Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/0af5486f4dc6f9e76f0f56b6af1e8f/659_bNS-T1-TRNA-1_A23MVY2LT4_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/01/abfbefebb896799a5a678a07d0dacb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/abfbefebb896799a5a678a07d0dacb/.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 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 659_bNS-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam --METRICS_FILE 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:57:32.362 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:57:32 GMT 2026] MarkDuplicates --INPUT 659_bNS-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam --METRICS_FILE 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:57:32 GMT 2026] Executing as ?@nf-01abfbefebb896799a5a678a07d0dacb-c56c6-86ffh on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO	2026-06-08 08:57:32	MarkDuplicates	Start of doWork freeMemory: 105492088; totalMemory: 134217728; maxMemory: 63585648640
INFO	2026-06-08 08:57:32	MarkDuplicates	Reading input file and constructing read end information.
INFO	2026-06-08 08:57:32	MarkDuplicates	Will retain up to 230382784 data points before spilling to disk.
INFO	2026-06-08 08:57:36	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:02s.  Time for last 1,000,000:    2s.  Last read position: chr1:1,336,084
INFO	2026-06-08 08:57:36	MarkDuplicates	Tracking 3822 as yet unmatched pairs. 340 records in RAM.
INFO	2026-06-08 08:57:38	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    2s.  Last read position: chr1:2,189,601
INFO	2026-06-08 08:57:38	MarkDuplicates	Tracking 7394 as yet unmatched pairs. 348 records in RAM.
INFO	2026-06-08 08:57:40	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    1s.  Last read position: chr1:6,785,547
INFO	2026-06-08 08:57:40	MarkDuplicates	Tracking 13864 as yet unmatched pairs. 3180 records in RAM.
INFO	2026-06-08 08:57:42	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    2s.  Last read position: chr1:9,653,570
INFO	2026-06-08 08:57:42	MarkDuplicates	Tracking 13484 as yet unmatched pairs. 63 records in RAM.
INFO	2026-06-08 08:57:44	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    1s.  Last read position: chr1:12,276,136
INFO	2026-06-08 08:57:44	MarkDuplicates	Tracking 16786 as yet unmatched pairs. 323 records in RAM.
INFO	2026-06-08 08:57:46	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    2s.  Last read position: chr1:16,936,689
INFO	2026-06-08 08:57:46	MarkDuplicates	Tracking 19490 as yet unmatched pairs. 208 records in RAM.
INFO	2026-06-08 08:57:49	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    2s.  Last read position: chr1:19,597,089
INFO	2026-06-08 08:57:49	MarkDuplicates	Tracking 25185 as yet unmatched pairs. 2856 records in RAM.
INFO	2026-06-08 08:57:51	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    2s.  Last read position: chr1:21,834,841
INFO	2026-06-08 08:57:51	MarkDuplicates	Tracking 26152 as yet unmatched pairs. 769 records in RAM.
INFO	2026-06-08 08:57:54	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    2s.  Last read position: chr1:22,521,646
INFO	2026-06-08 08:57:54	MarkDuplicates	Tracking 28757 as yet unmatched pairs. 196 records in RAM.
INFO	2026-06-08 08:57:56	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    2s.  Last read position: chr1:23,337,761
INFO	2026-06-08 08:57:56	MarkDuplicates	Tracking 32644 as yet unmatched pairs. 1225 records in RAM.
INFO	2026-06-08 08:57:58	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    1s.  Last read position: chr1:26,284,144
INFO	2026-06-08 08:57:58	MarkDuplicates	Tracking 35004 as yet unmatched pairs. 730 records in RAM.
INFO	2026-06-08 08:57:59	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    1s.  Last read position: chr1:27,550,669
INFO	2026-06-08 08:57:59	MarkDuplicates	Tracking 37589 as yet unmatched pairs. 419 records in RAM.
INFO	2026-06-08 08:58:02	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    2s.  Last read position: chr1:31,028,805
INFO	2026-06-08 08:58:02	MarkDuplicates	Tracking 41122 as yet unmatched pairs. 900 records in RAM.
INFO	2026-06-08 08:58:04	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    2s.  Last read position: chr1:32,754,121
INFO	2026-06-08 08:58:04	MarkDuplicates	Tracking 44090 as yet unmatched pairs. 753 records in RAM.
INFO	2026-06-08 08:58:05	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    1s.  Last read position: chr1:35,609,262
INFO	2026-06-08 08:58:05	MarkDuplicates	Tracking 47564 as yet unmatched pairs. 1156 records in RAM.
INFO	2026-06-08 08:58:07	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    1s.  Last read position: chr1:39,283,944
INFO	2026-06-08 08:58:07	MarkDuplicates	Tracking 50351 as yet unmatched pairs. 866 records in RAM.
INFO	2026-06-08 08:58:09	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    1s.  Last read position: chr1:39,562,370
INFO	2026-06-08 08:58:09	MarkDuplicates	Tracking 53870 as yet unmatched pairs. 1823 records in RAM.
INFO	2026-06-08 08:58:12	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    2s.  Last read position: chr1:43,307,226
INFO	2026-06-08 08:58:12	MarkDuplicates	Tracking 55492 as yet unmatched pairs. 434 records in RAM.
INFO	2026-06-08 08:58:14	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    2s.  Last read position: chr1:44,776,680
INFO	2026-06-08 08:58:14	MarkDuplicates	Tracking 66561 as yet unmatched pairs. 8316 records in RAM.
INFO	2026-06-08 08:58:16	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    2s.  Last read position: chr1:47,219,011
INFO	2026-06-08 08:58:16	MarkDuplicates	Tracking 61112 as yet unmatched pairs. 163 records in RAM.
INFO	2026-06-08 08:58:18	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    1s.  Last read position: chr1:54,787,720
INFO	2026-06-08 08:58:18	MarkDuplicates	Tracking 63961 as yet unmatched pairs. 132 records in RAM.
INFO	2026-06-08 08:58:20	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    2s.  Last read position: chr1:65,570,718
INFO	2026-06-08 08:58:20	MarkDuplicates	Tracking 66960 as yet unmatched pairs. 172 records in RAM.
INFO	2026-06-08 08:58:22	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    1s.  Last read position: chr1:85,581,490
INFO	2026-06-08 08:58:22	MarkDuplicates	Tracking 71585 as yet unmatched pairs. 2038 records in RAM.
INFO	2026-06-08 08:58:24	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    1s.  Last read position: chr1:94,821,028
INFO	2026-06-08 08:58:24	MarkDuplicates	Tracking 72564 as yet unmatched pairs. 311 records in RAM.
INFO	2026-06-08 08:58:25	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    1s.  Last read position: chr1:109,237,750
INFO	2026-06-08 08:58:25	MarkDuplicates	Tracking 75268 as yet unmatched pairs. 571 records in RAM.
INFO	2026-06-08 08:58:27	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    2s.  Last read position: chr1:112,699,710
INFO	2026-06-08 08:58:27	MarkDuplicates	Tracking 77873 as yet unmatched pairs. 278 records in RAM.
INFO	2026-06-08 08:58:29	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    1s.  Last read position: chr1:114,730,523
INFO	2026-06-08 08:58:29	MarkDuplicates	Tracking 81695 as yet unmatched pairs. 1335 records in RAM.
INFO	2026-06-08 08:58:30	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    1s.  Last read position: chr1:119,919,404
INFO	2026-06-08 08:58:30	MarkDuplicates	Tracking 85916 as yet unmatched pairs. 2949 records in RAM.
INFO	2026-06-08 08:58:32	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    1s.  Last read position: chr1:120,833,707
INFO	2026-06-08 08:58:32	MarkDuplicates	Tracking 85930 as yet unmatched pairs. 468 records in RAM.
INFO	2026-06-08 08:58:34	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    1s.  Last read position: chr1:146,156,461
INFO	2026-06-08 08:58:34	MarkDuplicates	Tracking 88743 as yet unmatched pairs. 1464 records in RAM.
INFO	2026-06-08 08:58:35	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    1s.  Last read position: chr1:148,953,038
INFO	2026-06-08 08:58:35	MarkDuplicates	Tracking 89257 as yet unmatched pairs. 411 records in RAM.
INFO	2026-06-08 08:58:37	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    2s.  Last read position: chr1:150,081,390
INFO	2026-06-08 08:58:37	MarkDuplicates	Tracking 91173 as yet unmatched pairs. 533 records in RAM.
INFO	2026-06-08 08:58:39	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    1s.  Last read position: chr1:150,747,781
INFO	2026-06-08 08:58:39	MarkDuplicates	Tracking 94822 as yet unmatched pairs. 1316 records in RAM.
INFO	2026-06-08 08:58:41	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    2s.  Last read position: chr1:151,400,177
INFO	2026-06-08 08:58:41	MarkDuplicates	Tracking 97904 as yet unmatched pairs. 1637 records in RAM.
INFO	2026-06-08 08:58:43	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    2s.  Last read position: chr1:153,662,446
INFO	2026-06-08 08:58:43	MarkDuplicates	Tracking 99898 as yet unmatched pairs. 895 records in RAM.
INFO	2026-06-08 08:58:45	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    2s.  Last read position: chr1:154,172,973
INFO	2026-06-08 08:58:45	MarkDuplicates	Tracking 107735 as yet unmatched pairs. 6029 records in RAM.
INFO	2026-06-08 08:58:47	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    1s.  Last read position: chr1:154,929,081
INFO	2026-06-08 08:58:47	MarkDuplicates	Tracking 105134 as yet unmatched pairs. 718 records in RAM.
INFO	2026-06-08 08:58:49	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    2s.  Last read position: chr1:155,186,070
INFO	2026-06-08 08:58:49	MarkDuplicates	Tracking 114534 as yet unmatched pairs. 6848 records in RAM.
INFO	2026-06-08 08:58:51	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    1s.  Last read position: chr1:155,190,062
INFO	2026-06-08 08:58:51	MarkDuplicates	Tracking 112273 as yet unmatched pairs. 2500 records in RAM.
INFO	2026-06-08 08:58:53	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    1s.  Last read position: chr1:155,346,468
INFO	2026-06-08 08:58:53	MarkDuplicates	Tracking 112173 as yet unmatched pairs. 332 records in RAM.
