsed time: 00:10:55s.  Time for last 1,000,000:    2s.  Last read position: chr10:32,015,659
INFO	2026-06-08 09:51:06	MarkDuplicates	Tracking 535183 as yet unmatched pairs. 29265 records in RAM.
INFO	2026-06-08 09:51:08	MarkDuplicates	Read   305,000,000 records.  Elapsed time: 00:10:58s.  Time for last 1,000,000:    2s.  Last read position: chr10:32,929,969
INFO	2026-06-08 09:51:08	MarkDuplicates	Tracking 532485 as yet unmatched pairs. 26547 records in RAM.
INFO	2026-06-08 09:51:10	MarkDuplicates	Read   306,000,000 records.  Elapsed time: 00:11:00s.  Time for last 1,000,000:    1s.  Last read position: chr10:37,165,116
INFO	2026-06-08 09:51:10	MarkDuplicates	Tracking 536493 as yet unmatched pairs. 30537 records in RAM.
INFO	2026-06-08 09:51:12	MarkDuplicates	Read   307,000,000 records.  Elapsed time: 00:11:02s.  Time for last 1,000,000:    2s.  Last read position: chr10:37,193,233
INFO	2026-06-08 09:51:12	MarkDuplicates	Tracking 536490 as yet unmatched pairs. 30529 records in RAM.
INFO	2026-06-08 09:51:14	MarkDuplicates	Read   308,000,000 records.  Elapsed time: 00:11:04s.  Time for last 1,000,000:    1s.  Last read position: chr10:43,100,673
INFO	2026-06-08 09:51:14	MarkDuplicates	Tracking 535401 as yet unmatched pairs. 29367 records in RAM.
INFO	2026-06-08 09:51:16	MarkDuplicates	Read   309,000,000 records.  Elapsed time: 00:11:06s.  Time for last 1,000,000:    2s.  Last read position: chr10:43,112,181
INFO	2026-06-08 09:51:16	MarkDuplicates	Tracking 543705 as yet unmatched pairs. 37648 records in RAM.
INFO	2026-06-08 09:51:18	MarkDuplicates	Read   310,000,000 records.  Elapsed time: 00:11:08s.  Time for last 1,000,000:    2s.  Last read position: chr10:43,387,328
INFO	2026-06-08 09:51:18	MarkDuplicates	Tracking 524894 as yet unmatched pairs. 18713 records in RAM.
INFO	2026-06-08 09:51:20	MarkDuplicates	Read   311,000,000 records.  Elapsed time: 00:11:10s.  Time for last 1,000,000:    1s.  Last read position: chr10:48,015,669
INFO	2026-06-08 09:51:20	MarkDuplicates	Tracking 522820 as yet unmatched pairs. 16638 records in RAM.
INFO	2026-06-08 09:51:22	MarkDuplicates	Read   312,000,000 records.  Elapsed time: 00:11:12s.  Time for last 1,000,000:    2s.  Last read position: chr10:67,912,938
INFO	2026-06-08 09:51:22	MarkDuplicates	Tracking 521184 as yet unmatched pairs. 14965 records in RAM.
INFO	2026-06-08 09:51:24	MarkDuplicates	Read   313,000,000 records.  Elapsed time: 00:11:14s.  Time for last 1,000,000:    1s.  Last read position: chr10:72,861,686
INFO	2026-06-08 09:51:24	MarkDuplicates	Tracking 519421 as yet unmatched pairs. 13177 records in RAM.
INFO	2026-06-08 09:51:26	MarkDuplicates	Read   314,000,000 records.  Elapsed time: 00:11:16s.  Time for last 1,000,000:    2s.  Last read position: chr10:77,806,757
INFO	2026-06-08 09:51:26	MarkDuplicates	Tracking 518333 as yet unmatched pairs. 12069 records in RAM.
INFO	2026-06-08 09:51:28	MarkDuplicates	Read   315,000,000 records.  Elapsed time: 00:11:18s.  Time for last 1,000,000:    2s.  Last read position: chr10:87,094,527
INFO	2026-06-08 09:51:28	MarkDuplicates	Tracking 516826 as yet unmatched pairs. 10549 records in RAM.
INFO	2026-06-08 09:51:30	MarkDuplicates	Read   316,000,000 records.  Elapsed time: 00:11:20s.  Time for last 1,000,000:    1s.  Last read position: chr10:95,664,192
INFO	2026-06-08 09:51:30	MarkDuplicates	Tracking 515200 as yet unmatched pairs. 8902 records in RAM.
INFO	2026-06-08 09:51:33	MarkDuplicates	Read   317,000,000 records.  Elapsed time: 00:11:22s.  Time for last 1,000,000:    2s.  Last read position: chr10:100,360,793
INFO	2026-06-08 09:51:33	MarkDuplicates	Tracking 514609 as yet unmatched pairs. 8301 records in RAM.
INFO	2026-06-08 09:51:35	MarkDuplicates	Read   318,000,000 records.  Elapsed time: 00:11:25s.  Time for last 1,000,000:    2s.  Last read position: chr10:102,401,843
INFO	2026-06-08 09:51:35	MarkDuplicates	Tracking 512157 as yet unmatched pairs. 5811 records in RAM.
INFO	2026-06-08 09:51:37	MarkDuplicates	Read   319,000,000 records.  Elapsed time: 00:11:27s.  Time for last 1,000,000:    1s.  Last read position: chr10:114,473,015
INFO	2026-06-08 09:51:37	MarkDuplicates	Tracking 510584 as yet unmatched pairs. 4224 records in RAM.
INFO	2026-06-08 09:51:39	MarkDuplicates	Read   320,000,000 records.  Elapsed time: 00:11:29s.  Time for last 1,000,000:    2s.  Last read position: chr10:119,917,984
INFO	2026-06-08 09:51:39	MarkDuplicates	Tracking 509069 as yet unmatched pairs. 2689 records in RAM.
INFO	2026-06-08 09:51:41	MarkDuplicates	Read   321,000,000 records.  Elapsed time: 00:11:31s.  Time for last 1,000,000:    2s.  Last read position: chr10:127,127,708
INFO	2026-06-08 09:51:41	MarkDuplicates	Tracking 507630 as yet unmatched pairs. 1219 records in RAM.
INFO	2026-06-08 09:51:44	MarkDuplicates	Read   322,000,000 records.  Elapsed time: 00:11:34s.  Time for last 1,000,000:    2s.  Last read position: chr11:320,610
INFO	2026-06-08 09:51:44	MarkDuplicates	Tracking 508223 as yet unmatched pairs. 65460 records in RAM.
INFO	2026-06-08 09:51:46	MarkDuplicates	Read   323,000,000 records.  Elapsed time: 00:11:36s.  Time for last 1,000,000:    2s.  Last read position: chr11:555,262
INFO	2026-06-08 09:51:46	MarkDuplicates	Tracking 504927 as yet unmatched pairs. 62150 records in RAM.
INFO	2026-06-08 09:51:49	MarkDuplicates	Read   324,000,000 records.  Elapsed time: 00:11:38s.  Time for last 1,000,000:    2s.  Last read position: chr11:597,404
INFO	2026-06-08 09:51:49	MarkDuplicates	Tracking 506044 as yet unmatched pairs. 63258 records in RAM.
INFO	2026-06-08 09:51:51	MarkDuplicates	Read   325,000,000 records.  Elapsed time: 00:11:40s.  Time for last 1,000,000:    1s.  Last read position: chr11:613,861
INFO	2026-06-08 09:51:51	MarkDuplicates	Tracking 500255 as yet unmatched pairs. 57459 records in RAM.
INFO	2026-06-08 09:51:53	MarkDuplicates	Read   326,000,000 records.  Elapsed time: 00:11:43s.  Time for last 1,000,000:    2s.  Last read position: chr11:822,467
INFO	2026-06-08 09:51:53	MarkDuplicates	Tracking 497906 as yet unmatched pairs. 55098 records in RAM.
INFO	2026-06-08 09:51:55	MarkDuplicates	Read   327,000,000 records.  Elapsed time: 00:11:45s.  Time for last 1,000,000:    2s.  Last read position: chr11:1,390,318
INFO	2026-06-08 09:51:55	MarkDuplicates	Tracking 495175 as yet unmatched pairs. 52348 records in RAM.
INFO	2026-06-08 09:51:57	MarkDuplicates	Read   328,000,000 records.  Elapsed time: 00:11:47s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,753,492
INFO	2026-06-08 09:51:57	MarkDuplicates	Tracking 505111 as yet unmatched pairs. 62270 records in RAM.
INFO	2026-06-08 09:51:59	MarkDuplicates	Read   329,000,000 records.  Elapsed time: 00:11:49s.  Time for last 1,000,000:    2s.  Last read position: chr11:1,757,417
INFO	2026-06-08 09:51:59	MarkDuplicates	Tracking 505167 as yet unmatched pairs. 62315 records in RAM.
INFO	2026-06-08 09:52:01	MarkDuplicates	Read   330,000,000 records.  Elapsed time: 00:11:51s.  Time for last 1,000,000:    2s.  Last read position: chr11:1,761,407
INFO	2026-06-08 09:52:01	MarkDuplicates	Tracking 500917 as yet unmatched pairs. 58057 records in RAM.
INFO	2026-06-08 09:52:03	MarkDuplicates	Read   331,000,000 records.  Elapsed time: 00:11:53s.  Time for last 1,000,000:    1s.  Last read position: chr11:3,693,315
INFO	2026-06-08 09:52:03	MarkDuplicates	Tracking 488485 as yet unmatched pairs. 45618 records in RAM.
INFO	2026-06-08 09:52:06	MarkDuplicates	Read   332,000,000 records.  Elapsed time: 00:11:55s.  Time for last 1,000,000:    2s.  Last read position: chr11:6,566,177
INFO	2026-06-08 09:52:06	MarkDuplicates	Tracking 486398 as yet unmatched pairs. 43518 records in RAM.
INFO	2026-06-08 09:52:07	MarkDuplicates	Read   333,000,000 records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:    1s.  Last read position: chr11:9,574,305
INFO	2026-06-08 09:52:07	MarkDuplicates	Tracking 485160 as yet unmatched pairs. 42272 records in RAM.
INFO	2026-06-08 09:52:10	MarkDuplicates	Read   334,000,000 records.  Elapsed time: 00:12:00s.  Time for last 1,000,000:    2s.  Last read position: chr11:12,881,897
INFO	2026-06-08 09:52:10	MarkDuplicates	Tracking 483613 as yet unmatched pairs. 40714 records in RAM.
INFO	2026-06-08 09:52:12	MarkDuplicates	Read   335,000,000 records.  Elapsed time: 00:12:02s.  Time for last 1,000,000:    2s.  Last read position: chr11:18,400,941
INFO	2026-06-08 09:52:12	MarkDuplicates	Tracking 482815 as yet unmatched pairs. 39902 records in RAM.
INFO	2026-06-08 09:52:14	MarkDuplicates	Read   336,000,000 records.  Elapsed time: 00:12:04s.  Time for last 1,000,000:    1s.  Last read position: chr11:32,934,239
INFO	2026-06-08 09:52:14	MarkDuplicates	Tracking 480528 as yet unmatched pairs. 37515 records in RAM.
INFO	2026-06-08 09:52:16	MarkDuplicates	Read   337,000,000 records.  Elapsed time: 00:12:06s.  Time for last 1,000,000:    2s.  Last read position: chr11:43,342,658
INFO	2026-06-08 09:52:16	MarkDuplicates	Tracking 478840 as yet unmatched pairs. 35805 records in RAM.
INFO	2026-06-08 09:52:18	MarkDuplicates	Read   338,000,000 records.  Elapsed time: 00:12:08s.  Time for last 1,000,000:    2s.  Last read position: chr11:46,428,627
INFO	2026-06-08 09:52:18	MarkDuplicates	Tracking 477374 as yet unmatched pairs. 34319 records in RAM.
INFO	2026-06-08 09:52:20	MarkDuplicates	Read   339,000,000 records.  Elapsed time: 00:12:10s.  Time for last 1,000,000:    1s.  Last read position: chr11:47,573,670
INFO	2026-06-08 09:52:20	MarkDuplicates	Tracking 475854 as yet unmatched pairs. 32790 records in RAM.
INFO	2026-06-08 09:52:23	MarkDuplicates	Read   340,000,000 records.  Elapsed time: 00:12:12s.  Time for last 1,000,000:    2s.  Last read position: chr11:57,801,757
INFO	2026-06-08 09:52:23	MarkDuplicates	Tracking 475707 as yet unmatched pairs. 32627 records in RAM.
INFO	2026-06-08 09:52:25	MarkDuplicates	Read   341,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:    2s.  Last read position: chr11:61,533,042
INFO	2026-06-08 09:52:25	MarkDuplicates	Tracking 473151 as yet unmatched pairs. 30057 records in RAM.
INFO	2026-06-08 09:52:27	MarkDuplicates	Read   342,000,000 records.  Elapsed time: 00:12:17s.  Time for last 1,000,000:    1s.  Last read position: chr11:62,523,978
INFO	2026-06-08 09:52:27	MarkDuplicates	Tracking 471872 as yet unmatched pairs. 28777 records in RAM.
INFO	2026-06-08 09:52:29	MarkDuplicates	Read   343,000,000 records.  Elapsed time: 00:12:19s.  Time for last 1,000,000:    2s.  Last read position: chr11:62,612,529
INFO	2026-06-08 09:52:29	MarkDuplicates	Tracking 469814 as yet unmatched pairs. 26715 records in RAM.
INFO	2026-06-08 09:52:31	MarkDuplicates	Read   344,000,000 records.  Elapsed time: 00:12:21s.  Time for last 1,000,000:    2s.  Last read position: chr11:63,997,555
INFO	2026-06-08 09:52:31	MarkDuplicates	Tracking 468210 as yet unmatched pairs. 25085 records in RAM.
INFO	2026-06-08 09:52:33	MarkDuplicates	Read   345,000,000 records.  Elapsed time: 00:12:23s.  Time for last 1,000,000:    1s.  Last read position: chr11:65,079,455
INFO	2026-06-08 09:52:33	MarkDuplicates	Tracking 466299 as yet unmatched pairs. 23170 records in RAM.
INFO	2026-06-08 09:52:35	MarkDuplicates	Read   346,000,000 records.  Elapsed time: 00:12:25s.  Time for last 1,000,000:    2s.  Last read position: chr11:65,605,765
INFO	2026-06-08 09:52:35	MarkDuplicates	Tracking 464556 as yet unmatched pairs. 21346 records in RAM.
INFO	2026-06-08 09:52:37	MarkDuplicates	Read   347,000,000 records.  Elapsed time: 00:12:27s.  Time for last 1,000,000:    1s.  Last read position: chr11:66,284,910
INFO	2026-06-08 09:52:37	MarkDuplicates	Tracking 463524 as yet unmatched pairs. 20312 records in RAM.
INFO	2026-06-08 09:52:39	MarkDuplicates	Read   348,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:    2s.  Last read position: chr11:67,401,153
INFO	2026-06-08 09:52:39	MarkDuplicates	Tracking 461210 as yet unmatched pairs. 17987 records in RAM.
INFO	2026-06-08 09:52:41	MarkDuplicates	Read   349,000,000 records.  Elapsed time: 00:12:31s.  Time for last 1,000,000:    2s.  Last read position: chr11:68,892,506
INFO	2026-06-08 09:52:41	MarkDuplicates	Tracking 459693 as yet unmatched pairs. 16451 records in RAM.
INFO	2026-06-08 09:52:43	MarkDuplicates	Read   350,000,000 records.  Elapsed time: 00:12:33s.  Time for last 1,000,000:    1s.  Last read position: chr11:70,326,749
INFO	2026-06-08 09:52:43	MarkDuplicates	Tracking 457631 as yet unmatched pairs. 14366 records in RAM.