INFO	2026-06-08 08:58:55	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    1s.  Last read position: chr1:156,070,286
INFO	2026-06-08 08:58:55	MarkDuplicates	Tracking 114825 as yet unmatched pairs. 403 records in RAM.
INFO	2026-06-08 08:58:56	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    1s.  Last read position: chr1:156,138,822
INFO	2026-06-08 08:58:56	MarkDuplicates	Tracking 124895 as yet unmatched pairs. 6849 records in RAM.
INFO	2026-06-08 08:58:58	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    2s.  Last read position: chr1:157,125,810
INFO	2026-06-08 08:58:58	MarkDuplicates	Tracking 121330 as yet unmatched pairs. 298 records in RAM.
INFO	2026-06-08 08:59:00	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    1s.  Last read position: chr1:160,420,429
INFO	2026-06-08 08:59:00	MarkDuplicates	Tracking 123821 as yet unmatched pairs. 123 records in RAM.
INFO	2026-06-08 08:59:01	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    1s.  Last read position: chr1:161,544,834
INFO	2026-06-08 08:59:01	MarkDuplicates	Tracking 127894 as yet unmatched pairs. 1368 records in RAM.
INFO	2026-06-08 08:59:03	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    1s.  Last read position: chr1:168,312,705
INFO	2026-06-08 08:59:03	MarkDuplicates	Tracking 129491 as yet unmatched pairs. 120 records in RAM.
INFO	2026-06-08 08:59:04	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    1s.  Last read position: chr1:171,796,549
INFO	2026-06-08 08:59:04	MarkDuplicates	Tracking 132326 as yet unmatched pairs. 232 records in RAM.
INFO	2026-06-08 08:59:06	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    1s.  Last read position: chr1:180,632,108
INFO	2026-06-08 08:59:06	MarkDuplicates	Tracking 135883 as yet unmatched pairs. 1101 records in RAM.
INFO	2026-06-08 08:59:08	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    1s.  Last read position: chr1:183,132,453
INFO	2026-06-08 08:59:08	MarkDuplicates	Tracking 138187 as yet unmatched pairs. 368 records in RAM.
INFO	2026-06-08 08:59:10	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    1s.  Last read position: chr1:186,336,568
INFO	2026-06-08 08:59:10	MarkDuplicates	Tracking 141682 as yet unmatched pairs. 1251 records in RAM.
INFO	2026-06-08 08:59:11	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    1s.  Last read position: chr1:200,909,142
INFO	2026-06-08 08:59:11	MarkDuplicates	Tracking 143229 as yet unmatched pairs. 307 records in RAM.
INFO	2026-06-08 08:59:13	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:    2s.  Last read position: chr1:202,944,987
INFO	2026-06-08 08:59:13	MarkDuplicates	Tracking 148344 as yet unmatched pairs. 2435 records in RAM.
INFO	2026-06-08 08:59:15	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    1s.  Last read position: chr1:204,259,366
INFO	2026-06-08 08:59:15	MarkDuplicates	Tracking 149113 as yet unmatched pairs. 498 records in RAM.
INFO	2026-06-08 08:59:17	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    1s.  Last read position: chr1:206,934,419
INFO	2026-06-08 08:59:17	MarkDuplicates	Tracking 152726 as yet unmatched pairs. 1443 records in RAM.
INFO	2026-06-08 08:59:18	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    1s.  Last read position: chr1:207,359,552
INFO	2026-06-08 08:59:18	MarkDuplicates	Tracking 156255 as yet unmatched pairs. 2118 records in RAM.
INFO	2026-06-08 08:59:20	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    1s.  Last read position: chr1:211,663,322
INFO	2026-06-08 08:59:20	MarkDuplicates	Tracking 156862 as yet unmatched pairs. 23 records in RAM.
INFO	2026-06-08 08:59:22	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    1s.  Last read position: chr1:223,544,800
INFO	2026-06-08 08:59:22	MarkDuplicates	Tracking 159672 as yet unmatched pairs. 162 records in RAM.
INFO	2026-06-08 08:59:24	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    2s.  Last read position: chr1:225,519,489
INFO	2026-06-08 08:59:24	MarkDuplicates	Tracking 162463 as yet unmatched pairs. 193 records in RAM.
INFO	2026-06-08 08:59:26	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    2s.  Last read position: chr1:226,736,761
INFO	2026-06-08 08:59:26	MarkDuplicates	Tracking 166028 as yet unmatched pairs. 1006 records in RAM.
INFO	2026-06-08 08:59:27	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    1s.  Last read position: chr1:228,743,282
INFO	2026-06-08 08:59:27	MarkDuplicates	Tracking 169189 as yet unmatched pairs. 533 records in RAM.
INFO	2026-06-08 08:59:30	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:    2s.  Last read position: chr1:234,609,404
INFO	2026-06-08 08:59:30	MarkDuplicates	Tracking 172749 as yet unmatched pairs. 822 records in RAM.
INFO	2026-06-08 08:59:32	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    1s.  Last read position: chr1:244,841,946
INFO	2026-06-08 08:59:32	MarkDuplicates	Tracking 175404 as yet unmatched pairs. 705 records in RAM.
INFO	2026-06-08 08:59:35	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    3s.  Last read position: chr2:1,684,080
INFO	2026-06-08 08:59:35	MarkDuplicates	Tracking 177977 as yet unmatched pairs. 176626 records in RAM.
INFO	2026-06-08 08:59:37	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    2s.  Last read position: chr2:20,037,592
INFO	2026-06-08 08:59:37	MarkDuplicates	Tracking 182861 as yet unmatched pairs. 181481 records in RAM.
INFO	2026-06-08 08:59:39	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    2s.  Last read position: chr2:25,743,905
INFO	2026-06-08 08:59:39	MarkDuplicates	Tracking 183991 as yet unmatched pairs. 182599 records in RAM.
INFO	2026-06-08 08:59:41	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    1s.  Last read position: chr2:28,657,682
INFO	2026-06-08 08:59:41	MarkDuplicates	Tracking 186985 as yet unmatched pairs. 185555 records in RAM.
INFO	2026-06-08 08:59:43	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    2s.  Last read position: chr2:32,916,253
INFO	2026-06-08 08:59:43	MarkDuplicates	Tracking 235629 as yet unmatched pairs. 185332 records in RAM.
INFO	2026-06-08 08:59:44	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    1s.  Last read position: chr2:32,916,264
INFO	2026-06-08 08:59:44	MarkDuplicates	Tracking 392382 as yet unmatched pairs. 176135 records in RAM.
INFO	2026-06-08 08:59:47	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    2s.  Last read position: chr2:32,916,264
INFO	2026-06-08 08:59:47	MarkDuplicates	Tracking 1080661 as yet unmatched pairs. 134904 records in RAM.
INFO	2026-06-08 08:59:49	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    1s.  Last read position: chr2:32,916,406
INFO	2026-06-08 08:59:49	MarkDuplicates	Tracking 1496664 as yet unmatched pairs. 109580 records in RAM.
INFO	2026-06-08 08:59:50	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    1s.  Last read position: chr2:32,916,406
INFO	2026-06-08 08:59:50	MarkDuplicates	Tracking 1501507 as yet unmatched pairs. 109310 records in RAM.
INFO	2026-06-08 08:59:51	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    1s.  Last read position: chr2:36,476,953
INFO	2026-06-08 08:59:51	MarkDuplicates	Tracking 1591038 as yet unmatched pairs. 104140 records in RAM.
INFO	2026-06-08 08:59:53	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    1s.  Last read position: chr2:42,708,938
INFO	2026-06-08 08:59:53	MarkDuplicates	Tracking 1587844 as yet unmatched pairs. 100927 records in RAM.
INFO	2026-06-08 08:59:55	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    2s.  Last read position: chr2:46,382,486
INFO	2026-06-08 08:59:55	MarkDuplicates	Tracking 1587324 as yet unmatched pairs. 100370 records in RAM.
INFO	2026-06-08 08:59:57	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    1s.  Last read position: chr2:54,649,146
INFO	2026-06-08 08:59:57	MarkDuplicates	Tracking 1583238 as yet unmatched pairs. 96247 records in RAM.
INFO	2026-06-08 08:59:59	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    1s.  Last read position: chr2:61,839,777
INFO	2026-06-08 08:59:59	MarkDuplicates	Tracking 1578697 as yet unmatched pairs. 91684 records in RAM.
INFO	2026-06-08 09:00:01	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    1s.  Last read position: chr2:70,087,839
INFO	2026-06-08 09:00:01	MarkDuplicates	Tracking 1577464 as yet unmatched pairs. 90420 records in RAM.
INFO	2026-06-08 09:00:02	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    1s.  Last read position: chr2:74,370,230
INFO	2026-06-08 09:00:02	MarkDuplicates	Tracking 1573664 as yet unmatched pairs. 86601 records in RAM.
INFO	2026-06-08 09:00:04	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    1s.  Last read position: chr2:85,550,940
INFO	2026-06-08 09:00:04	MarkDuplicates	Tracking 1570683 as yet unmatched pairs. 83606 records in RAM.
INFO	2026-06-08 09:00:06	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    1s.  Last read position: chr2:85,663,706
INFO	2026-06-08 09:00:06	MarkDuplicates	Tracking 1593676 as yet unmatched pairs. 106540 records in RAM.
INFO	2026-06-08 09:00:08	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    1s.  Last read position: chr2:85,667,147
INFO	2026-06-08 09:00:08	MarkDuplicates	Tracking 1585987 as yet unmatched pairs. 98822 records in RAM.
INFO	2026-06-08 09:00:10	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    2s.  Last read position: chr2:95,288,494
INFO	2026-06-08 09:00:10	MarkDuplicates	Tracking 1562456 as yet unmatched pairs. 75269 records in RAM.
INFO	2026-06-08 09:00:12	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:    1s.  Last read position: chr2:99,376,626
INFO	2026-06-08 09:00:12	MarkDuplicates	Tracking 1558257 as yet unmatched pairs. 71042 records in RAM.
INFO	2026-06-08 09:00:13	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    1s.  Last read position: chr2:108,754,925
INFO	2026-06-08 09:00:13	MarkDuplicates	Tracking 1557207 as yet unmatched pairs. 69975 records in RAM.
INFO	2026-06-08 09:00:15	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    2s.  Last read position: chr2:111,847,733
INFO	2026-06-08 09:00:15	MarkDuplicates	Tracking 1554088 as yet unmatched pairs. 66848 records in RAM.
INFO	2026-06-08 09:00:18	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    2s.  Last read position: chr2:121,216,610
INFO	2026-06-08 09:00:18	MarkDuplicates	Tracking 1551670 as yet unmatched pairs. 64416 records in RAM.
INFO	2026-06-08 09:00:20	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    1s.  Last read position: chr2:135,058,027
INFO	2026-06-08 09:00:20	MarkDuplicates	Tracking 1549331 as yet unmatched pairs. 62036 records in RAM.
INFO	2026-06-08 09:00:21	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    1s.  Last read position: chr2:157,415,631
INFO	2026-06-08 09:00:21	MarkDuplicates	Tracking 1546729 as yet unmatched pairs. 59420 records in RAM.
INFO	2026-06-08 09:00:23	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    1s.  Last read position: chr2:169,238,255
INFO	2026-06-08 09:00:23	MarkDuplicates	Tracking 1543614 as yet unmatched pairs. 56290 records in RAM.
INFO	2026-06-08 09:00:25	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    1s.  Last read position: chr2:177,219,143
INFO	2026-06-08 09:00:25	MarkDuplicates	Tracking 1542459 as yet unmatched pairs. 55102 records in RAM.
INFO	2026-06-08 09:00:27	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    1s.  Last read position: chr2:188,974,417
INFO	2026-06-08 09:00:27	MarkDuplicates	Tracking 1541347 as yet unmatched pairs. 53965 records in RAM.
INFO	2026-06-08 09:00:28	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    1s.  Last read position: chr2:189,039,411
INFO	2026-06-08 09:00:28	MarkDuplicates	Tracking 1536529 as yet unmatched pairs. 49120 records in RAM.
INFO	2026-06-08 09:00:30	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    1s.  Last read position: chr2:191,835,953
INFO	2026-06-08 09:00:30	MarkDuplicates	Tracking 1534688 as yet unmatched pairs. 47259 records in RAM.
INFO	2026-06-08 09:00:32	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    1s.  Last read position: chr2:201,193,077
INFO	2026-06-08 09:00:32	MarkDuplicates	Tracking 1530100 as yet unmatched pairs. 42657 records in RAM.
INFO	2026-06-08 09:00:34	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    1s.  Last read position: chr2:207,711,993
INFO	2026-06-08 09:00:34	MarkDuplicates	Tracking 1527505 as yet unmatched pairs. 40037 records in RAM.
INFO	2026-06-08 09:00:36	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    1s.  Last read position: chr2:215,367,908
INFO	2026-06-08 09:00:36	MarkDuplicates	Tracking 1532870 as yet unmatched pairs. 45384 records in RAM.
INFO	2026-06-08 09:00:37	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    1s.  Last read position: chr2:215,372,356
INFO	2026-06-08 09:00:37	MarkDuplicates	Tracking 1542648 as yet unmatched pairs. 55160 records in RAM.
INFO	2026-06-08 09:00:39	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    1s.  Last read position: chr2:215,379,251
INFO	2026-06-08 09:00:39	MarkDuplicates	Tracking 1537939 as yet unmatched pairs. 50427 records in RAM.
INFO	2026-06-08 09:00:41	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    1s.  Last read position: chr2:215,388,283
INFO	2026-06-08 09:00:41	MarkDuplicates	Tracking 1534726 as yet unmatched pairs. 47214 records in RAM.
INFO	2026-06-08 09:00:43	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,406,252
INFO	2026-06-08 09:00:43	MarkDuplicates	Tracking 1527927 as yet unmatched pairs. 40411 records in RAM.
INFO	2026-06-08 09:00:45	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    1s.  Last read position: chr2:215,410,105
INFO	2026-06-08 09:00:45	MarkDuplicates	Tracking 1523149 as yet unmatched pairs. 35625 records in RAM.
INFO	2026-06-08 09:00:47	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    2s.  Last read position: chr2:215,428,267
INFO	2026-06-08 09:00:47	MarkDuplicates	Tracking 1519766 as yet unmatched pairs. 32237 records in RAM.
INFO	2026-06-08 09:00:49	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    1s.  Last read position: chr2:216,499,354
INFO	2026-06-08 09:00:49	MarkDuplicates	Tracking 1522126 as yet unmatched pairs. 34581 records in RAM.
INFO	2026-06-08 09:00:51	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    1s.  Last read position: chr2:218,385,099
INFO	2026-06-08 09:00:51	MarkDuplicates	Tracking 1503988 as yet unmatched pairs. 16425 records in RAM.
INFO	2026-06-08 09:00:52	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:    1s.  Last read position: chr2:219,570,689
INFO	2026-06-08 09:00:52	MarkDuplicates	Tracking 1500738 as yet unmatched pairs. 13151 records in RAM.
INFO	2026-06-08 09:00:54	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    2s.  Last read position: chr2:231,455,190
INFO	2026-06-08 09:00:54	MarkDuplicates	Tracking 1498170 as yet unmatched pairs. 10552 records in RAM.
INFO	2026-06-08 09:00:56	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    1s.  Last read position: chr2:237,340,726
INFO	2026-06-08 09:00:56	MarkDuplicates	Tracking 1497081 as yet unmatched pairs. 9446 records in RAM.
INFO	2026-06-08 09:00:58	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    1s.  Last read position: chr2:237,518,594
INFO	2026-06-08 09:00:58	MarkDuplicates	Tracking 1493121 as yet unmatched pairs. 5472 records in RAM.
INFO	2026-06-08 09:01:00	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    1s.  Last read position: chr2:241,239,719
INFO	2026-06-08 09:01:00	MarkDuplicates	Tracking 1490020 as yet unmatched pairs. 2353 records in RAM.
INFO	2026-06-08 09:01:02	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    2s.  Last read position: chr3:9,450,254
INFO	2026-06-08 09:01:02	MarkDuplicates	Tracking 1486518 as yet unmatched pairs. 78469 records in RAM.
INFO	2026-06-08 09:01:04	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    1s.  Last read position: chr3:12,839,450
INFO	2026-06-08 09:01:04	MarkDuplicates	Tracking 1488403 as yet unmatched pairs. 80329 records in RAM.
INFO	2026-06-08 09:01:06	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    1s.  Last read position: chr3:17,010,816
INFO	2026-06-08 09:01:06	MarkDuplicates	Tracking 1480955 as yet unmatched pairs. 72850 records in RAM.
INFO	2026-06-08 09:01:07	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    1s.  Last read position: chr3:33,581,715
INFO	2026-06-08 09:01:07	MarkDuplicates	Tracking 1478097 as yet unmatched pairs. 69962 records in RAM.
INFO	2026-06-08 09:01:09	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    1s.  Last read position: chr3:39,411,697
INFO	2026-06-08 09:01:09	MarkDuplicates	Tracking 1480467 as yet unmatched pairs. 72312 records in RAM.
INFO	2026-06-08 09:01:11	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    1s.  Last read position: chr3:42,698,708
INFO	2026-06-08 09:01:11	MarkDuplicates	Tracking 1472145 as yet unmatched pairs. 63974 records in RAM.
INFO	2026-06-08 09:01:13	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    2s.  Last read position: chr3:47,411,897
INFO	2026-06-08 09:01:13	MarkDuplicates	Tracking 1469378 as yet unmatched pairs. 61186 records in RAM.
INFO	2026-06-08 09:01:15	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    2s.  Last read position: chr3:48,694,831
INFO	2026-06-08 09:01:15	MarkDuplicates	Tracking 1467591 as yet unmatched pairs. 59390 records in RAM.
INFO	2026-06-08 09:01:17	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    2s.  Last read position: chr3:49,163,136
INFO	2026-06-08 09:01:17	MarkDuplicates	Tracking 1462945 as yet unmatched pairs. 54719 records in RAM.
INFO	2026-06-08 09:01:19	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    1s.  Last read position: chr3:50,065,030
INFO	2026-06-08 09:01:19	MarkDuplicates	Tracking 1459802 as yet unmatched pairs. 51561 records in RAM.
INFO	2026-06-08 09:01:21	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    1s.  Last read position: chr3:51,993,707
INFO	2026-06-08 09:01:21	MarkDuplicates	Tracking 1457593 as yet unmatched pairs. 49334 records in RAM.
INFO	2026-06-08 09:01:22	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    1s.  Last read position: chr3:52,737,585
INFO	2026-06-08 09:01:22	MarkDuplicates	Tracking 1453887 as yet unmatched pairs. 45622 records in RAM.
INFO	2026-06-08 09:01:24	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    1s.  Last read position: chr3:58,169,632
INFO	2026-06-08 09:01:24	MarkDuplicates	Tracking 1451922 as yet unmatched pairs. 43618 records in RAM.
INFO	2026-06-08 09:01:26	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    1s.  Last read position: chr3:73,384,524
INFO	2026-06-08 09:01:26	MarkDuplicates	Tracking 1448498 as yet unmatched pairs. 40149 records in RAM.
INFO	2026-06-08 09:01:28	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    1s.  Last read position: chr3:100,794,959
INFO	2026-06-08 09:01:28	MarkDuplicates	Tracking 1446053 as yet unmatched pairs. 37664 records in RAM.
INFO	2026-06-08 09:01:30	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    2s.  Last read position: chr3:113,026,797
INFO	2026-06-08 09:01:30	MarkDuplicates	Tracking 1443154 as yet unmatched pairs. 34744 records in RAM.
INFO	2026-06-08 09:01:32	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    1s.  Last read position: chr3:122,577,841
INFO	2026-06-08 09:01:32	MarkDuplicates	Tracking 1440671 as yet unmatched pairs. 32235 records in RAM.
INFO	2026-06-08 09:01:33	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    1s.  Last read position: chr3:127,005,006
INFO	2026-06-08 09:01:33	MarkDuplicates	Tracking 1438151 as yet unmatched pairs. 29680 records in RAM.
INFO	2026-06-08 09:01:35	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:04:01s.  Time for last 1,000,000:    1s.  Last read position: chr3:129,302,099
INFO	2026-06-08 09:01:35	MarkDuplicates	Tracking 1434897 as yet unmatched pairs. 26409 records in RAM.