INFO	2026-06-08 09:52:45	MarkDuplicates	Read   351,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:    2s.  Last read position: chr11:72,009,324
INFO	2026-06-08 09:52:45	MarkDuplicates	Tracking 456610 as yet unmatched pairs. 13319 records in RAM.
INFO	2026-06-08 09:52:48	MarkDuplicates	Read   352,000,000 records.  Elapsed time: 00:12:38s.  Time for last 1,000,000:    2s.  Last read position: chr11:73,976,853
INFO	2026-06-08 09:52:48	MarkDuplicates	Tracking 454704 as yet unmatched pairs. 11393 records in RAM.
INFO	2026-06-08 09:52:50	MarkDuplicates	Read   353,000,000 records.  Elapsed time: 00:12:40s.  Time for last 1,000,000:    1s.  Last read position: chr11:77,702,227
INFO	2026-06-08 09:52:50	MarkDuplicates	Tracking 452983 as yet unmatched pairs. 9661 records in RAM.
INFO	2026-06-08 09:52:52	MarkDuplicates	Read   354,000,000 records.  Elapsed time: 00:12:42s.  Time for last 1,000,000:    2s.  Last read position: chr11:86,807,806
INFO	2026-06-08 09:52:52	MarkDuplicates	Tracking 452093 as yet unmatched pairs. 8753 records in RAM.
INFO	2026-06-08 09:52:54	MarkDuplicates	Read   355,000,000 records.  Elapsed time: 00:12:44s.  Time for last 1,000,000:    2s.  Last read position: chr11:103,996,147
INFO	2026-06-08 09:52:54	MarkDuplicates	Tracking 449273 as yet unmatched pairs. 5924 records in RAM.
INFO	2026-06-08 09:52:56	MarkDuplicates	Read   356,000,000 records.  Elapsed time: 00:12:46s.  Time for last 1,000,000:    2s.  Last read position: chr11:118,379,665
INFO	2026-06-08 09:52:56	MarkDuplicates	Tracking 448319 as yet unmatched pairs. 4948 records in RAM.
INFO	2026-06-08 09:52:59	MarkDuplicates	Read   357,000,000 records.  Elapsed time: 00:12:49s.  Time for last 1,000,000:    2s.  Last read position: chr11:119,182,243
INFO	2026-06-08 09:52:59	MarkDuplicates	Tracking 446344 as yet unmatched pairs. 2971 records in RAM.
INFO	2026-06-08 09:53:01	MarkDuplicates	Read   358,000,000 records.  Elapsed time: 00:12:51s.  Time for last 1,000,000:    2s.  Last read position: chr11:125,597,080
INFO	2026-06-08 09:53:01	MarkDuplicates	Tracking 445433 as yet unmatched pairs. 2056 records in RAM.
INFO	2026-06-08 09:53:04	MarkDuplicates	Read   359,000,000 records.  Elapsed time: 00:12:53s.  Time for last 1,000,000:    2s.  Last read position: chr12:19,042
INFO	2026-06-08 09:53:04	MarkDuplicates	Tracking 443765 as yet unmatched pairs. 48252 records in RAM.
INFO	2026-06-08 09:53:06	MarkDuplicates	Read   360,000,000 records.  Elapsed time: 00:12:56s.  Time for last 1,000,000:    2s.  Last read position: chr12:2,861,221
INFO	2026-06-08 09:53:06	MarkDuplicates	Tracking 442111 as yet unmatched pairs. 46586 records in RAM.
INFO	2026-06-08 09:53:08	MarkDuplicates	Read   361,000,000 records.  Elapsed time: 00:12:58s.  Time for last 1,000,000:    2s.  Last read position: chr12:6,492,320
INFO	2026-06-08 09:53:08	MarkDuplicates	Tracking 441503 as yet unmatched pairs. 45975 records in RAM.
INFO	2026-06-08 09:53:10	MarkDuplicates	Read   362,000,000 records.  Elapsed time: 00:13:00s.  Time for last 1,000,000:    2s.  Last read position: chr12:6,869,363
INFO	2026-06-08 09:53:10	MarkDuplicates	Tracking 439480 as yet unmatched pairs. 43948 records in RAM.
INFO	2026-06-08 09:53:12	MarkDuplicates	Read   363,000,000 records.  Elapsed time: 00:13:02s.  Time for last 1,000,000:    2s.  Last read position: chr12:8,921,610
INFO	2026-06-08 09:53:12	MarkDuplicates	Tracking 437556 as yet unmatched pairs. 42022 records in RAM.
INFO	2026-06-08 09:53:14	MarkDuplicates	Read   364,000,000 records.  Elapsed time: 00:13:04s.  Time for last 1,000,000:    1s.  Last read position: chr12:12,908,276
INFO	2026-06-08 09:53:14	MarkDuplicates	Tracking 437849 as yet unmatched pairs. 42291 records in RAM.
INFO	2026-06-08 09:53:16	MarkDuplicates	Read   365,000,000 records.  Elapsed time: 00:13:06s.  Time for last 1,000,000:    2s.  Last read position: chr12:19,359,534
INFO	2026-06-08 09:53:16	MarkDuplicates	Tracking 434849 as yet unmatched pairs. 39283 records in RAM.
INFO	2026-06-08 09:53:19	MarkDuplicates	Read   366,000,000 records.  Elapsed time: 00:13:08s.  Time for last 1,000,000:    2s.  Last read position: chr12:32,824,115
INFO	2026-06-08 09:53:19	MarkDuplicates	Tracking 433191 as yet unmatched pairs. 37621 records in RAM.
INFO	2026-06-08 09:53:21	MarkDuplicates	Read   367,000,000 records.  Elapsed time: 00:13:10s.  Time for last 1,000,000:    1s.  Last read position: chr12:47,798,943
INFO	2026-06-08 09:53:21	MarkDuplicates	Tracking 432915 as yet unmatched pairs. 37336 records in RAM.
INFO	2026-06-08 09:53:23	MarkDuplicates	Read   368,000,000 records.  Elapsed time: 00:13:13s.  Time for last 1,000,000:    2s.  Last read position: chr12:49,045,920
INFO	2026-06-08 09:53:23	MarkDuplicates	Tracking 430650 as yet unmatched pairs. 35062 records in RAM.
INFO	2026-06-08 09:53:25	MarkDuplicates	Read   369,000,000 records.  Elapsed time: 00:13:15s.  Time for last 1,000,000:    2s.  Last read position: chr12:49,752,489
INFO	2026-06-08 09:53:25	MarkDuplicates	Tracking 432511 as yet unmatched pairs. 36915 records in RAM.
INFO	2026-06-08 09:53:27	MarkDuplicates	Read   370,000,000 records.  Elapsed time: 00:13:17s.  Time for last 1,000,000:    1s.  Last read position: chr12:51,377,232
INFO	2026-06-08 09:53:27	MarkDuplicates	Tracking 427705 as yet unmatched pairs. 32105 records in RAM.
INFO	2026-06-08 09:53:29	MarkDuplicates	Read   371,000,000 records.  Elapsed time: 00:13:19s.  Time for last 1,000,000:    2s.  Last read position: chr12:53,059,610
INFO	2026-06-08 09:53:29	MarkDuplicates	Tracking 425764 as yet unmatched pairs. 30152 records in RAM.
INFO	2026-06-08 09:53:31	MarkDuplicates	Read   372,000,000 records.  Elapsed time: 00:13:21s.  Time for last 1,000,000:    2s.  Last read position: chr12:53,483,356
INFO	2026-06-08 09:53:31	MarkDuplicates	Tracking 424026 as yet unmatched pairs. 28404 records in RAM.
INFO	2026-06-08 09:53:33	MarkDuplicates	Read   373,000,000 records.  Elapsed time: 00:13:23s.  Time for last 1,000,000:    1s.  Last read position: chr12:55,412,904
INFO	2026-06-08 09:53:33	MarkDuplicates	Tracking 422586 as yet unmatched pairs. 26960 records in RAM.
INFO	2026-06-08 09:53:35	MarkDuplicates	Read   374,000,000 records.  Elapsed time: 00:13:25s.  Time for last 1,000,000:    2s.  Last read position: chr12:56,142,611
INFO	2026-06-08 09:53:35	MarkDuplicates	Tracking 421096 as yet unmatched pairs. 25466 records in RAM.
INFO	2026-06-08 09:53:38	MarkDuplicates	Read   375,000,000 records.  Elapsed time: 00:13:27s.  Time for last 1,000,000:    2s.  Last read position: chr12:56,603,414
INFO	2026-06-08 09:53:38	MarkDuplicates	Tracking 419705 as yet unmatched pairs. 24061 records in RAM.
INFO	2026-06-08 09:53:39	MarkDuplicates	Read   376,000,000 records.  Elapsed time: 00:13:29s.  Time for last 1,000,000:    1s.  Last read position: chr12:57,099,308
INFO	2026-06-08 09:53:39	MarkDuplicates	Tracking 421341 as yet unmatched pairs. 25696 records in RAM.
INFO	2026-06-08 09:53:42	MarkDuplicates	Read   377,000,000 records.  Elapsed time: 00:13:32s.  Time for last 1,000,000:    2s.  Last read position: chr12:57,297,339
INFO	2026-06-08 09:53:42	MarkDuplicates	Tracking 416441 as yet unmatched pairs. 20794 records in RAM.
INFO	2026-06-08 09:53:44	MarkDuplicates	Read   378,000,000 records.  Elapsed time: 00:13:34s.  Time for last 1,000,000:    2s.  Last read position: chr12:62,495,012
INFO	2026-06-08 09:53:44	MarkDuplicates	Tracking 415253 as yet unmatched pairs. 19588 records in RAM.
INFO	2026-06-08 09:53:46	MarkDuplicates	Read   379,000,000 records.  Elapsed time: 00:13:36s.  Time for last 1,000,000:    2s.  Last read position: chr12:69,348,514
INFO	2026-06-08 09:53:46	MarkDuplicates	Tracking 413439 as yet unmatched pairs. 17746 records in RAM.
INFO	2026-06-08 09:53:49	MarkDuplicates	Read   380,000,000 records.  Elapsed time: 00:13:38s.  Time for last 1,000,000:    2s.  Last read position: chr12:91,158,388
INFO	2026-06-08 09:53:49	MarkDuplicates	Tracking 412099 as yet unmatched pairs. 16384 records in RAM.
INFO	2026-06-08 09:53:51	MarkDuplicates	Read   381,000,000 records.  Elapsed time: 00:13:41s.  Time for last 1,000,000:    2s.  Last read position: chr12:96,282,544
INFO	2026-06-08 09:53:51	MarkDuplicates	Tracking 410592 as yet unmatched pairs. 14870 records in RAM.
INFO	2026-06-08 09:53:53	MarkDuplicates	Read   382,000,000 records.  Elapsed time: 00:13:43s.  Time for last 1,000,000:    2s.  Last read position: chr12:104,325,400
INFO	2026-06-08 09:53:53	MarkDuplicates	Tracking 408985 as yet unmatched pairs. 13242 records in RAM.
INFO	2026-06-08 09:53:55	MarkDuplicates	Read   383,000,000 records.  Elapsed time: 00:13:45s.  Time for last 1,000,000:    2s.  Last read position: chr12:110,345,367
INFO	2026-06-08 09:53:55	MarkDuplicates	Tracking 407921 as yet unmatched pairs. 12171 records in RAM.
INFO	2026-06-08 09:53:57	MarkDuplicates	Read   384,000,000 records.  Elapsed time: 00:13:47s.  Time for last 1,000,000:    2s.  Last read position: chr12:112,408,447
INFO	2026-06-08 09:53:57	MarkDuplicates	Tracking 406472 as yet unmatched pairs. 10717 records in RAM.
INFO	2026-06-08 09:54:00	MarkDuplicates	Read   385,000,000 records.  Elapsed time: 00:13:50s.  Time for last 1,000,000:    2s.  Last read position: chr12:116,237,572
INFO	2026-06-08 09:54:00	MarkDuplicates	Tracking 405890 as yet unmatched pairs. 10124 records in RAM.
INFO	2026-06-08 09:54:02	MarkDuplicates	Read   386,000,000 records.  Elapsed time: 00:13:52s.  Time for last 1,000,000:    2s.  Last read position: chr12:120,534,589
INFO	2026-06-08 09:54:02	MarkDuplicates	Tracking 403026 as yet unmatched pairs. 7244 records in RAM.
INFO	2026-06-08 09:54:04	MarkDuplicates	Read   387,000,000 records.  Elapsed time: 00:13:54s.  Time for last 1,000,000:    2s.  Last read position: chr12:122,481,522
INFO	2026-06-08 09:54:04	MarkDuplicates	Tracking 401141 as yet unmatched pairs. 5341 records in RAM.
INFO	2026-06-08 09:54:06	MarkDuplicates	Read   388,000,000 records.  Elapsed time: 00:13:56s.  Time for last 1,000,000:    2s.  Last read position: chr12:124,340,397
INFO	2026-06-08 09:54:06	MarkDuplicates	Tracking 399851 as yet unmatched pairs. 4034 records in RAM.
INFO	2026-06-08 09:54:09	MarkDuplicates	Read   389,000,000 records.  Elapsed time: 00:13:58s.  Time for last 1,000,000:    2s.  Last read position: chr12:131,961,162
INFO	2026-06-08 09:54:09	MarkDuplicates	Tracking 398201 as yet unmatched pairs. 2369 records in RAM.
INFO	2026-06-08 09:54:11	MarkDuplicates	Read   390,000,000 records.  Elapsed time: 00:14:01s.  Time for last 1,000,000:    2s.  Last read position: chr13:18,298,319
INFO	2026-06-08 09:54:11	MarkDuplicates	Tracking 395838 as yet unmatched pairs. 11860 records in RAM.
INFO	2026-06-08 09:54:13	MarkDuplicates	Read   391,000,000 records.  Elapsed time: 00:14:03s.  Time for last 1,000,000:    2s.  Last read position: chr13:24,224,155
INFO	2026-06-08 09:54:13	MarkDuplicates	Tracking 395105 as yet unmatched pairs. 11119 records in RAM.
INFO	2026-06-08 09:54:15	MarkDuplicates	Read   392,000,000 records.  Elapsed time: 00:14:05s.  Time for last 1,000,000:    2s.  Last read position: chr13:35,041,021
INFO	2026-06-08 09:54:15	MarkDuplicates	Tracking 393424 as yet unmatched pairs. 9423 records in RAM.
INFO	2026-06-08 09:54:17	MarkDuplicates	Read   393,000,000 records.  Elapsed time: 00:14:07s.  Time for last 1,000,000:    1s.  Last read position: chr13:44,434,552
INFO	2026-06-08 09:54:17	MarkDuplicates	Tracking 391978 as yet unmatched pairs. 7965 records in RAM.
INFO	2026-06-08 09:54:19	MarkDuplicates	Read   394,000,000 records.  Elapsed time: 00:14:09s.  Time for last 1,000,000:    2s.  Last read position: chr13:52,024,299
INFO	2026-06-08 09:54:19	MarkDuplicates	Tracking 390413 as yet unmatched pairs. 6385 records in RAM.
INFO	2026-06-08 09:54:21	MarkDuplicates	Read   395,000,000 records.  Elapsed time: 00:14:11s.  Time for last 1,000,000:    1s.  Last read position: chr13:85,796,174
INFO	2026-06-08 09:54:21	MarkDuplicates	Tracking 392183 as yet unmatched pairs. 8136 records in RAM.
INFO	2026-06-08 09:54:23	MarkDuplicates	Read   396,000,000 records.  Elapsed time: 00:14:13s.  Time for last 1,000,000:    2s.  Last read position: chr13:101,583,236
INFO	2026-06-08 09:54:23	MarkDuplicates	Tracking 387336 as yet unmatched pairs. 3273 records in RAM.
INFO	2026-06-08 09:54:25	MarkDuplicates	Read   397,000,000 records.  Elapsed time: 00:14:15s.  Time for last 1,000,000:    1s.  Last read position: chr13:113,070,101
INFO	2026-06-08 09:54:25	MarkDuplicates	Tracking 386516 as yet unmatched pairs. 2439 records in RAM.
INFO	2026-06-08 09:54:28	MarkDuplicates	Read   398,000,000 records.  Elapsed time: 00:14:17s.  Time for last 1,000,000:    2s.  Last read position: chr14:20,457,209
INFO	2026-06-08 09:54:28	MarkDuplicates	Tracking 384336 as yet unmatched pairs. 24215 records in RAM.
INFO	2026-06-08 09:54:30	MarkDuplicates	Read   399,000,000 records.  Elapsed time: 00:14:20s.  Time for last 1,000,000:    2s.  Last read position: chr14:22,904,311
INFO	2026-06-08 09:54:30	MarkDuplicates	Tracking 382319 as yet unmatched pairs. 22196 records in RAM.
INFO	2026-06-08 09:54:32	MarkDuplicates	Read   400,000,000 records.  Elapsed time: 00:14:22s.  Time for last 1,000,000:    1s.  Last read position: chr14:24,182,094
INFO	2026-06-08 09:54:32	MarkDuplicates	Tracking 380730 as yet unmatched pairs. 20591 records in RAM.
INFO	2026-06-08 09:54:34	MarkDuplicates	Read   401,000,000 records.  Elapsed time: 00:14:24s.  Time for last 1,000,000:    2s.  Last read position: chr14:32,092,401
INFO	2026-06-08 09:54:34	MarkDuplicates	Tracking 378999 as yet unmatched pairs. 18848 records in RAM.
INFO	2026-06-08 09:54:36	MarkDuplicates	Read   402,000,000 records.  Elapsed time: 00:14:26s.  Time for last 1,000,000:    1s.  Last read position: chr14:49,585,959
INFO	2026-06-08 09:54:36	MarkDuplicates	Tracking 378539 as yet unmatched pairs. 18371 records in RAM.
INFO	2026-06-08 09:54:38	MarkDuplicates	Read   403,000,000 records.  Elapsed time: 00:14:28s.  Time for last 1,000,000:    2s.  Last read position: chr14:55,351,445
INFO	2026-06-08 09:54:38	MarkDuplicates	Tracking 376157 as yet unmatched pairs. 15931 records in RAM.
INFO	2026-06-08 09:54:40	MarkDuplicates	Read   404,000,000 records.  Elapsed time: 00:14:30s.  Time for last 1,000,000:    2s.  Last read position: chr14:64,426,052
INFO	2026-06-08 09:54:40	MarkDuplicates	Tracking 374550 as yet unmatched pairs. 14312 records in RAM.
INFO	2026-06-08 09:54:42	MarkDuplicates	Read   405,000,000 records.  Elapsed time: 00:14:32s.  Time for last 1,000,000:    1s.  Last read position: chr14:69,885,718
INFO	2026-06-08 09:54:42	MarkDuplicates	Tracking 373080 as yet unmatched pairs. 12827 records in RAM.
INFO	2026-06-08 09:54:44	MarkDuplicates	Read   406,000,000 records.  Elapsed time: 00:14:34s.  Time for last 1,000,000:    2s.  Last read position: chr14:74,764,346
INFO	2026-06-08 09:54:44	MarkDuplicates	Tracking 371825 as yet unmatched pairs. 11564 records in RAM.
INFO	2026-06-08 09:54:46	MarkDuplicates	Read   407,000,000 records.  Elapsed time: 00:14:36s.  Time for last 1,000,000:    1s.  Last read position: chr14:88,609,298
INFO	2026-06-08 09:54:46	MarkDuplicates	Tracking 370164 as yet unmatched pairs. 9893 records in RAM.
INFO	2026-06-08 09:54:48	MarkDuplicates	Read   408,000,000 records.  Elapsed time: 00:14:38s.  Time for last 1,000,000:    2s.  Last read position: chr14:94,614,521
INFO	2026-06-08 09:54:48	MarkDuplicates	Tracking 370997 as yet unmatched pairs. 10722 records in RAM.
INFO	2026-06-08 09:54:50	MarkDuplicates	Read   409,000,000 records.  Elapsed time: 00:14:40s.  Time for last 1,000,000:    2s.  Last read position: chr14:100,239,400
INFO	2026-06-08 09:54:50	MarkDuplicates	Tracking 366862 as yet unmatched pairs. 6580 records in RAM.
INFO	2026-06-08 09:54:52	MarkDuplicates	Read   410,000,000 records.  Elapsed time: 00:14:42s.  Time for last 1,000,000:    1s.  Last read position: chr14:102,208,763
INFO	2026-06-08 09:54:52	MarkDuplicates	Tracking 365409 as yet unmatched pairs. 5113 records in RAM.
INFO	2026-06-08 09:54:54	MarkDuplicates	Read   411,000,000 records.  Elapsed time: 00:14:44s.  Time for last 1,000,000:    2s.  Last read position: chr14:104,773,251
INFO	2026-06-08 09:54:54	MarkDuplicates	Tracking 364718 as yet unmatched pairs. 4416 records in RAM.
INFO	2026-06-08 09:54:56	MarkDuplicates	Read   412,000,000 records.  Elapsed time: 00:14:46s.  Time for last 1,000,000:    1s.  Last read position: chr14:104,949,688
INFO	2026-06-08 09:54:56	MarkDuplicates	Tracking 365738 as yet unmatched pairs. 5427 records in RAM.
INFO	2026-06-08 09:54:59	MarkDuplicates	Read   413,000,000 records.  Elapsed time: 00:14:49s.  Time for last 1,000,000:    2s.  Last read position: chr15:21,373,141
INFO	2026-06-08 09:54:59	MarkDuplicates	Tracking 360241 as yet unmatched pairs. 31891 records in RAM.
INFO	2026-06-08 09:55:01	MarkDuplicates	Read   414,000,000 records.  Elapsed time: 00:14:51s.  Time for last 1,000,000:    2s.  Last read position: chr15:28,640,298
INFO	2026-06-08 09:55:01	MarkDuplicates	Tracking 359126 as yet unmatched pairs. 30766 records in RAM.
INFO	2026-06-08 09:55:03	MarkDuplicates	Read   415,000,000 records.  Elapsed time: 00:14:53s.  Time for last 1,000,000:    1s.  Last read position: chr15:34,529,092
INFO	2026-06-08 09:55:03	MarkDuplicates	Tracking 358065 as yet unmatched pairs. 29697 records in RAM.
INFO	2026-06-08 09:55:05	MarkDuplicates	Read   416,000,000 records.  Elapsed time: 00:14:55s.  Time for last 1,000,000:    2s.  Last read position: chr15:40,411,619
INFO	2026-06-08 09:55:05	MarkDuplicates	Tracking 356631 as yet unmatched pairs. 28253 records in RAM.
INFO	2026-06-08 09:55:07	MarkDuplicates	Read   417,000,000 records.  Elapsed time: 00:14:57s.  Time for last 1,000,000:    1s.  Last read position: chr15:41,740,048
INFO	2026-06-08 09:55:07	MarkDuplicates	Tracking 355451 as yet unmatched pairs. 27061 records in RAM.
INFO	2026-06-08 09:55:09	MarkDuplicates	Read   418,000,000 records.  Elapsed time: 00:14:59s.  Time for last 1,000,000:    2s.  Last read position: chr15:43,407,445
INFO	2026-06-08 09:55:09	MarkDuplicates	Tracking 353692 as yet unmatched pairs. 25289 records in RAM.
INFO	2026-06-08 09:55:11	MarkDuplicates	Read   419,000,000 records.  Elapsed time: 00:15:01s.  Time for last 1,000,000:    1s.  Last read position: chr15:43,792,995
INFO	2026-06-08 09:55:11	MarkDuplicates	Tracking 363885 as yet unmatched pairs. 35476 records in RAM.
INFO	2026-06-08 09:55:13	MarkDuplicates	Read   420,000,000 records.  Elapsed time: 00:15:03s.  Time for last 1,000,000:    2s.  Last read position: chr15:48,153,811
INFO	2026-06-08 09:55:13	MarkDuplicates	Tracking 350766 as yet unmatched pairs. 22350 records in RAM.
INFO	2026-06-08 09:55:15	MarkDuplicates	Read   421,000,000 records.  Elapsed time: 00:15:05s.  Time for last 1,000,000:    2s.  Last read position: chr15:52,205,875
INFO	2026-06-08 09:55:15	MarkDuplicates	Tracking 349496 as yet unmatched pairs. 21079 records in RAM.
INFO	2026-06-08 09:55:17	MarkDuplicates	Read   422,000,000 records.  Elapsed time: 00:15:07s.  Time for last 1,000,000:    1s.  Last read position: chr15:58,610,234
INFO	2026-06-08 09:55:17	MarkDuplicates	Tracking 348055 as yet unmatched pairs. 19637 records in RAM.
INFO	2026-06-08 09:55:19	MarkDuplicates	Read   423,000,000 records.  Elapsed time: 00:15:09s.  Time for last 1,000,000:    2s.  Last read position: chr15:63,326,177
INFO	2026-06-08 09:55:19	MarkDuplicates	Tracking 346848 as yet unmatched pairs. 18418 records in RAM.
INFO	2026-06-08 09:55:21	MarkDuplicates	Read   424,000,000 records.  Elapsed time: 00:15:11s.  Time for last 1,000,000:    1s.  Last read position: chr15:65,088,775
INFO	2026-06-08 09:55:21	MarkDuplicates	Tracking 344535 as yet unmatched pairs. 16092 records in RAM.
INFO	2026-06-08 09:55:23	MarkDuplicates	Read   425,000,000 records.  Elapsed time: 00:15:13s.  Time for last 1,000,000:    2s.  Last read position: chr15:69,255,992
INFO	2026-06-08 09:55:23	MarkDuplicates	Tracking 343185 as yet unmatched pairs. 14729 records in RAM.
INFO	2026-06-08 09:55:26	MarkDuplicates	Read   426,000,000 records.  Elapsed time: 00:15:15s.  Time for last 1,000,000:    2s.  Last read position: chr15:72,210,347
INFO	2026-06-08 09:55:26	MarkDuplicates	Tracking 342863 as yet unmatched pairs. 14400 records in RAM.
INFO	2026-06-08 09:55:28	MarkDuplicates	Read   427,000,000 records.  Elapsed time: 00:15:17s.  Time for last 1,000,000:    1s.  Last read position: chr15:74,032,684
INFO	2026-06-08 09:55:28	MarkDuplicates	Tracking 340588 as yet unmatched pairs. 12119 records in RAM.
INFO	2026-06-08 09:55:30	MarkDuplicates	Read   428,000,000 records.  Elapsed time: 00:15:20s.  Time for last 1,000,000:    2s.  Last read position: chr15:75,355,847
INFO	2026-06-08 09:55:30	MarkDuplicates	Tracking 338285 as yet unmatched pairs. 9810 records in RAM.
INFO	2026-06-08 09:55:32	MarkDuplicates	Read   429,000,000 records.  Elapsed time: 00:15:21s.  Time for last 1,000,000:    1s.  Last read position: chr15:78,490,681
INFO	2026-06-08 09:55:32	MarkDuplicates	Tracking 336350 as yet unmatched pairs. 7866 records in RAM.
INFO	2026-06-08 09:55:34	MarkDuplicates	Read   430,000,000 records.  Elapsed time: 00:15:24s.  Time for last 1,000,000:    2s.  Last read position: chr15:82,539,982
INFO	2026-06-08 09:55:34	MarkDuplicates	Tracking 335065 as yet unmatched pairs. 6576 records in RAM.
INFO	2026-06-08 09:55:36	MarkDuplicates	Read   431,000,000 records.  Elapsed time: 00:15:26s.  Time for last 1,000,000:    2s.  Last read position: chr15:88,475,153
INFO	2026-06-08 09:55:36	MarkDuplicates	Tracking 333473 as yet unmatched pairs. 4973 records in RAM.
INFO	2026-06-08 09:55:38	MarkDuplicates	Read   432,000,000 records.  Elapsed time: 00:15:28s.  Time for last 1,000,000:    1s.  Last read position: chr15:90,232,219
INFO	2026-06-08 09:55:38	MarkDuplicates	Tracking 333427 as yet unmatched pairs. 4913 records in RAM.
INFO	2026-06-08 09:55:40	MarkDuplicates	Read   433,000,000 records.  Elapsed time: 00:15:30s.  Time for last 1,000,000:    2s.  Last read position: chr15:92,956,489
INFO	2026-06-08 09:55:40	MarkDuplicates	Tracking 330418 as yet unmatched pairs. 1889 records in RAM.
INFO	2026-06-08 09:55:43	MarkDuplicates	Read   434,000,000 records.  Elapsed time: 00:15:32s.  Time for last 1,000,000:    2s.  Last read position: chr16:60,243
INFO	2026-06-08 09:55:43	MarkDuplicates	Tracking 329307 as yet unmatched pairs. 57988 records in RAM.
INFO	2026-06-08 09:55:44	MarkDuplicates	Read   435,000,000 records.  Elapsed time: 00:15:34s.  Time for last 1,000,000:    1s.  Last read position: chr16:590,374
INFO	2026-06-08 09:55:44	MarkDuplicates	Tracking 326953 as yet unmatched pairs. 55617 records in RAM.
INFO	2026-06-08 09:55:47	MarkDuplicates	Read   436,000,000 records.  Elapsed time: 00:15:37s.  Time for last 1,000,000:    2s.  Last read position: chr16:787,098
INFO	2026-06-08 09:55:47	MarkDuplicates	Tracking 324182 as yet unmatched pairs. 52836 records in RAM.
INFO	2026-06-08 09:55:49	MarkDuplicates	Read   437,000,000 records.  Elapsed time: 00:15:39s.  Time for last 1,000,000:    2s.  Last read position: chr16:1,632,319
INFO	2026-06-08 09:55:49	MarkDuplicates	Tracking 322208 as yet unmatched pairs. 50855 records in RAM.
INFO	2026-06-08 09:55:51	MarkDuplicates	Read   438,000,000 records.  Elapsed time: 00:15:41s.  Time for last 1,000,000:    1s.  Last read position: chr16:2,036,734
INFO	2026-06-08 09:55:51	MarkDuplicates	Tracking 321195 as yet unmatched pairs. 49832 records in RAM.
INFO	2026-06-08 09:55:53	MarkDuplicates	Read   439,000,000 records.  Elapsed time: 00:15:43s.  Time for last 1,000,000:    2s.  Last read position: chr16:2,176,560
INFO	2026-06-08 09:55:53	MarkDuplicates	Tracking 318828 as yet unmatched pairs. 47452 records in RAM.
INFO	2026-06-08 09:55:55	MarkDuplicates	Read   440,000,000 records.  Elapsed time: 00:15:45s.  Time for last 1,000,000:    1s.  Last read position: chr16:2,761,570
INFO	2026-06-08 09:55:55	MarkDuplicates	Tracking 318563 as yet unmatched pairs. 47187 records in RAM.
INFO	2026-06-08 09:55:57	MarkDuplicates	Read   441,000,000 records.  Elapsed time: 00:15:47s.  Time for last 1,000,000:    2s.  Last read position: chr16:2,767,791
INFO	2026-06-08 09:55:57	MarkDuplicates	Tracking 316260 as yet unmatched pairs. 44881 records in RAM.
INFO	2026-06-08 09:55:59	MarkDuplicates	Read   442,000,000 records.  Elapsed time: 00:15:49s.  Time for last 1,000,000:    2s.  Last read position: chr16:3,390,006
INFO	2026-06-08 09:55:59	MarkDuplicates	Tracking 313178 as yet unmatched pairs. 41790 records in RAM.