INFO	2026-06-08 09:01:37	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    1s.  Last read position: chr3:133,945,240
INFO	2026-06-08 09:01:37	MarkDuplicates	Tracking 1431975 as yet unmatched pairs. 23468 records in RAM.
INFO	2026-06-08 09:01:38	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:    1s.  Last read position: chr3:143,028,333
INFO	2026-06-08 09:01:38	MarkDuplicates	Tracking 1429375 as yet unmatched pairs. 20864 records in RAM.
INFO	2026-06-08 09:01:41	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    2s.  Last read position: chr3:151,448,111
INFO	2026-06-08 09:01:41	MarkDuplicates	Tracking 1426388 as yet unmatched pairs. 17862 records in RAM.
INFO	2026-06-08 09:01:43	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    1s.  Last read position: chr3:161,429,466
INFO	2026-06-08 09:01:43	MarkDuplicates	Tracking 1423410 as yet unmatched pairs. 14860 records in RAM.
INFO	2026-06-08 09:01:44	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    1s.  Last read position: chr3:179,656,789
INFO	2026-06-08 09:01:44	MarkDuplicates	Tracking 1421203 as yet unmatched pairs. 12609 records in RAM.
INFO	2026-06-08 09:01:46	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    1s.  Last read position: chr3:184,317,474
INFO	2026-06-08 09:01:46	MarkDuplicates	Tracking 1419139 as yet unmatched pairs. 10525 records in RAM.
INFO	2026-06-08 09:01:48	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    1s.  Last read position: chr3:187,729,245
INFO	2026-06-08 09:01:48	MarkDuplicates	Tracking 1416391 as yet unmatched pairs. 7768 records in RAM.
INFO	2026-06-08 09:01:50	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:    1s.  Last read position: chr3:194,359,829
INFO	2026-06-08 09:01:50	MarkDuplicates	Tracking 1413115 as yet unmatched pairs. 4461 records in RAM.
INFO	2026-06-08 09:01:51	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    1s.  Last read position: chr3:195,782,695
INFO	2026-06-08 09:01:51	MarkDuplicates	Tracking 1413150 as yet unmatched pairs. 4489 records in RAM.
INFO	2026-06-08 09:01:53	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    1s.  Last read position: chr3:198,134,341
INFO	2026-06-08 09:01:53	MarkDuplicates	Tracking 1408683 as yet unmatched pairs. 0 records in RAM.
INFO	2026-06-08 09:01:55	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    2s.  Last read position: chr4:1,717,154
INFO	2026-06-08 09:01:55	MarkDuplicates	Tracking 1406277 as yet unmatched pairs. 66756 records in RAM.
INFO	2026-06-08 09:01:57	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    1s.  Last read position: chr4:3,187,815
INFO	2026-06-08 09:01:57	MarkDuplicates	Tracking 1402254 as yet unmatched pairs. 62725 records in RAM.
INFO	2026-06-08 09:01:59	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    1s.  Last read position: chr4:8,227,452
INFO	2026-06-08 09:01:59	MarkDuplicates	Tracking 1398963 as yet unmatched pairs. 59410 records in RAM.
INFO	2026-06-08 09:02:00	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    1s.  Last read position: chr4:24,795,612
INFO	2026-06-08 09:02:00	MarkDuplicates	Tracking 1396672 as yet unmatched pairs. 57083 records in RAM.
INFO	2026-06-08 09:02:02	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    1s.  Last read position: chr4:25,662,733
INFO	2026-06-08 09:02:02	MarkDuplicates	Tracking 1457428 as yet unmatched pairs. 117816 records in RAM.
INFO	2026-06-08 09:02:04	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:04:30s.  Time for last 1,000,000:    1s.  Last read position: chr4:25,666,135
INFO	2026-06-08 09:02:04	MarkDuplicates	Tracking 1457714 as yet unmatched pairs. 118102 records in RAM.
INFO	2026-06-08 09:02:06	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    1s.  Last read position: chr4:25,669,645
INFO	2026-06-08 09:02:06	MarkDuplicates	Tracking 1432375 as yet unmatched pairs. 92747 records in RAM.
INFO	2026-06-08 09:02:09	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    2s.  Last read position: chr4:25,671,678
INFO	2026-06-08 09:02:09	MarkDuplicates	Tracking 1448690 as yet unmatched pairs. 109055 records in RAM.
INFO	2026-06-08 09:02:11	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    1s.  Last read position: chr4:25,674,331
INFO	2026-06-08 09:02:11	MarkDuplicates	Tracking 1412138 as yet unmatched pairs. 72483 records in RAM.
INFO	2026-06-08 09:02:12	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:    1s.  Last read position: chr4:25,676,212
INFO	2026-06-08 09:02:12	MarkDuplicates	Tracking 1434075 as yet unmatched pairs. 94420 records in RAM.
INFO	2026-06-08 09:02:14	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    1s.  Last read position: chr4:25,676,533
INFO	2026-06-08 09:02:14	MarkDuplicates	Tracking 1420947 as yet unmatched pairs. 81276 records in RAM.
INFO	2026-06-08 09:02:16	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    1s.  Last read position: chr4:39,103,288
INFO	2026-06-08 09:02:16	MarkDuplicates	Tracking 1374734 as yet unmatched pairs. 35049 records in RAM.
INFO	2026-06-08 09:02:17	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    1s.  Last read position: chr4:42,464,790
INFO	2026-06-08 09:02:17	MarkDuplicates	Tracking 1371818 as yet unmatched pairs. 32115 records in RAM.
INFO	2026-06-08 09:02:19	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    1s.  Last read position: chr4:56,483,261
INFO	2026-06-08 09:02:19	MarkDuplicates	Tracking 1369265 as yet unmatched pairs. 29544 records in RAM.
INFO	2026-06-08 09:02:20	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:04:47s.  Time for last 1,000,000:    1s.  Last read position: chr4:73,870,736
INFO	2026-06-08 09:02:20	MarkDuplicates	Tracking 1366352 as yet unmatched pairs. 26603 records in RAM.
INFO	2026-06-08 09:02:22	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    1s.  Last read position: chr4:77,871,744
INFO	2026-06-08 09:02:22	MarkDuplicates	Tracking 1363607 as yet unmatched pairs. 23849 records in RAM.
INFO	2026-06-08 09:02:24	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    1s.  Last read position: chr4:87,131,130
INFO	2026-06-08 09:02:24	MarkDuplicates	Tracking 1361151 as yet unmatched pairs. 21382 records in RAM.
INFO	2026-06-08 09:02:25	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:04:51s.  Time for last 1,000,000:    1s.  Last read position: chr4:99,076,407
INFO	2026-06-08 09:02:25	MarkDuplicates	Tracking 1358779 as yet unmatched pairs. 18984 records in RAM.
INFO	2026-06-08 09:02:27	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    2s.  Last read position: chr4:107,989,977
INFO	2026-06-08 09:02:27	MarkDuplicates	Tracking 1356593 as yet unmatched pairs. 16774 records in RAM.
INFO	2026-06-08 09:02:29	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:04:55s.  Time for last 1,000,000:    1s.  Last read position: chr4:121,671,574
INFO	2026-06-08 09:02:29	MarkDuplicates	Tracking 1353839 as yet unmatched pairs. 13995 records in RAM.
INFO	2026-06-08 09:02:31	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    2s.  Last read position: chr4:140,153,205
INFO	2026-06-08 09:02:31	MarkDuplicates	Tracking 1350286 as yet unmatched pairs. 10421 records in RAM.
INFO	2026-06-08 09:02:33	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    1s.  Last read position: chr4:151,102,999
INFO	2026-06-08 09:02:33	MarkDuplicates	Tracking 1353680 as yet unmatched pairs. 13797 records in RAM.
INFO	2026-06-08 09:02:35	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    1s.  Last read position: chr4:163,166,371
INFO	2026-06-08 09:02:35	MarkDuplicates	Tracking 1345027 as yet unmatched pairs. 5115 records in RAM.
INFO	2026-06-08 09:02:36	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    1s.  Last read position: chr4:183,280,879
INFO	2026-06-08 09:02:36	MarkDuplicates	Tracking 1342101 as yet unmatched pairs. 2175 records in RAM.
INFO	2026-06-08 09:02:39	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    2s.  Last read position: chr5:1,008,915
INFO	2026-06-08 09:02:39	MarkDuplicates	Tracking 1339034 as yet unmatched pairs. 106786 records in RAM.
INFO	2026-06-08 09:02:41	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    1s.  Last read position: chr5:6,633,715
INFO	2026-06-08 09:02:41	MarkDuplicates	Tracking 1335725 as yet unmatched pairs. 103456 records in RAM.
INFO	2026-06-08 09:02:43	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    1s.  Last read position: chr5:14,368,878
INFO	2026-06-08 09:02:43	MarkDuplicates	Tracking 1333186 as yet unmatched pairs. 100910 records in RAM.
INFO	2026-06-08 09:02:44	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    1s.  Last read position: chr5:17,354,217
INFO	2026-06-08 09:02:44	MarkDuplicates	Tracking 1329687 as yet unmatched pairs. 97375 records in RAM.
INFO	2026-06-08 09:02:46	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    1s.  Last read position: chr5:38,481,626
INFO	2026-06-08 09:02:46	MarkDuplicates	Tracking 1327881 as yet unmatched pairs. 95550 records in RAM.
INFO	2026-06-08 09:02:48	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    1s.  Last read position: chr5:43,535,578
INFO	2026-06-08 09:02:48	MarkDuplicates	Tracking 1325303 as yet unmatched pairs. 92964 records in RAM.
INFO	2026-06-08 09:02:49	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    1s.  Last read position: chr5:56,881,940
INFO	2026-06-08 09:02:49	MarkDuplicates	Tracking 1322108 as yet unmatched pairs. 89744 records in RAM.
INFO	2026-06-08 09:02:51	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    1s.  Last read position: chr5:69,419,437
INFO	2026-06-08 09:02:51	MarkDuplicates	Tracking 1319665 as yet unmatched pairs. 87290 records in RAM.