INFO	2026-06-08 09:56:01	MarkDuplicates	Read   443,000,000 records.  Elapsed time: 00:15:51s.  Time for last 1,000,000:    1s.  Last read position: chr16:4,466,216
INFO	2026-06-08 09:56:01	MarkDuplicates	Tracking 311607 as yet unmatched pairs. 40213 records in RAM.
INFO	2026-06-08 09:56:03	MarkDuplicates	Read   444,000,000 records.  Elapsed time: 00:15:53s.  Time for last 1,000,000:    2s.  Last read position: chr16:9,091,968
INFO	2026-06-08 09:56:03	MarkDuplicates	Tracking 310618 as yet unmatched pairs. 39224 records in RAM.
INFO	2026-06-08 09:56:05	MarkDuplicates	Read   445,000,000 records.  Elapsed time: 00:15:55s.  Time for last 1,000,000:    2s.  Last read position: chr16:14,247,132
INFO	2026-06-08 09:56:05	MarkDuplicates	Tracking 309545 as yet unmatched pairs. 38113 records in RAM.
INFO	2026-06-08 09:56:07	MarkDuplicates	Read   446,000,000 records.  Elapsed time: 00:15:57s.  Time for last 1,000,000:    1s.  Last read position: chr16:14,941,818
INFO	2026-06-08 09:56:07	MarkDuplicates	Tracking 307765 as yet unmatched pairs. 36333 records in RAM.
INFO	2026-06-08 09:56:09	MarkDuplicates	Read   447,000,000 records.  Elapsed time: 00:15:59s.  Time for last 1,000,000:    2s.  Last read position: chr16:16,182,366
INFO	2026-06-08 09:56:09	MarkDuplicates	Tracking 306072 as yet unmatched pairs. 34634 records in RAM.
INFO	2026-06-08 09:56:11	MarkDuplicates	Read   448,000,000 records.  Elapsed time: 00:16:01s.  Time for last 1,000,000:    1s.  Last read position: chr16:16,358,058
INFO	2026-06-08 09:56:11	MarkDuplicates	Tracking 306385 as yet unmatched pairs. 34943 records in RAM.
INFO	2026-06-08 09:56:12	MarkDuplicates	Read   449,000,000 records.  Elapsed time: 00:16:02s.  Time for last 1,000,000:    1s.  Last read position: chr16:18,379,963
INFO	2026-06-08 09:56:12	MarkDuplicates	Tracking 306359 as yet unmatched pairs. 34912 records in RAM.
INFO	2026-06-08 09:56:14	MarkDuplicates	Read   450,000,000 records.  Elapsed time: 00:16:04s.  Time for last 1,000,000:    1s.  Last read position: chr16:18,871,369
INFO	2026-06-08 09:56:14	MarkDuplicates	Tracking 304106 as yet unmatched pairs. 32659 records in RAM.
INFO	2026-06-08 09:56:16	MarkDuplicates	Read   451,000,000 records.  Elapsed time: 00:16:06s.  Time for last 1,000,000:    1s.  Last read position: chr16:21,403,832
INFO	2026-06-08 09:56:16	MarkDuplicates	Tracking 302870 as yet unmatched pairs. 31419 records in RAM.
INFO	2026-06-08 09:56:18	MarkDuplicates	Read   452,000,000 records.  Elapsed time: 00:16:08s.  Time for last 1,000,000:    1s.  Last read position: chr16:21,834,789
INFO	2026-06-08 09:56:18	MarkDuplicates	Tracking 301896 as yet unmatched pairs. 30439 records in RAM.
INFO	2026-06-08 09:56:20	MarkDuplicates	Read   453,000,000 records.  Elapsed time: 00:16:09s.  Time for last 1,000,000:    1s.  Last read position: chr16:21,980,553
INFO	2026-06-08 09:56:20	MarkDuplicates	Tracking 302313 as yet unmatched pairs. 30854 records in RAM.
INFO	2026-06-08 09:56:21	MarkDuplicates	Read   454,000,000 records.  Elapsed time: 00:16:11s.  Time for last 1,000,000:    1s.  Last read position: chr16:22,534,284
INFO	2026-06-08 09:56:21	MarkDuplicates	Tracking 301302 as yet unmatched pairs. 29843 records in RAM.
INFO	2026-06-08 09:56:23	MarkDuplicates	Read   455,000,000 records.  Elapsed time: 00:16:13s.  Time for last 1,000,000:    1s.  Last read position: chr16:24,823,578
INFO	2026-06-08 09:56:23	MarkDuplicates	Tracking 300267 as yet unmatched pairs. 28798 records in RAM.
INFO	2026-06-08 09:56:25	MarkDuplicates	Read   456,000,000 records.  Elapsed time: 00:16:15s.  Time for last 1,000,000:    1s.  Last read position: chr16:28,537,627
INFO	2026-06-08 09:56:25	MarkDuplicates	Tracking 299508 as yet unmatched pairs. 28021 records in RAM.
INFO	2026-06-08 09:56:27	MarkDuplicates	Read   457,000,000 records.  Elapsed time: 00:16:17s.  Time for last 1,000,000:    2s.  Last read position: chr16:28,983,877
INFO	2026-06-08 09:56:27	MarkDuplicates	Tracking 297448 as yet unmatched pairs. 25949 records in RAM.
INFO	2026-06-08 09:56:29	MarkDuplicates	Read   458,000,000 records.  Elapsed time: 00:16:19s.  Time for last 1,000,000:    1s.  Last read position: chr16:29,491,647
INFO	2026-06-08 09:56:29	MarkDuplicates	Tracking 298137 as yet unmatched pairs. 26637 records in RAM.
INFO	2026-06-08 09:56:31	MarkDuplicates	Read   459,000,000 records.  Elapsed time: 00:16:20s.  Time for last 1,000,000:    1s.  Last read position: chr16:29,987,694
INFO	2026-06-08 09:56:31	MarkDuplicates	Tracking 295729 as yet unmatched pairs. 24222 records in RAM.
INFO	2026-06-08 09:56:33	MarkDuplicates	Read   460,000,000 records.  Elapsed time: 00:16:23s.  Time for last 1,000,000:    2s.  Last read position: chr16:30,225,395
INFO	2026-06-08 09:56:33	MarkDuplicates	Tracking 293727 as yet unmatched pairs. 22220 records in RAM.
INFO	2026-06-08 09:56:34	MarkDuplicates	Read   461,000,000 records.  Elapsed time: 00:16:24s.  Time for last 1,000,000:    1s.  Last read position: chr16:30,665,673
INFO	2026-06-08 09:56:34	MarkDuplicates	Tracking 293156 as yet unmatched pairs. 21641 records in RAM.
INFO	2026-06-08 09:56:37	MarkDuplicates	Read   462,000,000 records.  Elapsed time: 00:16:26s.  Time for last 1,000,000:    2s.  Last read position: chr16:31,076,684
INFO	2026-06-08 09:56:37	MarkDuplicates	Tracking 291188 as yet unmatched pairs. 19666 records in RAM.
INFO	2026-06-08 09:56:39	MarkDuplicates	Read   463,000,000 records.  Elapsed time: 00:16:28s.  Time for last 1,000,000:    1s.  Last read position: chr16:31,189,784
INFO	2026-06-08 09:56:39	MarkDuplicates	Tracking 290165 as yet unmatched pairs. 18643 records in RAM.
INFO	2026-06-08 09:56:41	MarkDuplicates	Read   464,000,000 records.  Elapsed time: 00:16:31s.  Time for last 1,000,000:    2s.  Last read position: chr16:47,699,256
INFO	2026-06-08 09:56:41	MarkDuplicates	Tracking 288040 as yet unmatched pairs. 16517 records in RAM.
INFO	2026-06-08 09:56:43	MarkDuplicates	Read   465,000,000 records.  Elapsed time: 00:16:33s.  Time for last 1,000,000:    2s.  Last read position: chr16:53,314,376
INFO	2026-06-08 09:56:43	MarkDuplicates	Tracking 286527 as yet unmatched pairs. 14999 records in RAM.
INFO	2026-06-08 09:56:45	MarkDuplicates	Read   466,000,000 records.  Elapsed time: 00:16:35s.  Time for last 1,000,000:    1s.  Last read position: chr16:57,660,832
INFO	2026-06-08 09:56:45	MarkDuplicates	Tracking 285259 as yet unmatched pairs. 13722 records in RAM.
INFO	2026-06-08 09:56:47	MarkDuplicates	Read   467,000,000 records.  Elapsed time: 00:16:37s.  Time for last 1,000,000:    2s.  Last read position: chr16:67,233,735
INFO	2026-06-08 09:56:47	MarkDuplicates	Tracking 282847 as yet unmatched pairs. 11306 records in RAM.
INFO	2026-06-08 09:56:49	MarkDuplicates	Read   468,000,000 records.  Elapsed time: 00:16:39s.  Time for last 1,000,000:    1s.  Last read position: chr16:69,119,732
INFO	2026-06-08 09:56:49	MarkDuplicates	Tracking 281169 as yet unmatched pairs. 9626 records in RAM.
INFO	2026-06-08 09:56:51	MarkDuplicates	Read   469,000,000 records.  Elapsed time: 00:16:41s.  Time for last 1,000,000:    2s.  Last read position: chr16:71,626,312
INFO	2026-06-08 09:56:51	MarkDuplicates	Tracking 279630 as yet unmatched pairs. 8078 records in RAM.
INFO	2026-06-08 09:56:53	MarkDuplicates	Read   470,000,000 records.  Elapsed time: 00:16:43s.  Time for last 1,000,000:    1s.  Last read position: chr16:78,022,571
INFO	2026-06-08 09:56:53	MarkDuplicates	Tracking 280715 as yet unmatched pairs. 9153 records in RAM.
INFO	2026-06-08 09:56:55	MarkDuplicates	Read   471,000,000 records.  Elapsed time: 00:16:45s.  Time for last 1,000,000:    2s.  Last read position: chr16:84,880,557
INFO	2026-06-08 09:56:55	MarkDuplicates	Tracking 276312 as yet unmatched pairs. 4742 records in RAM.
INFO	2026-06-08 09:56:57	MarkDuplicates	Read   472,000,000 records.  Elapsed time: 00:16:47s.  Time for last 1,000,000:    2s.  Last read position: chr16:88,656,166
INFO	2026-06-08 09:56:57	MarkDuplicates	Tracking 274307 as yet unmatched pairs. 2733 records in RAM.
INFO	2026-06-08 09:56:59	MarkDuplicates	Read   473,000,000 records.  Elapsed time: 00:16:49s.  Time for last 1,000,000:    1s.  Last read position: chr16:89,656,694
INFO	2026-06-08 09:56:59	MarkDuplicates	Tracking 272425 as yet unmatched pairs. 837 records in RAM.
INFO	2026-06-08 09:57:02	MarkDuplicates	Read   474,000,000 records.  Elapsed time: 00:16:52s.  Time for last 1,000,000:    3s.  Last read position: chr17:1,364,998
INFO	2026-06-08 09:57:02	MarkDuplicates	Tracking 275558 as yet unmatched pairs. 92419 records in RAM.
INFO	2026-06-08 09:57:04	MarkDuplicates	Read   475,000,000 records.  Elapsed time: 00:16:54s.  Time for last 1,000,000:    1s.  Last read position: chr17:2,373,405
INFO	2026-06-08 09:57:04	MarkDuplicates	Tracking 269716 as yet unmatched pairs. 86570 records in RAM.
INFO	2026-06-08 09:57:07	MarkDuplicates	Read   476,000,000 records.  Elapsed time: 00:16:57s.  Time for last 1,000,000:    2s.  Last read position: chr17:4,895,163
INFO	2026-06-08 09:57:07	MarkDuplicates	Tracking 267776 as yet unmatched pairs. 84625 records in RAM.
INFO	2026-06-08 09:57:09	MarkDuplicates	Read   477,000,000 records.  Elapsed time: 00:16:59s.  Time for last 1,000,000:    2s.  Last read position: chr17:7,223,673
INFO	2026-06-08 09:57:09	MarkDuplicates	Tracking 266890 as yet unmatched pairs. 83738 records in RAM.
INFO	2026-06-08 09:57:11	MarkDuplicates	Read   478,000,000 records.  Elapsed time: 00:17:01s.  Time for last 1,000,000:    1s.  Last read position: chr17:7,513,610
INFO	2026-06-08 09:57:11	MarkDuplicates	Tracking 264948 as yet unmatched pairs. 81794 records in RAM.
INFO	2026-06-08 09:57:13	MarkDuplicates	Read   479,000,000 records.  Elapsed time: 00:17:03s.  Time for last 1,000,000:    2s.  Last read position: chr17:8,236,002
INFO	2026-06-08 09:57:13	MarkDuplicates	Tracking 263104 as yet unmatched pairs. 79948 records in RAM.
INFO	2026-06-08 09:57:15	MarkDuplicates	Read   480,000,000 records.  Elapsed time: 00:17:05s.  Time for last 1,000,000:    1s.  Last read position: chr17:16,382,284
INFO	2026-06-08 09:57:15	MarkDuplicates	Tracking 262706 as yet unmatched pairs. 79545 records in RAM.
INFO	2026-06-08 09:57:17	MarkDuplicates	Read   481,000,000 records.  Elapsed time: 00:17:07s.  Time for last 1,000,000:    2s.  Last read position: chr17:18,093,926
INFO	2026-06-08 09:57:17	MarkDuplicates	Tracking 259453 as yet unmatched pairs. 76291 records in RAM.
INFO	2026-06-08 09:57:19	MarkDuplicates	Read   482,000,000 records.  Elapsed time: 00:17:09s.  Time for last 1,000,000:    2s.  Last read position: chr17:27,301,857
INFO	2026-06-08 09:57:19	MarkDuplicates	Tracking 259366 as yet unmatched pairs. 76199 records in RAM.
INFO	2026-06-08 09:57:21	MarkDuplicates	Read   483,000,000 records.  Elapsed time: 00:17:11s.  Time for last 1,000,000:    1s.  Last read position: chr17:28,632,978
INFO	2026-06-08 09:57:21	MarkDuplicates	Tracking 258998 as yet unmatched pairs. 75828 records in RAM.
INFO	2026-06-08 09:57:24	MarkDuplicates	Read   484,000,000 records.  Elapsed time: 00:17:13s.  Time for last 1,000,000:    2s.  Last read position: chr17:28,758,584
INFO	2026-06-08 09:57:24	MarkDuplicates	Tracking 255055 as yet unmatched pairs. 71879 records in RAM.
INFO	2026-06-08 09:57:25	MarkDuplicates	Read   485,000,000 records.  Elapsed time: 00:17:15s.  Time for last 1,000,000:    1s.  Last read position: chr17:30,195,642
INFO	2026-06-08 09:57:25	MarkDuplicates	Tracking 253032 as yet unmatched pairs. 69855 records in RAM.
INFO	2026-06-08 09:57:28	MarkDuplicates	Read   486,000,000 records.  Elapsed time: 00:17:18s.  Time for last 1,000,000:    2s.  Last read position: chr17:31,973,178
INFO	2026-06-08 09:57:28	MarkDuplicates	Tracking 254689 as yet unmatched pairs. 71504 records in RAM.
INFO	2026-06-08 09:57:30	MarkDuplicates	Read   487,000,000 records.  Elapsed time: 00:17:20s.  Time for last 1,000,000:    2s.  Last read position: chr17:35,265,079
INFO	2026-06-08 09:57:30	MarkDuplicates	Tracking 250261 as yet unmatched pairs. 67064 records in RAM.
INFO	2026-06-08 09:57:32	MarkDuplicates	Read   488,000,000 records.  Elapsed time: 00:17:22s.  Time for last 1,000,000:    1s.  Last read position: chr17:37,205,810
INFO	2026-06-08 09:57:32	MarkDuplicates	Tracking 249285 as yet unmatched pairs. 66086 records in RAM.
INFO	2026-06-08 09:57:34	MarkDuplicates	Read   489,000,000 records.  Elapsed time: 00:17:24s.  Time for last 1,000,000:    1s.  Last read position: chr17:38,716,748
INFO	2026-06-08 09:57:34	MarkDuplicates	Tracking 249012 as yet unmatched pairs. 65806 records in RAM.
INFO	2026-06-08 09:57:36	MarkDuplicates	Read   490,000,000 records.  Elapsed time: 00:17:26s.  Time for last 1,000,000:    1s.  Last read position: chr17:39,707,094
INFO	2026-06-08 09:57:36	MarkDuplicates	Tracking 252057 as yet unmatched pairs. 68850 records in RAM.
INFO	2026-06-08 09:57:38	MarkDuplicates	Read   491,000,000 records.  Elapsed time: 00:17:28s.  Time for last 1,000,000:    2s.  Last read position: chr17:39,726,947
INFO	2026-06-08 09:57:38	MarkDuplicates	Tracking 249258 as yet unmatched pairs. 66051 records in RAM.
INFO	2026-06-08 09:57:40	MarkDuplicates	Read   492,000,000 records.  Elapsed time: 00:17:30s.  Time for last 1,000,000:    1s.  Last read position: chr17:40,399,998
INFO	2026-06-08 09:57:40	MarkDuplicates	Tracking 243098 as yet unmatched pairs. 59889 records in RAM.
INFO	2026-06-08 09:57:42	MarkDuplicates	Read   493,000,000 records.  Elapsed time: 00:17:32s.  Time for last 1,000,000:    2s.  Last read position: chr17:41,983,571
INFO	2026-06-08 09:57:42	MarkDuplicates	Tracking 241380 as yet unmatched pairs. 58169 records in RAM.
INFO	2026-06-08 09:57:44	MarkDuplicates	Read   494,000,000 records.  Elapsed time: 00:17:34s.  Time for last 1,000,000:    2s.  Last read position: chr17:43,180,802
INFO	2026-06-08 09:57:44	MarkDuplicates	Tracking 239797 as yet unmatched pairs. 56584 records in RAM.
INFO	2026-06-08 09:57:46	MarkDuplicates	Read   495,000,000 records.  Elapsed time: 00:17:36s.  Time for last 1,000,000:    1s.  Last read position: chr17:45,232,369
INFO	2026-06-08 09:57:46	MarkDuplicates	Tracking 238144 as yet unmatched pairs. 54928 records in RAM.
INFO	2026-06-08 09:57:48	MarkDuplicates	Read   496,000,000 records.  Elapsed time: 00:17:38s.  Time for last 1,000,000:    2s.  Last read position: chr17:47,668,249
INFO	2026-06-08 09:57:48	MarkDuplicates	Tracking 237728 as yet unmatched pairs. 54508 records in RAM.
INFO	2026-06-08 10:00:03	MarkDuplicates	Read   497,000,000 records.  Elapsed time: 00:19:53s.  Time for last 1,000,000:  134s.  Last read position: chr17:48,921,223
INFO	2026-06-08 10:00:03	MarkDuplicates	Tracking 235137 as yet unmatched pairs. 51912 records in RAM.
INFO	2026-06-08 10:00:05	MarkDuplicates	Read   498,000,000 records.  Elapsed time: 00:19:55s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,186,676
INFO	2026-06-08 10:00:05	MarkDuplicates	Tracking 238068 as yet unmatched pairs. 54838 records in RAM.
INFO	2026-06-08 10:00:08	MarkDuplicates	Read   499,000,000 records.  Elapsed time: 00:19:57s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,188,121
INFO	2026-06-08 10:00:08	MarkDuplicates	Tracking 258567 as yet unmatched pairs. 75335 records in RAM.
INFO	2026-06-08 10:00:10	MarkDuplicates	Read   500,000,000 records.  Elapsed time: 00:20:00s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,189,480
INFO	2026-06-08 10:00:10	MarkDuplicates	Tracking 254257 as yet unmatched pairs. 71025 records in RAM.
INFO	2026-06-08 10:00:12	MarkDuplicates	Read   501,000,000 records.  Elapsed time: 00:20:02s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,190,584
INFO	2026-06-08 10:00:12	MarkDuplicates	Tracking 237631 as yet unmatched pairs. 54390 records in RAM.
INFO	2026-06-08 10:00:15	MarkDuplicates	Read   502,000,000 records.  Elapsed time: 00:20:05s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,192,675
INFO	2026-06-08 10:00:15	MarkDuplicates	Tracking 258533 as yet unmatched pairs. 75290 records in RAM.
INFO	2026-06-08 10:00:17	MarkDuplicates	Read   503,000,000 records.  Elapsed time: 00:20:07s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,194,406
INFO	2026-06-08 10:00:17	MarkDuplicates	Tracking 252697 as yet unmatched pairs. 69454 records in RAM.
INFO	2026-06-08 10:00:19	MarkDuplicates	Read   504,000,000 records.  Elapsed time: 00:20:09s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,195,590
INFO	2026-06-08 10:00:19	MarkDuplicates	Tracking 249288 as yet unmatched pairs. 66034 records in RAM.
INFO	2026-06-08 10:00:22	MarkDuplicates	Read   505,000,000 records.  Elapsed time: 00:20:12s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,196,644
INFO	2026-06-08 10:00:22	MarkDuplicates	Tracking 251604 as yet unmatched pairs. 68350 records in RAM.
INFO	2026-06-08 10:00:24	MarkDuplicates	Read   506,000,000 records.  Elapsed time: 00:20:14s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,199,261
INFO	2026-06-08 10:00:24	MarkDuplicates	Tracking 238391 as yet unmatched pairs. 55131 records in RAM.
INFO	2026-06-08 10:00:27	MarkDuplicates	Read   507,000,000 records.  Elapsed time: 00:20:16s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,669,256
INFO	2026-06-08 10:00:27	MarkDuplicates	Tracking 218322 as yet unmatched pairs. 35059 records in RAM.
INFO	2026-06-08 10:00:29	MarkDuplicates	Read   508,000,000 records.  Elapsed time: 00:20:19s.  Time for last 1,000,000:    2s.  Last read position: chr17:57,873,652
INFO	2026-06-08 10:00:29	MarkDuplicates	Tracking 217877 as yet unmatched pairs. 34613 records in RAM.
INFO	2026-06-08 10:00:31	MarkDuplicates	Read   509,000,000 records.  Elapsed time: 00:20:21s.  Time for last 1,000,000:    2s.  Last read position: chr17:59,660,424
INFO	2026-06-08 10:00:31	MarkDuplicates	Tracking 220003 as yet unmatched pairs. 36729 records in RAM.
INFO	2026-06-08 10:00:33	MarkDuplicates	Read   510,000,000 records.  Elapsed time: 00:20:23s.  Time for last 1,000,000:    2s.  Last read position: chr17:59,683,115
INFO	2026-06-08 10:00:33	MarkDuplicates	Tracking 217075 as yet unmatched pairs. 33800 records in RAM.
INFO	2026-06-08 10:00:35	MarkDuplicates	Read   511,000,000 records.  Elapsed time: 00:20:25s.  Time for last 1,000,000:    2s.  Last read position: chr17:62,536,269
INFO	2026-06-08 10:00:35	MarkDuplicates	Tracking 212582 as yet unmatched pairs. 29303 records in RAM.
INFO	2026-06-08 10:00:38	MarkDuplicates	Read   512,000,000 records.  Elapsed time: 00:20:28s.  Time for last 1,000,000:    2s.  Last read position: chr17:64,193,688
INFO	2026-06-08 10:00:38	MarkDuplicates	Tracking 210707 as yet unmatched pairs. 27428 records in RAM.
INFO	2026-06-08 10:00:40	MarkDuplicates	Read   513,000,000 records.  Elapsed time: 00:20:30s.  Time for last 1,000,000:    2s.  Last read position: chr17:67,854,294
INFO	2026-06-08 10:00:40	MarkDuplicates	Tracking 209747 as yet unmatched pairs. 26464 records in RAM.
INFO	2026-06-08 10:00:42	MarkDuplicates	Read   514,000,000 records.  Elapsed time: 00:20:32s.  Time for last 1,000,000:    2s.  Last read position: chr17:72,649,254
INFO	2026-06-08 10:00:42	MarkDuplicates	Tracking 208049 as yet unmatched pairs. 24765 records in RAM.
INFO	2026-06-08 10:00:44	MarkDuplicates	Read   515,000,000 records.  Elapsed time: 00:20:34s.  Time for last 1,000,000:    2s.  Last read position: chr17:75,110,239
INFO	2026-06-08 10:00:44	MarkDuplicates	Tracking 206072 as yet unmatched pairs. 22788 records in RAM.
INFO	2026-06-08 10:00:47	MarkDuplicates	Read   516,000,000 records.  Elapsed time: 00:20:36s.  Time for last 1,000,000:    2s.  Last read position: chr17:75,629,271
INFO	2026-06-08 10:00:47	MarkDuplicates	Tracking 204833 as yet unmatched pairs. 21546 records in RAM.
INFO	2026-06-08 10:00:49	MarkDuplicates	Read   517,000,000 records.  Elapsed time: 00:20:39s.  Time for last 1,000,000:    2s.  Last read position: chr17:76,089,294
INFO	2026-06-08 10:00:49	MarkDuplicates	Tracking 202888 as yet unmatched pairs. 19599 records in RAM.
INFO	2026-06-08 10:00:51	MarkDuplicates	Read   518,000,000 records.  Elapsed time: 00:20:41s.  Time for last 1,000,000:    2s.  Last read position: chr17:78,120,943
INFO	2026-06-08 10:00:51	MarkDuplicates	Tracking 201829 as yet unmatched pairs. 18538 records in RAM.
INFO	2026-06-08 10:00:53	MarkDuplicates	Read   519,000,000 records.  Elapsed time: 00:20:43s.  Time for last 1,000,000:    2s.  Last read position: chr17:78,976,109
INFO	2026-06-08 10:00:53	MarkDuplicates	Tracking 202585 as yet unmatched pairs. 19290 records in RAM.
INFO	2026-06-08 10:00:56	MarkDuplicates	Read   520,000,000 records.  Elapsed time: 00:20:45s.  Time for last 1,000,000:    2s.  Last read position: chr17:80,287,947
INFO	2026-06-08 10:00:56	MarkDuplicates	Tracking 200656 as yet unmatched pairs. 17359 records in RAM.
INFO	2026-06-08 10:00:58	MarkDuplicates	Read   521,000,000 records.  Elapsed time: 00:20:48s.  Time for last 1,000,000:    2s.  Last read position: chr17:80,368,057
INFO	2026-06-08 10:00:58	MarkDuplicates	Tracking 196744 as yet unmatched pairs. 13441 records in RAM.
INFO	2026-06-08 10:01:00	MarkDuplicates	Read   522,000,000 records.  Elapsed time: 00:20:50s.  Time for last 1,000,000:    2s.  Last read position: chr17:81,511,451
INFO	2026-06-08 10:01:00	MarkDuplicates	Tracking 196046 as yet unmatched pairs. 12742 records in RAM.
INFO	2026-06-08 10:01:02	MarkDuplicates	Read   523,000,000 records.  Elapsed time: 00:20:52s.  Time for last 1,000,000:    2s.  Last read position: chr17:81,845,975
INFO	2026-06-08 10:01:02	MarkDuplicates	Tracking 194405 as yet unmatched pairs. 11083 records in RAM.
INFO	2026-06-08 10:01:04	MarkDuplicates	Read   524,000,000 records.  Elapsed time: 00:20:54s.  Time for last 1,000,000:    2s.  Last read position: chr17:82,030,700
INFO	2026-06-08 10:01:04	MarkDuplicates	Tracking 190452 as yet unmatched pairs. 7126 records in RAM.
INFO	2026-06-08 10:01:07	MarkDuplicates	Read   525,000,000 records.  Elapsed time: 00:20:57s.  Time for last 1,000,000:    2s.  Last read position: chr17:82,083,983
INFO	2026-06-08 10:01:07	MarkDuplicates	Tracking 195939 as yet unmatched pairs. 12606 records in RAM.
INFO	2026-06-08 10:01:09	MarkDuplicates	Read   526,000,000 records.  Elapsed time: 00:20:59s.  Time for last 1,000,000:    2s.  Last read position: chr17:82,089,248
INFO	2026-06-08 10:01:09	MarkDuplicates	Tracking 190704 as yet unmatched pairs. 7369 records in RAM.
INFO	2026-06-08 10:01:11	MarkDuplicates	Read   527,000,000 records.  Elapsed time: 00:21:01s.  Time for last 1,000,000:    2s.  Last read position: chr17:82,444,063
INFO	2026-06-08 10:01:11	MarkDuplicates	Tracking 185979 as yet unmatched pairs. 2636 records in RAM.
INFO	2026-06-08 10:01:14	MarkDuplicates	Read   528,000,000 records.  Elapsed time: 00:21:03s.  Time for last 1,000,000:    2s.  Last read position: chr18:6,729,828
INFO	2026-06-08 10:01:14	MarkDuplicates	Tracking 182610 as yet unmatched pairs. 8312 records in RAM.
INFO	2026-06-08 10:01:16	MarkDuplicates	Read   529,000,000 records.  Elapsed time: 00:21:06s.  Time for last 1,000,000:    2s.  Last read position: chr18:14,537,873
INFO	2026-06-08 10:01:16	MarkDuplicates	Tracking 183822 as yet unmatched pairs. 9518 records in RAM.
INFO	2026-06-08 10:01:18	MarkDuplicates	Read   530,000,000 records.  Elapsed time: 00:21:08s.  Time for last 1,000,000:    2s.  Last read position: chr18:26,052,684
INFO	2026-06-08 10:01:18	MarkDuplicates	Tracking 180613 as yet unmatched pairs. 6295 records in RAM.
INFO	2026-06-08 10:01:20	MarkDuplicates	Read   531,000,000 records.  Elapsed time: 00:21:10s.  Time for last 1,000,000:    2s.  Last read position: chr18:36,126,877
INFO	2026-06-08 10:01:20	MarkDuplicates	Tracking 180731 as yet unmatched pairs. 6405 records in RAM.
INFO	2026-06-08 10:01:22	MarkDuplicates	Read   532,000,000 records.  Elapsed time: 00:21:12s.  Time for last 1,000,000:    2s.  Last read position: chr18:54,291,962
INFO	2026-06-08 10:01:22	MarkDuplicates	Tracking 176922 as yet unmatched pairs. 2592 records in RAM.
INFO	2026-06-08 10:01:25	MarkDuplicates	Read   533,000,000 records.  Elapsed time: 00:21:14s.  Time for last 1,000,000:    2s.  Last read position: chr18:74,505,916
INFO	2026-06-08 10:01:25	MarkDuplicates	Tracking 175346 as yet unmatched pairs. 1016 records in RAM.
INFO	2026-06-08 10:01:27	MarkDuplicates	Read   534,000,000 records.  Elapsed time: 00:21:17s.  Time for last 1,000,000:    2s.  Last read position: chr19:757,340
INFO	2026-06-08 10:01:27	MarkDuplicates	Tracking 173680 as yet unmatched pairs. 81396 records in RAM.
INFO	2026-06-08 10:01:30	MarkDuplicates	Read   535,000,000 records.  Elapsed time: 00:21:20s.  Time for last 1,000,000:    2s.  Last read position: chr19:1,116,881
INFO	2026-06-08 10:01:30	MarkDuplicates	Tracking 172317 as yet unmatched pairs. 80018 records in RAM.
INFO	2026-06-08 10:01:32	MarkDuplicates	Read   536,000,000 records.  Elapsed time: 00:21:22s.  Time for last 1,000,000:    2s.  Last read position: chr19:1,599,474
INFO	2026-06-08 10:01:32	MarkDuplicates	Tracking 170907 as yet unmatched pairs. 78608 records in RAM.