INFO	2026-06-08 09:02:53	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:05:19s.  Time for last 1,000,000:    1s.  Last read position: chr5:73,068,908
INFO	2026-06-08 09:02:53	MarkDuplicates	Tracking 1317755 as yet unmatched pairs. 85369 records in RAM.
INFO	2026-06-08 09:02:54	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    1s.  Last read position: chr5:79,616,299
INFO	2026-06-08 09:02:54	MarkDuplicates	Tracking 1315122 as yet unmatched pairs. 82703 records in RAM.
INFO	2026-06-08 09:02:57	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    2s.  Last read position: chr5:83,553,477
INFO	2026-06-08 09:02:57	MarkDuplicates	Tracking 1313690 as yet unmatched pairs. 81251 records in RAM.
INFO	2026-06-08 09:02:58	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:05:25s.  Time for last 1,000,000:    1s.  Last read position: chr5:96,702,827
INFO	2026-06-08 09:02:58	MarkDuplicates	Tracking 1312244 as yet unmatched pairs. 79771 records in RAM.
INFO	2026-06-08 09:03:00	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    1s.  Last read position: chr5:112,821,907
INFO	2026-06-08 09:03:00	MarkDuplicates	Tracking 1307264 as yet unmatched pairs. 74768 records in RAM.
INFO	2026-06-08 09:03:02	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    1s.  Last read position: chr5:126,810,301
INFO	2026-06-08 09:03:02	MarkDuplicates	Tracking 1304535 as yet unmatched pairs. 72018 records in RAM.
INFO	2026-06-08 09:03:04	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    1s.  Last read position: chr5:134,158,458
INFO	2026-06-08 09:03:04	MarkDuplicates	Tracking 1304781 as yet unmatched pairs. 72246 records in RAM.
INFO	2026-06-08 09:03:05	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:05:31s.  Time for last 1,000,000:    1s.  Last read position: chr5:138,345,465
INFO	2026-06-08 09:03:05	MarkDuplicates	Tracking 1299300 as yet unmatched pairs. 66751 records in RAM.
INFO	2026-06-08 09:03:07	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    1s.  Last read position: chr5:138,933,818
INFO	2026-06-08 09:03:07	MarkDuplicates	Tracking 1298566 as yet unmatched pairs. 66003 records in RAM.
INFO	2026-06-08 09:03:08	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:05:35s.  Time for last 1,000,000:    1s.  Last read position: chr5:140,647,296
INFO	2026-06-08 09:03:08	MarkDuplicates	Tracking 1293311 as yet unmatched pairs. 60721 records in RAM.
INFO	2026-06-08 09:03:10	MarkDuplicates	Read   181,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    1s.  Last read position: chr5:141,366,044
INFO	2026-06-08 09:03:10	MarkDuplicates	Tracking 1290662 as yet unmatched pairs. 58067 records in RAM.
INFO	2026-06-08 09:03:12	MarkDuplicates	Read   182,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    1s.  Last read position: chr5:142,314,172
INFO	2026-06-08 09:03:12	MarkDuplicates	Tracking 1288410 as yet unmatched pairs. 55809 records in RAM.
INFO	2026-06-08 09:03:13	MarkDuplicates	Read   183,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,050,294
INFO	2026-06-08 09:03:13	MarkDuplicates	Tracking 1285477 as yet unmatched pairs. 52840 records in RAM.
INFO	2026-06-08 09:03:15	MarkDuplicates	Read   184,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,379,668
INFO	2026-06-08 09:03:15	MarkDuplicates	Tracking 1281671 as yet unmatched pairs. 49027 records in RAM.
INFO	2026-06-08 09:03:17	MarkDuplicates	Read   185,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,402,233
INFO	2026-06-08 09:03:17	MarkDuplicates	Tracking 1380554 as yet unmatched pairs. 147906 records in RAM.
INFO	2026-06-08 09:03:19	MarkDuplicates	Read   186,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    2s.  Last read position: chr5:150,404,690
INFO	2026-06-08 09:03:19	MarkDuplicates	Tracking 1338225 as yet unmatched pairs. 105576 records in RAM.
INFO	2026-06-08 09:03:21	MarkDuplicates	Read   187,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    2s.  Last read position: chr5:150,405,144
INFO	2026-06-08 09:03:21	MarkDuplicates	Tracking 1398349 as yet unmatched pairs. 165693 records in RAM.
INFO	2026-06-08 09:03:23	MarkDuplicates	Read   188,000,000 records.  Elapsed time: 00:05:49s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,406,947
INFO	2026-06-08 09:03:23	MarkDuplicates	Tracking 1318577 as yet unmatched pairs. 85917 records in RAM.
INFO	2026-06-08 09:03:25	MarkDuplicates	Read   189,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,521,439
INFO	2026-06-08 09:03:25	MarkDuplicates	Tracking 1266645 as yet unmatched pairs. 33975 records in RAM.
INFO	2026-06-08 09:03:26	MarkDuplicates	Read   190,000,000 records.  Elapsed time: 00:05:52s.  Time for last 1,000,000:    1s.  Last read position: chr5:151,664,225
INFO	2026-06-08 09:03:26	MarkDuplicates	Tracking 1265636 as yet unmatched pairs. 32950 records in RAM.
INFO	2026-06-08 09:03:28	MarkDuplicates	Read   191,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    1s.  Last read position: chr5:157,314,982
INFO	2026-06-08 09:03:28	MarkDuplicates	Tracking 1260666 as yet unmatched pairs. 27954 records in RAM.
INFO	2026-06-08 09:03:30	MarkDuplicates	Read   192,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    1s.  Last read position: chr5:168,806,474
INFO	2026-06-08 09:03:30	MarkDuplicates	Tracking 1258656 as yet unmatched pairs. 25921 records in RAM.
INFO	2026-06-08 09:03:31	MarkDuplicates	Read   193,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:    1s.  Last read position: chr5:171,391,799
INFO	2026-06-08 09:03:31	MarkDuplicates	Tracking 1279188 as yet unmatched pairs. 46435 records in RAM.
INFO	2026-06-08 09:03:33	MarkDuplicates	Read   194,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    1s.  Last read position: chr5:172,670,065
INFO	2026-06-08 09:03:33	MarkDuplicates	Tracking 1253499 as yet unmatched pairs. 20739 records in RAM.
INFO	2026-06-08 09:03:35	MarkDuplicates	Read   195,000,000 records.  Elapsed time: 00:06:01s.  Time for last 1,000,000:    1s.  Last read position: chr5:176,651,762
INFO	2026-06-08 09:03:35	MarkDuplicates	Tracking 1250469 as yet unmatched pairs. 17694 records in RAM.
INFO	2026-06-08 09:03:36	MarkDuplicates	Read   196,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    1s.  Last read position: chr5:177,605,188
INFO	2026-06-08 09:03:36	MarkDuplicates	Tracking 1247085 as yet unmatched pairs. 14286 records in RAM.
INFO	2026-06-08 09:03:38	MarkDuplicates	Read   197,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    1s.  Last read position: chr5:179,765,847
INFO	2026-06-08 09:03:38	MarkDuplicates	Tracking 1244312 as yet unmatched pairs. 11499 records in RAM.
INFO	2026-06-08 09:03:40	MarkDuplicates	Read   198,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    1s.  Last read position: chr5:179,824,283
INFO	2026-06-08 09:03:40	MarkDuplicates	Tracking 1261854 as yet unmatched pairs. 29037 records in RAM.
INFO	2026-06-08 09:03:42	MarkDuplicates	Read   199,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    1s.  Last read position: chr5:180,335,800
INFO	2026-06-08 09:03:42	MarkDuplicates	Tracking 1237732 as yet unmatched pairs. 4913 records in RAM.
INFO	2026-06-08 09:03:43	MarkDuplicates	Read   200,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    1s.  Last read position: chr5:181,238,181
INFO	2026-06-08 09:03:43	MarkDuplicates	Tracking 1248616 as yet unmatched pairs. 15791 records in RAM.
INFO	2026-06-08 09:03:46	MarkDuplicates	Read   201,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    2s.  Last read position: chr6:4,892,159
INFO	2026-06-08 09:03:46	MarkDuplicates	Tracking 1231031 as yet unmatched pairs. 74417 records in RAM.
INFO	2026-06-08 09:03:47	MarkDuplicates	Read   202,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    1s.  Last read position: chr6:11,094,364
INFO	2026-06-08 09:03:47	MarkDuplicates	Tracking 1227785 as yet unmatched pairs. 71165 records in RAM.
INFO	2026-06-08 09:03:49	MarkDuplicates	Read   203,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    1s.  Last read position: chr6:20,649,321
INFO	2026-06-08 09:03:49	MarkDuplicates	Tracking 1225175 as yet unmatched pairs. 68520 records in RAM.
INFO	2026-06-08 09:03:50	MarkDuplicates	Read   204,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    1s.  Last read position: chr6:27,138,599
INFO	2026-06-08 09:03:50	MarkDuplicates	Tracking 1222635 as yet unmatched pairs. 65965 records in RAM.
INFO	2026-06-08 09:03:52	MarkDuplicates	Read   205,000,000 records.  Elapsed time: 00:06:18s.  Time for last 1,000,000:    1s.  Last read position: chr6:30,489,549
INFO	2026-06-08 09:03:52	MarkDuplicates	Tracking 1220356 as yet unmatched pairs. 63677 records in RAM.
INFO	2026-06-08 09:03:54	MarkDuplicates	Read   206,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    1s.  Last read position: chr6:30,987,127
INFO	2026-06-08 09:03:54	MarkDuplicates	Tracking 1217054 as yet unmatched pairs. 60367 records in RAM.
INFO	2026-06-08 09:03:56	MarkDuplicates	Read   207,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,630,619
INFO	2026-06-08 09:03:56	MarkDuplicates	Tracking 1214959 as yet unmatched pairs. 58264 records in RAM.
INFO	2026-06-08 09:03:58	MarkDuplicates	Read   208,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,816,454
INFO	2026-06-08 09:03:58	MarkDuplicates	Tracking 1211612 as yet unmatched pairs. 54902 records in RAM.
INFO	2026-06-08 09:03:59	MarkDuplicates	Read   209,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,958,335
INFO	2026-06-08 09:03:59	MarkDuplicates	Tracking 1209363 as yet unmatched pairs. 52645 records in RAM.
INFO	2026-06-08 09:04:01	MarkDuplicates	Read   210,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    1s.  Last read position: chr6:32,056,703
INFO	2026-06-08 09:04:01	MarkDuplicates	Tracking 1209949 as yet unmatched pairs. 53223 records in RAM.
INFO	2026-06-08 09:04:02	MarkDuplicates	Read   211,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    1s.  Last read position: chr6:32,200,836
INFO	2026-06-08 09:04:02	MarkDuplicates	Tracking 1205003 as yet unmatched pairs. 48265 records in RAM.
INFO	2026-06-08 09:04:04	MarkDuplicates	Read   212,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    1s.  Last read position: chr6:32,843,030
INFO	2026-06-08 09:04:04	MarkDuplicates	Tracking 1202755 as yet unmatched pairs. 46007 records in RAM.
INFO	2026-06-08 09:04:06	MarkDuplicates	Read   213,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    1s.  Last read position: chr6:33,269,164
INFO	2026-06-08 09:04:06	MarkDuplicates	Tracking 1198763 as yet unmatched pairs. 42007 records in RAM.
INFO	2026-06-08 09:04:07	MarkDuplicates	Read   214,000,000 records.  Elapsed time: 00:06:33s.  Time for last 1,000,000:    1s.  Last read position: chr6:33,680,374
INFO	2026-06-08 09:04:07	MarkDuplicates	Tracking 1196101 as yet unmatched pairs. 39334 records in RAM.
INFO	2026-06-08 09:04:09	MarkDuplicates	Read   215,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    1s.  Last read position: chr6:36,225,320
INFO	2026-06-08 09:04:09	MarkDuplicates	Tracking 1193099 as yet unmatched pairs. 36317 records in RAM.
INFO	2026-06-08 09:04:11	MarkDuplicates	Read   216,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    2s.  Last read position: chr6:42,057,409
INFO	2026-06-08 09:04:11	MarkDuplicates	Tracking 1189980 as yet unmatched pairs. 33174 records in RAM.
INFO	2026-06-08 09:04:13	MarkDuplicates	Read   217,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    2s.  Last read position: chr6:43,771,024
INFO	2026-06-08 09:04:13	MarkDuplicates	Tracking 1187571 as yet unmatched pairs. 30746 records in RAM.
INFO	2026-06-08 09:04:15	MarkDuplicates	Read   218,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    1s.  Last read position: chr6:49,447,690
INFO	2026-06-08 09:04:15	MarkDuplicates	Tracking 1183761 as yet unmatched pairs. 26920 records in RAM.
INFO	2026-06-08 09:04:17	MarkDuplicates	Read   219,000,000 records.  Elapsed time: 00:06:43s.  Time for last 1,000,000:    1s.  Last read position: chr6:73,519,427
INFO	2026-06-08 09:04:17	MarkDuplicates	Tracking 1183007 as yet unmatched pairs. 26110 records in RAM.
INFO	2026-06-08 09:04:18	MarkDuplicates	Read   220,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:    1s.  Last read position: chr6:89,080,838
INFO	2026-06-08 09:04:18	MarkDuplicates	Tracking 1182148 as yet unmatched pairs. 25224 records in RAM.
INFO	2026-06-08 09:04:20	MarkDuplicates	Read   221,000,000 records.  Elapsed time: 00:06:46s.  Time for last 1,000,000:    1s.  Last read position: chr6:109,446,341
INFO	2026-06-08 09:04:20	MarkDuplicates	Tracking 1176330 as yet unmatched pairs. 19403 records in RAM.
INFO	2026-06-08 09:04:21	MarkDuplicates	Read   222,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    1s.  Last read position: chr6:117,387,787
INFO	2026-06-08 09:04:21	MarkDuplicates	Tracking 1175546 as yet unmatched pairs. 18587 records in RAM.
INFO	2026-06-08 09:04:23	MarkDuplicates	Read   223,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    1s.  Last read position: chr6:131,135,699
INFO	2026-06-08 09:04:23	MarkDuplicates	Tracking 1170650 as yet unmatched pairs. 13655 records in RAM.
INFO	2026-06-08 09:04:24	MarkDuplicates	Read   224,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:    1s.  Last read position: chr6:139,373,786
INFO	2026-06-08 09:04:24	MarkDuplicates	Tracking 1170690 as yet unmatched pairs. 13688 records in RAM.
INFO	2026-06-08 09:04:26	MarkDuplicates	Read   225,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    1s.  Last read position: chr6:151,353,353
INFO	2026-06-08 09:04:26	MarkDuplicates	Tracking 1164940 as yet unmatched pairs. 7923 records in RAM.
INFO	2026-06-08 09:04:28	MarkDuplicates	Read   226,000,000 records.  Elapsed time: 00:06:54s.  Time for last 1,000,000:    1s.  Last read position: chr6:158,769,876
INFO	2026-06-08 09:04:28	MarkDuplicates	Tracking 1161977 as yet unmatched pairs. 4955 records in RAM.
INFO	2026-06-08 09:04:29	MarkDuplicates	Read   227,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    1s.  Last read position: chr6:163,566,728
INFO	2026-06-08 09:04:29	MarkDuplicates	Tracking 1162205 as yet unmatched pairs. 5178 records in RAM.
INFO	2026-06-08 09:04:32	MarkDuplicates	Read   228,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    3s.  Last read position: chr7:919,987
INFO	2026-06-08 09:04:32	MarkDuplicates	Tracking 1156729 as yet unmatched pairs. 76840 records in RAM.
INFO	2026-06-08 09:04:34	MarkDuplicates	Read   229,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    1s.  Last read position: chr7:5,312,622
INFO	2026-06-08 09:04:34	MarkDuplicates	Tracking 1153306 as yet unmatched pairs. 73395 records in RAM.
INFO	2026-06-08 09:04:36	MarkDuplicates	Read   230,000,000 records.  Elapsed time: 00:07:02s.  Time for last 1,000,000:    1s.  Last read position: chr7:5,528,041
INFO	2026-06-08 09:04:36	MarkDuplicates	Tracking 1175157 as yet unmatched pairs. 95226 records in RAM.
INFO	2026-06-08 09:04:38	MarkDuplicates	Read   231,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    2s.  Last read position: chr7:5,529,538
INFO	2026-06-08 09:04:38	MarkDuplicates	Tracking 1157991 as yet unmatched pairs. 78047 records in RAM.
INFO	2026-06-08 09:04:40	MarkDuplicates	Read   232,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    1s.  Last read position: chr7:16,610,603
INFO	2026-06-08 09:04:40	MarkDuplicates	Tracking 1143702 as yet unmatched pairs. 63738 records in RAM.
INFO	2026-06-08 09:04:41	MarkDuplicates	Read   233,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    1s.  Last read position: chr7:27,794,364
INFO	2026-06-08 09:04:41	MarkDuplicates	Tracking 1141312 as yet unmatched pairs. 61334 records in RAM.
INFO	2026-06-08 09:04:43	MarkDuplicates	Read   234,000,000 records.  Elapsed time: 00:07:09s.  Time for last 1,000,000:    1s.  Last read position: chr7:40,094,602
INFO	2026-06-08 09:04:43	MarkDuplicates	Tracking 1138423 as yet unmatched pairs. 58419 records in RAM.
INFO	2026-06-08 09:04:45	MarkDuplicates	Read   235,000,000 records.  Elapsed time: 00:07:11s.  Time for last 1,000,000:    1s.  Last read position: chr7:44,113,724
INFO	2026-06-08 09:04:45	MarkDuplicates	Tracking 1136306 as yet unmatched pairs. 56282 records in RAM.
INFO	2026-06-08 09:04:46	MarkDuplicates	Read   236,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    1s.  Last read position: chr7:47,439,625
INFO	2026-06-08 09:04:46	MarkDuplicates	Tracking 1132451 as yet unmatched pairs. 52411 records in RAM.
INFO	2026-06-08 09:04:48	MarkDuplicates	Read   237,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    1s.  Last read position: chr7:56,079,760
INFO	2026-06-08 09:04:48	MarkDuplicates	Tracking 1130821 as yet unmatched pairs. 50777 records in RAM.
INFO	2026-06-08 09:04:49	MarkDuplicates	Read   238,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    1s.  Last read position: chr7:73,297,194
INFO	2026-06-08 09:04:49	MarkDuplicates	Tracking 1127608 as yet unmatched pairs. 47553 records in RAM.
INFO	2026-06-08 09:04:51	MarkDuplicates	Read   239,000,000 records.  Elapsed time: 00:07:17s.  Time for last 1,000,000:    1s.  Last read position: chr7:74,746,380
INFO	2026-06-08 09:04:51	MarkDuplicates	Tracking 1124449 as yet unmatched pairs. 44372 records in RAM.
INFO	2026-06-08 09:04:53	MarkDuplicates	Read   240,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    1s.  Last read position: chr7:76,302,841
INFO	2026-06-08 09:04:53	MarkDuplicates	Tracking 1130280 as yet unmatched pairs. 50184 records in RAM.
INFO	2026-06-08 09:04:54	MarkDuplicates	Read   241,000,000 records.  Elapsed time: 00:07:20s.  Time for last 1,000,000:    1s.  Last read position: chr7:84,983,705
INFO	2026-06-08 09:04:54	MarkDuplicates	Tracking 1119351 as yet unmatched pairs. 39249 records in RAM.
INFO	2026-06-08 09:04:56	MarkDuplicates	Read   242,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    1s.  Last read position: chr7:94,404,558
INFO	2026-06-08 09:04:56	MarkDuplicates	Tracking 1124098 as yet unmatched pairs. 43986 records in RAM.
INFO	2026-06-08 09:04:57	MarkDuplicates	Read   243,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    1s.  Last read position: chr7:94,428,354
INFO	2026-06-08 09:04:57	MarkDuplicates	Tracking 1115434 as yet unmatched pairs. 35312 records in RAM.
INFO	2026-06-08 09:04:59	MarkDuplicates	Read   244,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    1s.  Last read position: chr7:99,423,808
INFO	2026-06-08 09:04:59	MarkDuplicates	Tracking 1110787 as yet unmatched pairs. 30649 records in RAM.