INFO	2026-06-08 10:01:34	MarkDuplicates	Read   537,000,000 records.  Elapsed time: 00:21:24s.  Time for last 1,000,000:    2s.  Last read position: chr19:2,271,754
INFO	2026-06-08 10:01:34	MarkDuplicates	Tracking 167637 as yet unmatched pairs. 75337 records in RAM.
INFO	2026-06-08 10:01:37	MarkDuplicates	Read   538,000,000 records.  Elapsed time: 00:21:27s.  Time for last 1,000,000:    2s.  Last read position: chr19:3,730,369
INFO	2026-06-08 10:01:37	MarkDuplicates	Tracking 165658 as yet unmatched pairs. 73358 records in RAM.
INFO	2026-06-08 10:01:39	MarkDuplicates	Read   539,000,000 records.  Elapsed time: 00:21:29s.  Time for last 1,000,000:    2s.  Last read position: chr19:5,039,929
INFO	2026-06-08 10:01:39	MarkDuplicates	Tracking 163746 as yet unmatched pairs. 71444 records in RAM.
INFO	2026-06-08 10:01:41	MarkDuplicates	Read   540,000,000 records.  Elapsed time: 00:21:31s.  Time for last 1,000,000:    2s.  Last read position: chr19:6,416,372
INFO	2026-06-08 10:01:41	MarkDuplicates	Tracking 161521 as yet unmatched pairs. 69219 records in RAM.
INFO	2026-06-08 10:01:44	MarkDuplicates	Read   541,000,000 records.  Elapsed time: 00:21:33s.  Time for last 1,000,000:    2s.  Last read position: chr19:7,870,948
INFO	2026-06-08 10:01:44	MarkDuplicates	Tracking 159766 as yet unmatched pairs. 67464 records in RAM.
INFO	2026-06-08 10:01:46	MarkDuplicates	Read   542,000,000 records.  Elapsed time: 00:21:36s.  Time for last 1,000,000:    2s.  Last read position: chr19:10,115,478
INFO	2026-06-08 10:01:46	MarkDuplicates	Tracking 158105 as yet unmatched pairs. 65803 records in RAM.
INFO	2026-06-08 10:01:48	MarkDuplicates	Read   543,000,000 records.  Elapsed time: 00:21:38s.  Time for last 1,000,000:    2s.  Last read position: chr19:10,984,328
INFO	2026-06-08 10:01:48	MarkDuplicates	Tracking 156065 as yet unmatched pairs. 63761 records in RAM.
INFO	2026-06-08 10:01:50	MarkDuplicates	Read   544,000,000 records.  Elapsed time: 00:21:40s.  Time for last 1,000,000:    2s.  Last read position: chr19:12,646,570
INFO	2026-06-08 10:01:50	MarkDuplicates	Tracking 154546 as yet unmatched pairs. 62239 records in RAM.
INFO	2026-06-08 10:01:53	MarkDuplicates	Read   545,000,000 records.  Elapsed time: 00:21:42s.  Time for last 1,000,000:    2s.  Last read position: chr19:13,751,803
INFO	2026-06-08 10:01:53	MarkDuplicates	Tracking 152960 as yet unmatched pairs. 60653 records in RAM.
INFO	2026-06-08 10:01:55	MarkDuplicates	Read   546,000,000 records.  Elapsed time: 00:21:45s.  Time for last 1,000,000:    2s.  Last read position: chr19:14,516,770
INFO	2026-06-08 10:01:55	MarkDuplicates	Tracking 153975 as yet unmatched pairs. 61668 records in RAM.
INFO	2026-06-08 10:01:57	MarkDuplicates	Read   547,000,000 records.  Elapsed time: 00:21:47s.  Time for last 1,000,000:    2s.  Last read position: chr19:15,265,452
INFO	2026-06-08 10:01:57	MarkDuplicates	Tracking 150644 as yet unmatched pairs. 58328 records in RAM.
INFO	2026-06-08 10:01:59	MarkDuplicates	Read   548,000,000 records.  Elapsed time: 00:21:49s.  Time for last 1,000,000:    2s.  Last read position: chr19:17,232,447
INFO	2026-06-08 10:01:59	MarkDuplicates	Tracking 148248 as yet unmatched pairs. 55929 records in RAM.
INFO	2026-06-08 10:02:01	MarkDuplicates	Read   549,000,000 records.  Elapsed time: 00:21:51s.  Time for last 1,000,000:    2s.  Last read position: chr19:18,386,398
INFO	2026-06-08 10:02:01	MarkDuplicates	Tracking 145766 as yet unmatched pairs. 53444 records in RAM.
INFO	2026-06-08 10:02:04	MarkDuplicates	Read   550,000,000 records.  Elapsed time: 00:21:54s.  Time for last 1,000,000:    2s.  Last read position: chr19:19,180,632
INFO	2026-06-08 10:02:04	MarkDuplicates	Tracking 143161 as yet unmatched pairs. 50823 records in RAM.
INFO	2026-06-08 10:02:06	MarkDuplicates	Read   551,000,000 records.  Elapsed time: 00:21:56s.  Time for last 1,000,000:    2s.  Last read position: chr19:32,631,471
INFO	2026-06-08 10:02:06	MarkDuplicates	Tracking 142094 as yet unmatched pairs. 49755 records in RAM.
INFO	2026-06-08 10:02:08	MarkDuplicates	Read   552,000,000 records.  Elapsed time: 00:21:58s.  Time for last 1,000,000:    2s.  Last read position: chr19:35,122,918
INFO	2026-06-08 10:02:08	MarkDuplicates	Tracking 141217 as yet unmatched pairs. 48878 records in RAM.
INFO	2026-06-08 10:02:11	MarkDuplicates	Read   553,000,000 records.  Elapsed time: 00:22:00s.  Time for last 1,000,000:    2s.  Last read position: chr19:35,753,232
INFO	2026-06-08 10:02:11	MarkDuplicates	Tracking 137682 as yet unmatched pairs. 45341 records in RAM.
INFO	2026-06-08 10:02:13	MarkDuplicates	Read   554,000,000 records.  Elapsed time: 00:22:02s.  Time for last 1,000,000:    2s.  Last read position: chr19:38,264,887
INFO	2026-06-08 10:02:13	MarkDuplicates	Tracking 140684 as yet unmatched pairs. 48341 records in RAM.
INFO	2026-06-08 10:02:15	MarkDuplicates	Read   555,000,000 records.  Elapsed time: 00:22:05s.  Time for last 1,000,000:    2s.  Last read position: chr19:38,837,416
INFO	2026-06-08 10:02:15	MarkDuplicates	Tracking 136459 as yet unmatched pairs. 44113 records in RAM.
INFO	2026-06-08 10:02:17	MarkDuplicates	Read   556,000,000 records.  Elapsed time: 00:22:07s.  Time for last 1,000,000:    2s.  Last read position: chr19:39,826,726
INFO	2026-06-08 10:02:17	MarkDuplicates	Tracking 132989 as yet unmatched pairs. 40643 records in RAM.
INFO	2026-06-08 10:02:19	MarkDuplicates	Read   557,000,000 records.  Elapsed time: 00:22:09s.  Time for last 1,000,000:    2s.  Last read position: chr19:40,582,403
INFO	2026-06-08 10:02:19	MarkDuplicates	Tracking 131333 as yet unmatched pairs. 38986 records in RAM.
INFO	2026-06-08 10:02:22	MarkDuplicates	Read   558,000,000 records.  Elapsed time: 00:22:12s.  Time for last 1,000,000:    2s.  Last read position: chr19:41,302,791
INFO	2026-06-08 10:02:22	MarkDuplicates	Tracking 129450 as yet unmatched pairs. 37099 records in RAM.
INFO	2026-06-08 10:02:24	MarkDuplicates	Read   559,000,000 records.  Elapsed time: 00:22:14s.  Time for last 1,000,000:    2s.  Last read position: chr19:42,216,951
INFO	2026-06-08 10:02:24	MarkDuplicates	Tracking 127604 as yet unmatched pairs. 35253 records in RAM.
INFO	2026-06-08 10:02:26	MarkDuplicates	Read   560,000,000 records.  Elapsed time: 00:22:16s.  Time for last 1,000,000:    2s.  Last read position: chr19:42,293,167
INFO	2026-06-08 10:02:26	MarkDuplicates	Tracking 126742 as yet unmatched pairs. 34390 records in RAM.
INFO	2026-06-08 10:02:28	MarkDuplicates	Read   561,000,000 records.  Elapsed time: 00:22:18s.  Time for last 1,000,000:    2s.  Last read position: chr19:44,644,094
INFO	2026-06-08 10:02:28	MarkDuplicates	Tracking 124526 as yet unmatched pairs. 32169 records in RAM.
INFO	2026-06-08 10:02:31	MarkDuplicates	Read   562,000,000 records.  Elapsed time: 00:22:20s.  Time for last 1,000,000:    2s.  Last read position: chr19:44,820,803
INFO	2026-06-08 10:02:31	MarkDuplicates	Tracking 128457 as yet unmatched pairs. 36100 records in RAM.
INFO	2026-06-08 10:02:33	MarkDuplicates	Read   563,000,000 records.  Elapsed time: 00:22:23s.  Time for last 1,000,000:    2s.  Last read position: chr19:45,140,270
INFO	2026-06-08 10:02:33	MarkDuplicates	Tracking 121005 as yet unmatched pairs. 28648 records in RAM.
INFO	2026-06-08 10:02:35	MarkDuplicates	Read   564,000,000 records.  Elapsed time: 00:22:25s.  Time for last 1,000,000:    2s.  Last read position: chr19:45,786,661
INFO	2026-06-08 10:02:35	MarkDuplicates	Tracking 118512 as yet unmatched pairs. 26153 records in RAM.
INFO	2026-06-08 10:02:37	MarkDuplicates	Read   565,000,000 records.  Elapsed time: 00:22:27s.  Time for last 1,000,000:    2s.  Last read position: chr19:46,989,560
INFO	2026-06-08 10:02:37	MarkDuplicates	Tracking 117165 as yet unmatched pairs. 24803 records in RAM.
INFO	2026-06-08 10:02:40	MarkDuplicates	Read   566,000,000 records.  Elapsed time: 00:22:30s.  Time for last 1,000,000:    2s.  Last read position: chr19:48,325,541
INFO	2026-06-08 10:02:40	MarkDuplicates	Tracking 114377 as yet unmatched pairs. 22015 records in RAM.
INFO	2026-06-08 10:02:42	MarkDuplicates	Read   567,000,000 records.  Elapsed time: 00:22:32s.  Time for last 1,000,000:    2s.  Last read position: chr19:48,913,475
INFO	2026-06-08 10:02:42	MarkDuplicates	Tracking 113863 as yet unmatched pairs. 21500 records in RAM.
INFO	2026-06-08 10:02:44	MarkDuplicates	Read   568,000,000 records.  Elapsed time: 00:22:34s.  Time for last 1,000,000:    2s.  Last read position: chr19:49,447,411
INFO	2026-06-08 10:02:44	MarkDuplicates	Tracking 111001 as yet unmatched pairs. 18637 records in RAM.
INFO	2026-06-08 10:02:46	MarkDuplicates	Read   569,000,000 records.  Elapsed time: 00:22:36s.  Time for last 1,000,000:    2s.  Last read position: chr19:49,624,898
INFO	2026-06-08 10:02:46	MarkDuplicates	Tracking 109494 as yet unmatched pairs. 17130 records in RAM.
INFO	2026-06-08 10:02:49	MarkDuplicates	Read   570,000,000 records.  Elapsed time: 00:22:38s.  Time for last 1,000,000:    2s.  Last read position: chr19:49,851,359
INFO	2026-06-08 10:02:49	MarkDuplicates	Tracking 108799 as yet unmatched pairs. 16434 records in RAM.
INFO	2026-06-08 10:02:51	MarkDuplicates	Read   571,000,000 records.  Elapsed time: 00:22:41s.  Time for last 1,000,000:    2s.  Last read position: chr19:50,309,655
INFO	2026-06-08 10:02:51	MarkDuplicates	Tracking 105994 as yet unmatched pairs. 13625 records in RAM.
INFO	2026-06-08 10:02:53	MarkDuplicates	Read   572,000,000 records.  Elapsed time: 00:22:43s.  Time for last 1,000,000:    2s.  Last read position: chr19:52,613,954
INFO	2026-06-08 10:02:53	MarkDuplicates	Tracking 104194 as yet unmatched pairs. 11825 records in RAM.
INFO	2026-06-08 10:02:55	MarkDuplicates	Read   573,000,000 records.  Elapsed time: 00:22:45s.  Time for last 1,000,000:    2s.  Last read position: chr19:54,162,672
INFO	2026-06-08 10:02:55	MarkDuplicates	Tracking 103894 as yet unmatched pairs. 11525 records in RAM.
INFO	2026-06-08 10:02:58	MarkDuplicates	Read   574,000,000 records.  Elapsed time: 00:22:47s.  Time for last 1,000,000:    2s.  Last read position: chr19:54,456,733
INFO	2026-06-08 10:02:58	MarkDuplicates	Tracking 105008 as yet unmatched pairs. 12636 records in RAM.
INFO	2026-06-08 10:03:00	MarkDuplicates	Read   575,000,000 records.  Elapsed time: 00:22:50s.  Time for last 1,000,000:    2s.  Last read position: chr19:55,346,515
INFO	2026-06-08 10:03:00	MarkDuplicates	Tracking 99507 as yet unmatched pairs. 7130 records in RAM.
INFO	2026-06-08 10:03:02	MarkDuplicates	Read   576,000,000 records.  Elapsed time: 00:22:52s.  Time for last 1,000,000:    2s.  Last read position: chr19:55,691,997
INFO	2026-06-08 10:03:02	MarkDuplicates	Tracking 97969 as yet unmatched pairs. 5588 records in RAM.
INFO	2026-06-08 10:03:04	MarkDuplicates	Read   577,000,000 records.  Elapsed time: 00:22:54s.  Time for last 1,000,000:    2s.  Last read position: chr19:57,813,282
INFO	2026-06-08 10:03:04	MarkDuplicates	Tracking 97624 as yet unmatched pairs. 5243 records in RAM.
INFO	2026-06-08 10:03:06	MarkDuplicates	Read   578,000,000 records.  Elapsed time: 00:22:56s.  Time for last 1,000,000:    1s.  Last read position: chr19:57,933,753
INFO	2026-06-08 10:03:06	MarkDuplicates	Tracking 93955 as yet unmatched pairs. 1572 records in RAM.
INFO	2026-06-08 10:03:09	MarkDuplicates	Read   579,000,000 records.  Elapsed time: 00:22:58s.  Time for last 1,000,000:    2s.  Last read position: chr20:1,164,328
INFO	2026-06-08 10:03:09	MarkDuplicates	Tracking 92065 as yet unmatched pairs. 26194 records in RAM.
INFO	2026-06-08 10:03:11	MarkDuplicates	Read   580,000,000 records.  Elapsed time: 00:23:01s.  Time for last 1,000,000:    2s.  Last read position: chr20:3,923,313
INFO	2026-06-08 10:03:11	MarkDuplicates	Tracking 90183 as yet unmatched pairs. 24312 records in RAM.
INFO	2026-06-08 10:03:13	MarkDuplicates	Read   581,000,000 records.  Elapsed time: 00:23:03s.  Time for last 1,000,000:    2s.  Last read position: chr20:17,975,881
INFO	2026-06-08 10:03:13	MarkDuplicates	Tracking 88638 as yet unmatched pairs. 22760 records in RAM.
INFO	2026-06-08 10:03:15	MarkDuplicates	Read   582,000,000 records.  Elapsed time: 00:23:05s.  Time for last 1,000,000:    2s.  Last read position: chr20:25,221,371
INFO	2026-06-08 10:03:15	MarkDuplicates	Tracking 87208 as yet unmatched pairs. 21329 records in RAM.
INFO	2026-06-08 10:03:17	MarkDuplicates	Read   583,000,000 records.  Elapsed time: 00:23:07s.  Time for last 1,000,000:    2s.  Last read position: chr20:33,619,516
INFO	2026-06-08 10:03:17	MarkDuplicates	Tracking 85557 as yet unmatched pairs. 19670 records in RAM.
INFO	2026-06-08 10:03:20	MarkDuplicates	Read   584,000,000 records.  Elapsed time: 00:23:10s.  Time for last 1,000,000:    2s.  Last read position: chr20:35,509,997
INFO	2026-06-08 10:03:20	MarkDuplicates	Tracking 83807 as yet unmatched pairs. 17920 records in RAM.
INFO	2026-06-08 10:03:22	MarkDuplicates	Read   585,000,000 records.  Elapsed time: 00:23:12s.  Time for last 1,000,000:    2s.  Last read position: chr20:36,862,742
INFO	2026-06-08 10:03:22	MarkDuplicates	Tracking 82078 as yet unmatched pairs. 16191 records in RAM.
INFO	2026-06-08 10:03:24	MarkDuplicates	Read   586,000,000 records.  Elapsed time: 00:23:14s.  Time for last 1,000,000:    2s.  Last read position: chr20:41,484,355
INFO	2026-06-08 10:03:24	MarkDuplicates	Tracking 80634 as yet unmatched pairs. 14743 records in RAM.
INFO	2026-06-08 10:03:27	MarkDuplicates	Read   587,000,000 records.  Elapsed time: 00:23:16s.  Time for last 1,000,000:    2s.  Last read position: chr20:45,843,579
INFO	2026-06-08 10:03:27	MarkDuplicates	Tracking 78719 as yet unmatched pairs. 12820 records in RAM.
INFO	2026-06-08 10:03:29	MarkDuplicates	Read   588,000,000 records.  Elapsed time: 00:23:18s.  Time for last 1,000,000:    2s.  Last read position: chr20:49,025,347
INFO	2026-06-08 10:03:29	MarkDuplicates	Tracking 77082 as yet unmatched pairs. 11181 records in RAM.
INFO	2026-06-08 10:03:31	MarkDuplicates	Read   589,000,000 records.  Elapsed time: 00:23:21s.  Time for last 1,000,000:    2s.  Last read position: chr20:53,576,154
INFO	2026-06-08 10:03:31	MarkDuplicates	Tracking 75889 as yet unmatched pairs. 9986 records in RAM.
INFO	2026-06-08 10:03:33	MarkDuplicates	Read   590,000,000 records.  Elapsed time: 00:23:23s.  Time for last 1,000,000:    2s.  Last read position: chr20:58,903,552
INFO	2026-06-08 10:03:33	MarkDuplicates	Tracking 76684 as yet unmatched pairs. 10781 records in RAM.
INFO	2026-06-08 10:03:35	MarkDuplicates	Read   591,000,000 records.  Elapsed time: 00:23:25s.  Time for last 1,000,000:    2s.  Last read position: chr20:62,309,281
INFO	2026-06-08 10:03:35	MarkDuplicates	Tracking 73756 as yet unmatched pairs. 7852 records in RAM.
INFO	2026-06-08 10:03:38	MarkDuplicates	Read   592,000,000 records.  Elapsed time: 00:23:28s.  Time for last 1,000,000:    2s.  Last read position: chr20:62,353,237
INFO	2026-06-08 10:03:38	MarkDuplicates	Tracking 71516 as yet unmatched pairs. 5611 records in RAM.
INFO	2026-06-08 10:03:40	MarkDuplicates	Read   593,000,000 records.  Elapsed time: 00:23:30s.  Time for last 1,000,000:    2s.  Last read position: chr20:63,560,300
INFO	2026-06-08 10:03:40	MarkDuplicates	Tracking 68165 as yet unmatched pairs. 2259 records in RAM.
INFO	2026-06-08 10:03:42	MarkDuplicates	Read   594,000,000 records.  Elapsed time: 00:23:32s.  Time for last 1,000,000:    2s.  Last read position: chr21:5,117,097
INFO	2026-06-08 10:03:42	MarkDuplicates	Tracking 65991 as yet unmatched pairs. 12515 records in RAM.
INFO	2026-06-08 10:03:44	MarkDuplicates	Read   595,000,000 records.  Elapsed time: 00:23:34s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,400,294
INFO	2026-06-08 10:03:44	MarkDuplicates	Tracking 65244 as yet unmatched pairs. 11765 records in RAM.
INFO	2026-06-08 10:03:46	MarkDuplicates	Read   596,000,000 records.  Elapsed time: 00:23:36s.  Time for last 1,000,000:    1s.  Last read position: chr21:26,170,567
INFO	2026-06-08 10:03:46	MarkDuplicates	Tracking 64706 as yet unmatched pairs. 11225 records in RAM.
INFO	2026-06-08 10:03:48	MarkDuplicates	Read   597,000,000 records.  Elapsed time: 00:23:38s.  Time for last 1,000,000:    2s.  Last read position: chr21:33,552,855
INFO	2026-06-08 10:03:48	MarkDuplicates	Tracking 63739 as yet unmatched pairs. 10253 records in RAM.
INFO	2026-06-08 10:03:50	MarkDuplicates	Read   598,000,000 records.  Elapsed time: 00:23:40s.  Time for last 1,000,000:    2s.  Last read position: chr21:36,936,844
INFO	2026-06-08 10:03:50	MarkDuplicates	Tracking 61271 as yet unmatched pairs. 7785 records in RAM.
INFO	2026-06-08 10:03:52	MarkDuplicates	Read   599,000,000 records.  Elapsed time: 00:23:42s.  Time for last 1,000,000:    2s.  Last read position: chr21:39,348,929
INFO	2026-06-08 10:03:52	MarkDuplicates	Tracking 59321 as yet unmatched pairs. 5834 records in RAM.
INFO	2026-06-08 10:03:55	MarkDuplicates	Read   600,000,000 records.  Elapsed time: 00:23:45s.  Time for last 1,000,000:    2s.  Last read position: chr21:43,791,371
INFO	2026-06-08 10:03:55	MarkDuplicates	Tracking 57548 as yet unmatched pairs. 4057 records in RAM.
INFO	2026-06-08 10:03:57	MarkDuplicates	Read   601,000,000 records.  Elapsed time: 00:23:47s.  Time for last 1,000,000:    2s.  Last read position: chr21:45,981,856
INFO	2026-06-08 10:03:57	MarkDuplicates	Tracking 57049 as yet unmatched pairs. 3557 records in RAM.
INFO	2026-06-08 10:03:59	MarkDuplicates	Read   602,000,000 records.  Elapsed time: 00:23:49s.  Time for last 1,000,000:    2s.  Last read position: chr21:46,459,099
INFO	2026-06-08 10:03:59	MarkDuplicates	Tracking 54549 as yet unmatched pairs. 1057 records in RAM.
INFO	2026-06-08 10:04:01	MarkDuplicates	Read   603,000,000 records.  Elapsed time: 00:23:51s.  Time for last 1,000,000:    2s.  Last read position: chr22:20,446,470
INFO	2026-06-08 10:04:01	MarkDuplicates	Tracking 52030 as yet unmatched pairs. 21750 records in RAM.
INFO	2026-06-08 10:04:04	MarkDuplicates	Read   604,000,000 records.  Elapsed time: 00:23:54s.  Time for last 1,000,000:    2s.  Last read position: chr22:23,292,579
INFO	2026-06-08 10:04:04	MarkDuplicates	Tracking 50750 as yet unmatched pairs. 20469 records in RAM.
INFO	2026-06-08 10:04:06	MarkDuplicates	Read   605,000,000 records.  Elapsed time: 00:23:56s.  Time for last 1,000,000:    2s.  Last read position: chr22:26,560,970
INFO	2026-06-08 10:04:06	MarkDuplicates	Tracking 48425 as yet unmatched pairs. 18137 records in RAM.
INFO	2026-06-08 10:04:08	MarkDuplicates	Read   606,000,000 records.  Elapsed time: 00:23:58s.  Time for last 1,000,000:    2s.  Last read position: chr22:29,125,336
INFO	2026-06-08 10:04:08	MarkDuplicates	Tracking 46952 as yet unmatched pairs. 16654 records in RAM.
INFO	2026-06-08 10:04:10	MarkDuplicates	Read   607,000,000 records.  Elapsed time: 00:24:00s.  Time for last 1,000,000:    2s.  Last read position: chr22:29,694,784
INFO	2026-06-08 10:04:10	MarkDuplicates	Tracking 45219 as yet unmatched pairs. 14921 records in RAM.
INFO	2026-06-08 10:04:13	MarkDuplicates	Read   608,000,000 records.  Elapsed time: 00:24:03s.  Time for last 1,000,000:    2s.  Last read position: chr22:33,626,271
INFO	2026-06-08 10:04:13	MarkDuplicates	Tracking 43610 as yet unmatched pairs. 13312 records in RAM.
INFO	2026-06-08 10:04:15	MarkDuplicates	Read   609,000,000 records.  Elapsed time: 00:24:05s.  Time for last 1,000,000:    2s.  Last read position: chr22:37,232,834
INFO	2026-06-08 10:04:15	MarkDuplicates	Tracking 41731 as yet unmatched pairs. 11433 records in RAM.
INFO	2026-06-08 10:04:17	MarkDuplicates	Read   610,000,000 records.  Elapsed time: 00:24:07s.  Time for last 1,000,000:    2s.  Last read position: chr22:38,726,282
INFO	2026-06-08 10:04:17	MarkDuplicates	Tracking 40114 as yet unmatched pairs. 9816 records in RAM.
INFO	2026-06-08 10:04:19	MarkDuplicates	Read   611,000,000 records.  Elapsed time: 00:24:09s.  Time for last 1,000,000:    2s.  Last read position: chr22:41,205,346
INFO	2026-06-08 10:04:19	MarkDuplicates	Tracking 38424 as yet unmatched pairs. 8123 records in RAM.
INFO	2026-06-08 10:04:22	MarkDuplicates	Read   612,000,000 records.  Elapsed time: 00:24:11s.  Time for last 1,000,000:    2s.  Last read position: chr22:44,187,846
INFO	2026-06-08 10:04:22	MarkDuplicates	Tracking 36729 as yet unmatched pairs. 6428 records in RAM.
INFO	2026-06-08 10:04:24	MarkDuplicates	Read   613,000,000 records.  Elapsed time: 00:24:14s.  Time for last 1,000,000:    2s.  Last read position: chr22:46,535,284
INFO	2026-06-08 10:04:24	MarkDuplicates	Tracking 36492 as yet unmatched pairs. 6188 records in RAM.
INFO	2026-06-08 10:04:26	MarkDuplicates	Read   614,000,000 records.  Elapsed time: 00:24:16s.  Time for last 1,000,000:    2s.  Last read position: chr22:50,288,767
INFO	2026-06-08 10:04:26	MarkDuplicates	Tracking 33857 as yet unmatched pairs. 3551 records in RAM.
INFO	2026-06-08 10:04:28	MarkDuplicates	Read   615,000,000 records.  Elapsed time: 00:24:18s.  Time for last 1,000,000:    2s.  Last read position: chr22:50,721,024
INFO	2026-06-08 10:04:28	MarkDuplicates	Tracking 31003 as yet unmatched pairs. 697 records in RAM.
INFO	2026-06-08 10:04:31	MarkDuplicates	Read   616,000,000 records.  Elapsed time: 00:24:21s.  Time for last 1,000,000:    2s.  Last read position: chrX:9,684,048
INFO	2026-06-08 10:04:31	MarkDuplicates	Tracking 29300 as yet unmatched pairs. 25839 records in RAM.
INFO	2026-06-08 10:04:33	MarkDuplicates	Read   617,000,000 records.  Elapsed time: 00:24:23s.  Time for last 1,000,000:    2s.  Last read position: chrX:19,542,000
INFO	2026-06-08 10:04:33	MarkDuplicates	Tracking 27652 as yet unmatched pairs. 24188 records in RAM.
INFO	2026-06-08 10:04:35	MarkDuplicates	Read   618,000,000 records.  Elapsed time: 00:24:25s.  Time for last 1,000,000:    2s.  Last read position: chrX:40,073,299
INFO	2026-06-08 10:04:35	MarkDuplicates	Tracking 27115 as yet unmatched pairs. 23651 records in RAM.
INFO	2026-06-08 10:04:37	MarkDuplicates	Read   619,000,000 records.  Elapsed time: 00:24:27s.  Time for last 1,000,000:    2s.  Last read position: chrX:46,758,732
INFO	2026-06-08 10:04:37	MarkDuplicates	Tracking 24905 as yet unmatched pairs. 21439 records in RAM.
INFO	2026-06-08 10:04:40	MarkDuplicates	Read   620,000,000 records.  Elapsed time: 00:24:30s.  Time for last 1,000,000:    2s.  Last read position: chrX:48,818,217
INFO	2026-06-08 10:04:40	MarkDuplicates	Tracking 23260 as yet unmatched pairs. 19794 records in RAM.
INFO	2026-06-08 10:04:42	MarkDuplicates	Read   621,000,000 records.  Elapsed time: 00:24:32s.  Time for last 1,000,000:    2s.  Last read position: chrX:51,900,188
INFO	2026-06-08 10:04:42	MarkDuplicates	Tracking 21994 as yet unmatched pairs. 18528 records in RAM.
INFO	2026-06-08 10:04:44	MarkDuplicates	Read   622,000,000 records.  Elapsed time: 00:24:34s.  Time for last 1,000,000:    2s.  Last read position: chrX:53,583,753
INFO	2026-06-08 10:04:44	MarkDuplicates	Tracking 20391 as yet unmatched pairs. 16925 records in RAM.
INFO	2026-06-08 10:04:46	MarkDuplicates	Read   623,000,000 records.  Elapsed time: 00:24:36s.  Time for last 1,000,000:    2s.  Last read position: chrX:57,135,943
INFO	2026-06-08 10:04:46	MarkDuplicates	Tracking 18685 as yet unmatched pairs. 15219 records in RAM.
INFO	2026-06-08 10:04:48	MarkDuplicates	Read   624,000,000 records.  Elapsed time: 00:24:38s.  Time for last 1,000,000:    2s.  Last read position: chrX:71,303,868
INFO	2026-06-08 10:04:48	MarkDuplicates	Tracking 16568 as yet unmatched pairs. 13102 records in RAM.
INFO	2026-06-08 10:04:51	MarkDuplicates	Read   625,000,000 records.  Elapsed time: 00:24:41s.  Time for last 1,000,000:    2s.  Last read position: chrX:77,600,395
INFO	2026-06-08 10:04:51	MarkDuplicates	Tracking 15586 as yet unmatched pairs. 12120 records in RAM.
INFO	2026-06-08 10:04:53	MarkDuplicates	Read   626,000,000 records.  Elapsed time: 00:24:43s.  Time for last 1,000,000:    2s.  Last read position: chrX:101,391,521
INFO	2026-06-08 10:04:53	MarkDuplicates	Tracking 14814 as yet unmatched pairs. 11348 records in RAM.
INFO	2026-06-08 10:04:55	MarkDuplicates	Read   627,000,000 records.  Elapsed time: 00:24:45s.  Time for last 1,000,000:    2s.  Last read position: chrX:111,708,071
INFO	2026-06-08 10:04:55	MarkDuplicates	Tracking 12368 as yet unmatched pairs. 8902 records in RAM.
INFO	2026-06-08 10:04:57	MarkDuplicates	Read   628,000,000 records.  Elapsed time: 00:24:47s.  Time for last 1,000,000:    2s.  Last read position: chrX:129,810,904
INFO	2026-06-08 10:04:57	MarkDuplicates	Tracking 11001 as yet unmatched pairs. 7535 records in RAM.