INFO	2026-06-08 09:05:01	MarkDuplicates	Read   245,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,578,417
INFO	2026-06-08 09:05:01	MarkDuplicates	Tracking 1108084 as yet unmatched pairs. 27937 records in RAM.
INFO	2026-06-08 09:06:00	MarkDuplicates	Read   246,000,000 records.  Elapsed time: 00:08:26s.  Time for last 1,000,000:   59s.  Last read position: chr7:101,316,496
INFO	2026-06-08 09:06:00	MarkDuplicates	Tracking 1104712 as yet unmatched pairs. 24564 records in RAM.
INFO	2026-06-08 09:06:02	MarkDuplicates	Read   247,000,000 records.  Elapsed time: 00:08:28s.  Time for last 1,000,000:    1s.  Last read position: chr7:102,660,211
INFO	2026-06-08 09:06:02	MarkDuplicates	Tracking 1104129 as yet unmatched pairs. 23980 records in RAM.
INFO	2026-06-08 09:06:04	MarkDuplicates	Read   248,000,000 records.  Elapsed time: 00:08:30s.  Time for last 1,000,000:    1s.  Last read position: chr7:111,740,893
INFO	2026-06-08 09:06:04	MarkDuplicates	Tracking 1100593 as yet unmatched pairs. 20429 records in RAM.
INFO	2026-06-08 09:06:06	MarkDuplicates	Read   249,000,000 records.  Elapsed time: 00:08:32s.  Time for last 1,000,000:    1s.  Last read position: chr7:122,663,469
INFO	2026-06-08 09:06:06	MarkDuplicates	Tracking 1098877 as yet unmatched pairs. 18704 records in RAM.
INFO	2026-06-08 09:06:07	MarkDuplicates	Read   250,000,000 records.  Elapsed time: 00:08:33s.  Time for last 1,000,000:    1s.  Last read position: chr7:128,479,176
INFO	2026-06-08 09:06:07	MarkDuplicates	Tracking 1095296 as yet unmatched pairs. 15107 records in RAM.
INFO	2026-06-08 09:06:09	MarkDuplicates	Read   251,000,000 records.  Elapsed time: 00:08:35s.  Time for last 1,000,000:    1s.  Last read position: chr7:137,513,841
INFO	2026-06-08 09:06:09	MarkDuplicates	Tracking 1092747 as yet unmatched pairs. 12534 records in RAM.
INFO	2026-06-08 09:06:10	MarkDuplicates	Read   252,000,000 records.  Elapsed time: 00:08:37s.  Time for last 1,000,000:    1s.  Last read position: chr7:140,800,409
INFO	2026-06-08 09:06:10	MarkDuplicates	Tracking 1090122 as yet unmatched pairs. 9906 records in RAM.
INFO	2026-06-08 09:06:12	MarkDuplicates	Read   253,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:    1s.  Last read position: chr7:149,154,070
INFO	2026-06-08 09:06:12	MarkDuplicates	Tracking 1086989 as yet unmatched pairs. 6761 records in RAM.
INFO	2026-06-08 09:06:14	MarkDuplicates	Read   254,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:    1s.  Last read position: chr7:151,081,630
INFO	2026-06-08 09:06:14	MarkDuplicates	Tracking 1084673 as yet unmatched pairs. 4437 records in RAM.
INFO	2026-06-08 09:06:15	MarkDuplicates	Read   255,000,000 records.  Elapsed time: 00:08:41s.  Time for last 1,000,000:    1s.  Last read position: chr7:158,759,452
INFO	2026-06-08 09:06:15	MarkDuplicates	Tracking 1081619 as yet unmatched pairs. 1366 records in RAM.
INFO	2026-06-08 09:06:18	MarkDuplicates	Read   256,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    2s.  Last read position: chr8:11,847,785
INFO	2026-06-08 09:06:18	MarkDuplicates	Tracking 1081883 as yet unmatched pairs. 65752 records in RAM.
INFO	2026-06-08 09:06:19	MarkDuplicates	Read   257,000,000 records.  Elapsed time: 00:08:45s.  Time for last 1,000,000:    1s.  Last read position: chr8:18,075,561
INFO	2026-06-08 09:06:19	MarkDuplicates	Tracking 1075389 as yet unmatched pairs. 59246 records in RAM.
INFO	2026-06-08 09:06:21	MarkDuplicates	Read   258,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    1s.  Last read position: chr8:22,164,030
INFO	2026-06-08 09:06:21	MarkDuplicates	Tracking 1077191 as yet unmatched pairs. 61035 records in RAM.
INFO	2026-06-08 09:06:23	MarkDuplicates	Read   259,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    2s.  Last read position: chr8:23,111,757
INFO	2026-06-08 09:06:23	MarkDuplicates	Tracking 1069460 as yet unmatched pairs. 53296 records in RAM.
INFO	2026-06-08 09:06:25	MarkDuplicates	Read   260,000,000 records.  Elapsed time: 00:08:51s.  Time for last 1,000,000:    1s.  Last read position: chr8:28,113,018
INFO	2026-06-08 09:06:25	MarkDuplicates	Tracking 1065807 as yet unmatched pairs. 49629 records in RAM.
INFO	2026-06-08 09:06:26	MarkDuplicates	Read   261,000,000 records.  Elapsed time: 00:08:52s.  Time for last 1,000,000:    1s.  Last read position: chr8:37,844,684
INFO	2026-06-08 09:06:26	MarkDuplicates	Tracking 1062879 as yet unmatched pairs. 46683 records in RAM.
INFO	2026-06-08 09:06:28	MarkDuplicates	Read   262,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    1s.  Last read position: chr8:38,820,199
INFO	2026-06-08 09:06:28	MarkDuplicates	Tracking 1063267 as yet unmatched pairs. 47064 records in RAM.
INFO	2026-06-08 09:06:29	MarkDuplicates	Read   263,000,000 records.  Elapsed time: 00:08:55s.  Time for last 1,000,000:    1s.  Last read position: chr8:42,398,733
INFO	2026-06-08 09:06:29	MarkDuplicates	Tracking 1058185 as yet unmatched pairs. 41976 records in RAM.
INFO	2026-06-08 09:06:31	MarkDuplicates	Read   264,000,000 records.  Elapsed time: 00:08:57s.  Time for last 1,000,000:    1s.  Last read position: chr8:53,967,972
INFO	2026-06-08 09:06:31	MarkDuplicates	Tracking 1054685 as yet unmatched pairs. 38470 records in RAM.
INFO	2026-06-08 09:06:33	MarkDuplicates	Read   265,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:    1s.  Last read position: chr8:65,745,411
INFO	2026-06-08 09:06:33	MarkDuplicates	Tracking 1051793 as yet unmatched pairs. 35565 records in RAM.
INFO	2026-06-08 09:06:34	MarkDuplicates	Read   266,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    1s.  Last read position: chr8:76,704,551
INFO	2026-06-08 09:06:34	MarkDuplicates	Tracking 1049564 as yet unmatched pairs. 33324 records in RAM.
INFO	2026-06-08 09:06:36	MarkDuplicates	Read   267,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    1s.  Last read position: chr8:96,593,563
INFO	2026-06-08 09:06:36	MarkDuplicates	Tracking 1047197 as yet unmatched pairs. 30941 records in RAM.
INFO	2026-06-08 09:06:38	MarkDuplicates	Read   268,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    1s.  Last read position: chr8:100,713,086
INFO	2026-06-08 09:06:38	MarkDuplicates	Tracking 1046847 as yet unmatched pairs. 30582 records in RAM.
INFO	2026-06-08 09:06:39	MarkDuplicates	Read   269,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:    1s.  Last read position: chr8:108,217,377
INFO	2026-06-08 09:06:39	MarkDuplicates	Tracking 1043308 as yet unmatched pairs. 27023 records in RAM.
INFO	2026-06-08 09:06:41	MarkDuplicates	Read   270,000,000 records.  Elapsed time: 00:09:07s.  Time for last 1,000,000:    1s.  Last read position: chr8:123,253,717
INFO	2026-06-08 09:06:41	MarkDuplicates	Tracking 1038403 as yet unmatched pairs. 22097 records in RAM.
INFO	2026-06-08 09:06:42	MarkDuplicates	Read   271,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    1s.  Last read position: chr8:132,794,410
INFO	2026-06-08 09:06:42	MarkDuplicates	Tracking 1035339 as yet unmatched pairs. 19020 records in RAM.
INFO	2026-06-08 09:06:44	MarkDuplicates	Read   272,000,000 records.  Elapsed time: 00:09:10s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,021,701
INFO	2026-06-08 09:06:44	MarkDuplicates	Tracking 1034738 as yet unmatched pairs. 18405 records in RAM.
INFO	2026-06-08 09:06:45	MarkDuplicates	Read   273,000,000 records.  Elapsed time: 00:09:12s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,816,559
INFO	2026-06-08 09:06:45	MarkDuplicates	Tracking 1028983 as yet unmatched pairs. 12636 records in RAM.
INFO	2026-06-08 09:06:47	MarkDuplicates	Read   274,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,864,850
INFO	2026-06-08 09:06:47	MarkDuplicates	Tracking 1027202 as yet unmatched pairs. 10855 records in RAM.
INFO	2026-06-08 09:06:48	MarkDuplicates	Read   275,000,000 records.  Elapsed time: 00:09:14s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,924,398
INFO	2026-06-08 09:06:48	MarkDuplicates	Tracking 1024333 as yet unmatched pairs. 7970 records in RAM.
INFO	2026-06-08 09:06:50	MarkDuplicates	Read   276,000,000 records.  Elapsed time: 00:09:16s.  Time for last 1,000,000:    1s.  Last read position: chr8:144,179,543
INFO	2026-06-08 09:06:50	MarkDuplicates	Tracking 1020448 as yet unmatched pairs. 4077 records in RAM.
INFO	2026-06-08 09:06:51	MarkDuplicates	Read   277,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:    1s.  Last read position: chr8:144,842,127
INFO	2026-06-08 09:06:51	MarkDuplicates	Tracking 1016879 as yet unmatched pairs. 503 records in RAM.
INFO	2026-06-08 09:06:53	MarkDuplicates	Read   278,000,000 records.  Elapsed time: 00:09:19s.  Time for last 1,000,000:    1s.  Last read position: chr9:14,120,523
INFO	2026-06-08 09:06:53	MarkDuplicates	Tracking 1018135 as yet unmatched pairs. 61223 records in RAM.
INFO	2026-06-08 09:06:55	MarkDuplicates	Read   279,000,000 records.  Elapsed time: 00:09:21s.  Time for last 1,000,000:    1s.  Last read position: chr9:32,572,801
INFO	2026-06-08 09:06:55	MarkDuplicates	Tracking 1011831 as yet unmatched pairs. 54899 records in RAM.
INFO	2026-06-08 09:06:57	MarkDuplicates	Read   280,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    1s.  Last read position: chr9:35,072,337
INFO	2026-06-08 09:06:57	MarkDuplicates	Tracking 1009779 as yet unmatched pairs. 52843 records in RAM.
INFO	2026-06-08 09:06:58	MarkDuplicates	Read   281,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    1s.  Last read position: chr9:36,147,838
INFO	2026-06-08 09:06:58	MarkDuplicates	Tracking 1006072 as yet unmatched pairs. 49129 records in RAM.
INFO	2026-06-08 09:07:00	MarkDuplicates	Read   282,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    1s.  Last read position: chr9:72,909,702
INFO	2026-06-08 09:07:00	MarkDuplicates	Tracking 1002938 as yet unmatched pairs. 45976 records in RAM.
INFO	2026-06-08 09:07:02	MarkDuplicates	Read   283,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    1s.  Last read position: chr9:87,700,199
INFO	2026-06-08 09:07:02	MarkDuplicates	Tracking 1000180 as yet unmatched pairs. 43205 records in RAM.
INFO	2026-06-08 09:07:03	MarkDuplicates	Read   284,000,000 records.  Elapsed time: 00:09:29s.  Time for last 1,000,000:    1s.  Last read position: chr9:94,441,007
INFO	2026-06-08 09:07:03	MarkDuplicates	Tracking 997374 as yet unmatched pairs. 40379 records in RAM.
INFO	2026-06-08 09:07:05	MarkDuplicates	Read   285,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:    1s.  Last read position: chr9:104,817,351
INFO	2026-06-08 09:07:05	MarkDuplicates	Tracking 994600 as yet unmatched pairs. 37587 records in RAM.
INFO	2026-06-08 09:07:06	MarkDuplicates	Read   286,000,000 records.  Elapsed time: 00:09:32s.  Time for last 1,000,000:    1s.  Last read position: chr9:111,897,176
INFO	2026-06-08 09:07:06	MarkDuplicates	Tracking 991875 as yet unmatched pairs. 34850 records in RAM.
INFO	2026-06-08 09:07:08	MarkDuplicates	Read   287,000,000 records.  Elapsed time: 00:09:34s.  Time for last 1,000,000:    1s.  Last read position: chr9:115,035,282
INFO	2026-06-08 09:07:08	MarkDuplicates	Tracking 991564 as yet unmatched pairs. 34530 records in RAM.
INFO	2026-06-08 09:07:10	MarkDuplicates	Read   288,000,000 records.  Elapsed time: 00:09:36s.  Time for last 1,000,000:    1s.  Last read position: chr9:121,302,125
INFO	2026-06-08 09:07:10	MarkDuplicates	Tracking 986783 as yet unmatched pairs. 29748 records in RAM.
INFO	2026-06-08 09:07:11	MarkDuplicates	Read   289,000,000 records.  Elapsed time: 00:09:37s.  Time for last 1,000,000:    1s.  Last read position: chr9:125,241,061
INFO	2026-06-08 09:07:11	MarkDuplicates	Tracking 984659 as yet unmatched pairs. 27613 records in RAM.
INFO	2026-06-08 09:07:13	MarkDuplicates	Read   290,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    1s.  Last read position: chr9:127,872,821
INFO	2026-06-08 09:07:13	MarkDuplicates	Tracking 979887 as yet unmatched pairs. 22829 records in RAM.
INFO	2026-06-08 09:07:15	MarkDuplicates	Read   291,000,000 records.  Elapsed time: 00:09:41s.  Time for last 1,000,000:    1s.  Last read position: chr9:128,693,703
INFO	2026-06-08 09:07:15	MarkDuplicates	Tracking 976900 as yet unmatched pairs. 19832 records in RAM.
INFO	2026-06-08 09:07:16	MarkDuplicates	Read   292,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:    1s.  Last read position: chr9:130,872,146
INFO	2026-06-08 09:07:16	MarkDuplicates	Tracking 975590 as yet unmatched pairs. 18518 records in RAM.
INFO	2026-06-08 09:07:18	MarkDuplicates	Read   293,000,000 records.  Elapsed time: 00:09:44s.  Time for last 1,000,000:    1s.  Last read position: chr9:132,376,022
INFO	2026-06-08 09:07:18	MarkDuplicates	Tracking 970445 as yet unmatched pairs. 13366 records in RAM.
INFO	2026-06-08 09:07:20	MarkDuplicates	Read   294,000,000 records.  Elapsed time: 00:09:46s.  Time for last 1,000,000:    1s.  Last read position: chr9:134,730,350
INFO	2026-06-08 09:07:20	MarkDuplicates	Tracking 967658 as yet unmatched pairs. 10562 records in RAM.
INFO	2026-06-08 09:07:21	MarkDuplicates	Read   295,000,000 records.  Elapsed time: 00:09:48s.  Time for last 1,000,000:    1s.  Last read position: chr9:136,464,446
INFO	2026-06-08 09:07:21	MarkDuplicates	Tracking 964626 as yet unmatched pairs. 7527 records in RAM.
INFO	2026-06-08 09:07:23	MarkDuplicates	Read   296,000,000 records.  Elapsed time: 00:09:49s.  Time for last 1,000,000:    1s.  Last read position: chr9:136,979,999
INFO	2026-06-08 09:07:23	MarkDuplicates	Tracking 962952 as yet unmatched pairs. 5840 records in RAM.
INFO	2026-06-08 09:07:25	MarkDuplicates	Read   297,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:    1s.  Last read position: chr9:137,744,079
INFO	2026-06-08 09:07:25	MarkDuplicates	Tracking 957480 as yet unmatched pairs. 356 records in RAM.
INFO	2026-06-08 09:07:27	MarkDuplicates	Read   298,000,000 records.  Elapsed time: 00:09:53s.  Time for last 1,000,000:    2s.  Last read position: chr10:7,566,142
INFO	2026-06-08 09:07:27	MarkDuplicates	Tracking 954823 as yet unmatched pairs. 53923 records in RAM.
INFO	2026-06-08 09:07:29	MarkDuplicates	Read   299,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    1s.  Last read position: chr10:17,898,033
INFO	2026-06-08 09:07:29	MarkDuplicates	Tracking 951861 as yet unmatched pairs. 50931 records in RAM.
INFO	2026-06-08 09:07:30	MarkDuplicates	Read   300,000,000 records.  Elapsed time: 00:09:57s.  Time for last 1,000,000:    1s.  Last read position: chr10:30,027,526
INFO	2026-06-08 09:07:30	MarkDuplicates	Tracking 949228 as yet unmatched pairs. 48281 records in RAM.
INFO	2026-06-08 09:07:32	MarkDuplicates	Read   301,000,000 records.  Elapsed time: 00:09:58s.  Time for last 1,000,000:    1s.  Last read position: chr10:34,382,590
INFO	2026-06-08 09:07:32	MarkDuplicates	Tracking 946575 as yet unmatched pairs. 45611 records in RAM.
INFO	2026-06-08 09:07:34	MarkDuplicates	Read   302,000,000 records.  Elapsed time: 00:10:00s.  Time for last 1,000,000:    1s.  Last read position: chr10:46,010,788
INFO	2026-06-08 09:07:34	MarkDuplicates	Tracking 946070 as yet unmatched pairs. 45080 records in RAM.
INFO	2026-06-08 09:07:35	MarkDuplicates	Read   303,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    1s.  Last read position: chr10:59,653,673
INFO	2026-06-08 09:07:35	MarkDuplicates	Tracking 941679 as yet unmatched pairs. 40678 records in RAM.
INFO	2026-06-08 09:07:37	MarkDuplicates	Read   304,000,000 records.  Elapsed time: 00:10:03s.  Time for last 1,000,000:    1s.  Last read position: chr10:69,227,206
INFO	2026-06-08 09:07:37	MarkDuplicates	Tracking 938664 as yet unmatched pairs. 37652 records in RAM.
INFO	2026-06-08 09:07:39	MarkDuplicates	Read   305,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:    1s.  Last read position: chr10:72,274,972
INFO	2026-06-08 09:07:39	MarkDuplicates	Tracking 943232 as yet unmatched pairs. 42204 records in RAM.
INFO	2026-06-08 09:07:40	MarkDuplicates	Read   306,000,000 records.  Elapsed time: 00:10:06s.  Time for last 1,000,000:    1s.  Last read position: chr10:74,842,995
INFO	2026-06-08 09:07:40	MarkDuplicates	Tracking 932686 as yet unmatched pairs. 31640 records in RAM.
INFO	2026-06-08 09:07:42	MarkDuplicates	Read   307,000,000 records.  Elapsed time: 00:10:08s.  Time for last 1,000,000:    1s.  Last read position: chr10:79,557,362
INFO	2026-06-08 09:07:42	MarkDuplicates	Tracking 956832 as yet unmatched pairs. 55760 records in RAM.
INFO	2026-06-08 09:07:44	MarkDuplicates	Read   308,000,000 records.  Elapsed time: 00:10:10s.  Time for last 1,000,000:    1s.  Last read position: chr10:79,610,905
INFO	2026-06-08 09:07:44	MarkDuplicates	Tracking 926793 as yet unmatched pairs. 25708 records in RAM.
INFO	2026-06-08 09:07:45	MarkDuplicates	Read   309,000,000 records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:    1s.  Last read position: chr10:80,082,161
INFO	2026-06-08 09:07:45	MarkDuplicates	Tracking 924933 as yet unmatched pairs. 23845 records in RAM.
INFO	2026-06-08 09:07:46	MarkDuplicates	Read   310,000,000 records.  Elapsed time: 00:10:13s.  Time for last 1,000,000:    1s.  Last read position