INFO	2026-06-08 10:05:00	MarkDuplicates	Read   629,000,000 records.  Elapsed time: 00:24:49s.  Time for last 1,000,000:    2s.  Last read position: chrX:150,727,214
INFO	2026-06-08 10:05:00	MarkDuplicates	Tracking 9402 as yet unmatched pairs. 5936 records in RAM.
INFO	2026-06-08 10:05:02	MarkDuplicates	Read   630,000,000 records.  Elapsed time: 00:24:52s.  Time for last 1,000,000:    2s.  Last read position: chrX:153,910,017
INFO	2026-06-08 10:05:02	MarkDuplicates	Tracking 7823 as yet unmatched pairs. 4357 records in RAM.
INFO	2026-06-08 10:05:04	MarkDuplicates	Read   631,000,000 records.  Elapsed time: 00:24:54s.  Time for last 1,000,000:    2s.  Last read position: chrX:154,364,681
INFO	2026-06-08 10:05:04	MarkDuplicates	Tracking 6718 as yet unmatched pairs. 3252 records in RAM.
INFO	2026-06-08 10:05:06	MarkDuplicates	Read   632,000,000 records.  Elapsed time: 00:24:56s.  Time for last 1,000,000:    2s.  Last read position: chrX:154,562,929
INFO	2026-06-08 10:05:06	MarkDuplicates	Tracking 4013 as yet unmatched pairs. 547 records in RAM.
INFO	2026-06-08 10:05:08	MarkDuplicates	Read   633,000,000 records.  Elapsed time: 00:24:58s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:154,401
INFO	2026-06-08 10:05:08	MarkDuplicates	Tracking 2553 as yet unmatched pairs. 22 records in RAM.
INFO	2026-06-08 10:05:10	MarkDuplicates	Read   634,000,000 records.  Elapsed time: 00:24:59s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:176,091
INFO	2026-06-08 10:05:10	MarkDuplicates	Tracking 69 as yet unmatched pairs. 31 records in RAM.
INFO	2026-06-08 10:05:10	MarkDuplicates	Read 634280796 records. 0 pairs never matched.
INFO	2026-06-08 10:05:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 58509362600; totalMemory: 83550535680; maxMemory: 127137742848
INFO	2026-06-08 10:05:56	MarkDuplicates	Will retain up to 2147483642 duplicate indices before spilling to disk.
INFO	2026-06-08 10:06:01	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2026-06-08 10:06:29	OpticalDuplicateFinder	Large duplicate set. size = 1294
INFO	2026-06-08 10:06:29	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-27,015
INFO	2026-06-08 10:06:36	OpticalDuplicateFinder	Large duplicate set. size = 1058
INFO	2026-06-08 10:06:36	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:15,166
INFO	2026-06-08 10:06:58	OpticalDuplicateFinder	Large duplicate set. size = 1017
INFO	2026-06-08 10:06:58	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:27,956
INFO	2026-06-08 10:07:26	MarkDuplicates	Traversing fragment information and detecting duplicates.
WARNING	2026-06-08 10:07:26	SortingCollection	There is not enough memory per file for buffering. Reading will be unbuffered.
INFO	2026-06-08 10:08:48	MarkDuplicates	Sorting list of duplicate records.
INFO	2026-06-08 10:08:50	MarkDuplicates	After generateDuplicateIndexes freeMemory: 203987592; totalMemory: 234881024; maxMemory: 127137742848
INFO	2026-06-08 10:08:50	MarkDuplicates	Marking 310207365 records as duplicates.
INFO	2026-06-08 10:08:50	MarkDuplicates	Found 21342683 optical duplicate clusters.
INFO	2026-06-08 10:08:51	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2026-06-08 10:09:08	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:00:17s.  Time for last 10,000,000:   17s.  Last read position: chr1:28,743,707
INFO	2026-06-08 10:09:24	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:00:33s.  Time for last 10,000,000:   16s.  Last read position: chr1:102,962,738
INFO	2026-06-08 10:09:41	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:00:50s.  Time for last 10,000,000:   16s.  Last read position: chr1:149,887,155
INFO	2026-06-08 10:09:57	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:01:06s.  Time for last 10,000,000:   16s.  Last read position: chr1:156,050,479
INFO	2026-06-08 10:10:14	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:01:23s.  Time for last 10,000,000:   16s.  Last read position: chr1:186,346,247
INFO	2026-06-08 10:10:31	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:01:40s.  Time for last 10,000,000:   16s.  Last read position: chr1:234,430,051
INFO	2026-06-08 10:10:47	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:01:56s.  Time for last 10,000,000:   16s.  Last read position: chr2:32,916,260
INFO	2026-06-08 10:11:04	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:02:13s.  Time for last 10,000,000:   16s.  Last read position: chr2:74,369,152
INFO	2026-06-08 10:11:21	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:02:30s.  Time for last 10,000,000:   16s.  Last read position: chr2:127,651,667
INFO	2026-06-08 10:11:38	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:02:47s.  Time for last 10,000,000:   17s.  Last read position: chr2:203,391,075
INFO	2026-06-08 10:11:54	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:03:03s.  Time for last 10,000,000:   16s.  Last read position: chr2:215,433,337
INFO	2026-06-08 10:12:12	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:03:20s.  Time for last 10,000,000:   17s.  Last read position: chr3:16,270,978
INFO	2026-06-08 10:12:29	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:03:38s.  Time for last 10,000,000:   17s.  Last read position: chr3:52,522,041
INFO	2026-06-08 10:12:46	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:03:55s.  Time for last 10,000,000:   17s.  Last read position: chr3:149,129,922
INFO	2026-06-08 10:13:03	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:04:12s.  Time for last 10,000,000:   17s.  Last read position: chr4:6,863,505
INFO	2026-06-08 10:13:20	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:04:29s.  Time for last 10,000,000:   17s.  Last read position: chr4:150,607,879
INFO	2026-06-08 10:13:37	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:04:46s.  Time for last 10,000,000:   17s.  Last read position: chr5:73,752,970
INFO	2026-06-08 10:13:54	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:05:03s.  Time for last 10,000,000:   17s.  Last read position: chr5:141,189,277
INFO	2026-06-08 10:14:11	MarkDuplicates	Written   190,000,000 records.  Elapsed time: 00:05:20s.  Time for last 10,000,000:   16s.  Last read position: chr5:177,460,485
INFO	2026-06-08 10:14:28	MarkDuplicates	Written   200,000,000 records.  Elapsed time: 00:05:37s.  Time for last 10,000,000:   16s.  Last read position: chr6:30,660,118
INFO	2026-06-08 10:14:44	MarkDuplicates	Written   210,000,000 records.  Elapsed time: 00:05:53s.  Time for last 10,000,000:   16s.  Last read position: chr6:36,978,078
INFO	2026-06-08 10:15:01	MarkDuplicates	Written   220,000,000 records.  Elapsed time: 00:06:10s.  Time for last 10,000,000:   17s.  Last read position: chr6:136,275,555
INFO	2026-06-08 10:15:18	MarkDuplicates	Written   230,000,000 records.  Elapsed time: 00:06:27s.  Time for last 10,000,000:   16s.  Last read position: chr7:5,361,593
INFO	2026-06-08 10:15:35	MarkDuplicates	Written   240,000,000 records.  Elapsed time: 00:06:44s.  Time for last 10,000,000:   16s.  Last read position: chr7:44,885,025
INFO	2026-06-08 10:15:52	MarkDuplicates	Written   250,000,000 records.  Elapsed time: 00:07:01s.  Time for last 10,000,000:   16s.  Last read position: chr7:100,374,353
INFO	2026-06-08 10:16:09	MarkDuplicates	Written   260,000,000 records.  Elapsed time: 00:07:18s.  Time for last 10,000,000:   16s.  Last read position: chr7:152,816,575
INFO	2026-06-08 10:16:26	MarkDuplicates	Written   270,000,000 records.  Elapsed time: 00:07:35s.  Time for last 10,000,000:   17s.  Last read position: chr8:89,786,612
INFO	2026-06-08 10:16:42	MarkDuplicates	Written   280,000,000 records.  Elapsed time: 00:07:51s.  Time for last 10,000,000:   16s.  Last read position: chr8:144,243,377
INFO	2026-06-08 10:16:59	MarkDuplicates	Written   290,000,000 records.  Elapsed time: 00:08:08s.  Time for last 10,000,000:   16s.  Last read position: chr9:124,321,461
INFO	2026-06-08 10:17:15	MarkDuplicates	Written   300,000,000 records.  Elapsed time: 00:08:24s.  Time for last 10,000,000:   16s.  Last read position: chr10:3,149,673
INFO	2026-06-08 10:17:31	MarkDuplicates	Written   310,000,000 records.  Elapsed time: 00:08:40s.  Time for last 10,000,000:   16s.  Last read position: chr10:43,387,328
INFO	2026-06-08 10:17:48	MarkDuplicates	Written   320,000,000 records.  Elapsed time: 00:08:57s.  Time for last 10,000,000:   16s.  Last read position: chr10:119,917,984
INFO	2026-06-08 10:18:04	MarkDuplicates	Written   330,000,000 records.  Elapsed time: 00:09:13s.  Time for last 10,000,000:   16s.  Last read position: chr11:1,761,407
INFO	2026-06-08 10:18:21	MarkDuplicates	Written   340,000,000 records.  Elapsed time: 00:09:30s.  Time for last 10,000,000:   16s.  Last read position: chr11:57,801,757
INFO	2026-06-08 10:18:37	MarkDuplicates	Written   350,000,000 records.  Elapsed time: 00:09:46s.  Time for last 10,000,000:   16s.  Last read position: chr11:70,326,749
INFO	2026-06-08 10:18:53	MarkDuplicates	Written   360,000,000 records.  Elapsed time: 00:10:02s.  Time for last 10,000,000:   16s.  Last read position: chr12:2,861,221
INFO	2026-06-08 10:19:10	MarkDuplicates	Written   370,000,000 records.  Elapsed time: 00:10:19s.  Time for last 10,000,000:   16s.  Last read position: chr12:51,377,232
INFO	2026-06-08 10:19:26	MarkDuplicates	Written   380,000,000 records.  Elapsed time: 00:10:35s.  Time for last 10,000,000:   16s.  Last read position: chr12:91,158,388
INFO	2026-06-08 10:19:43	MarkDuplicates	Written   390,000,000 records.  Elapsed time: 00:10:52s.  Time for last 10,000,000:   16s.  Last read position: chr13:18,298,319
INFO	2026-06-08 10:19:59	MarkDuplicates	Written   400,000,000 records.  Elapsed time: 00:11:08s.  Time for last 10,000,000:   16s.  Last read position: chr14:24,182,094
INFO	2026-06-08 10:20:16	MarkDuplicates	Written   410,000,000 records.  Elapsed time: 00:11:25s.  Time for last 10,000,000:   16s.  Last read position: chr14:102,208,763
INFO	2026-06-08 10:20:32	MarkDuplicates	Written   420,000,000 records.  Elapsed time: 00:11:41s.  Time for last 10,000,000:   16s.  Last read position: chr15:48,153,811
INFO	2026-06-08 10:20:49	MarkDuplicates	Written   430,000,000 records.  Elapsed time: 00:11:58s.  Time for last 10,000,000:   16s.  Last read position: chr15:82,539,982
INFO	2026-06-08 10:21:05	MarkDuplicates	Written   440,000,000 records.  Elapsed time: 00:12:14s.  Time for last 10,000,000:   16s.  Last read position: chr16:2,761,570
INFO	2026-06-08 10:21:21	MarkDuplicates	Written   450,000,000 records.  Elapsed time: 00:12:30s.  Time for last 10,000,000:   16s.  Last read position: chr16:18,871,369
INFO	2026-06-08 10:21:38	MarkDuplicates	Written   460,000,000 records.  Elapsed time: 00:12:47s.  Time for last 10,000,000:   16s.  Last read position: chr16:30,225,395
INFO	2026-06-08 10:21:54	MarkDuplicates	Written   470,000,000 records.  Elapsed time: 00:13:03s.  Time for last 10,000,000:   16s.  Last read position: chr16:78,022,571
INFO	2026-06-08 10:22:11	MarkDuplicates	Written   480,000,000 records.  Elapsed time: 00:13:20s.  Time for last 10,000,000:   16s.  Last read position: chr17:16,382,284
INFO	2026-06-08 10:22:27	MarkDuplicates	Written   490,000,000 records.  Elapsed time: 00:13:36s.  Time for last 10,000,000:   16s.  Last read position: chr17:39,707,094
INFO	2026-06-08 10:22:43	MarkDuplicates	Written   500,000,000 records.  Elapsed time: 00:13:52s.  Time for last 10,000,000:   16s.  Last read position: chr17:50,189,480
INFO	2026-06-08 10:23:00	MarkDuplicates	Written   510,000,000 records.  Elapsed time: 00:14:09s.  Time for last 10,000,000:   16s.  Last read position: chr17:59,683,115
INFO	2026-06-08 10:23:16	MarkDuplicates	Written   520,000,000 records.  Elapsed time: 00:14:25s.  Time for last 10,000,000:   16s.  Last read position: chr17:80,287,947
INFO	2026-06-08 10:23:33	MarkDuplicates	Written   530,000,000 records.  Elapsed time: 00:14:42s.  Time for last 10,000,000:   16s.  Last read position: chr18:26,052,684
INFO	2026-06-08 10:23:50	MarkDuplicates	Written   540,000,000 records.  Elapsed time: 00:14:59s.  Time for last 10,000,000:   16s.  Last read position: chr19:6,416,372
INFO	2026-06-08 10:24:06	MarkDuplicates	Written   550,000,000 records.  Elapsed time: 00:15:15s.  Time for last 10,000,000:   16s.  Last read position: chr19:19,180,632
INFO	2026-06-08 10:24:23	MarkDuplicates	Written   560,000,000 records.  Elapsed time: 00:15:32s.  Time for last 10,000,000:   16s.  Last read position: chr19:42,293,167
INFO	2026-06-08 10:24:39	MarkDuplicates	Written   570,000,000 records.  Elapsed time: 00:15:48s.  Time for last 10,000,000:   16s.  Last read position: chr19:49,851,359
INFO	2026-06-08 10:24:56	MarkDuplicates	Written   580,000,000 records.  Elapsed time: 00:16:05s.  Time for last 10,000,000:   16s.  Last read position: chr20:3,923,313
INFO	2026-06-08 10:25:12	MarkDuplicates	Written   590,000,000 records.  Elapsed time: 00:16:21s.  Time for last 10,000,000:   16s.  Last read position: chr20:58,903,552
INFO	2026-06-08 10:25:28	MarkDuplicates	Written   600,000,000 records.  Elapsed time: 00:16:37s.  Time for last 10,000,000:   16s.  Last read position: chr21:43,791,371
INFO	2026-06-08 10:25:45	MarkDuplicates	Written   610,000,000 records.  Elapsed time: 00:16:54s.  Time for last 10,000,000:   16s.  Last read position: chr22:38,726,282
INFO	2026-06-08 10:26:01	MarkDuplicates	Written   620,000,000 records.  Elapsed time: 00:17:10s.  Time for last 10,000,000:   16s.  Last read position: chrX:48,818,217
INFO	2026-06-08 10:26:17	MarkDuplicates	Written   630,000,000 records.  Elapsed time: 00:17:26s.  Time for last 10,000,000:   16s.  Last read position: chrX:153,910,017
INFO	2026-06-08 10:26:32	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2026-06-08 10:26:32	MarkDuplicates	Duplicate Index cleanup.
INFO	2026-06-08 10:26:32	MarkDuplicates	Getting Memory Stats.
INFO	2026-06-08 10:26:32	MarkDuplicates	Before output close freeMemory: 203933520; totalMemory: 234881024; maxMemory: 127137742848
INFO	2026-06-08 10:26:32	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2026-06-08 10:26:32	MarkDuplicates	After output close freeMemory: 104190016; totalMemory: 134217728; maxMemory: 127137742848
[Mon Jun 08 10:26:32 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 46.43 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory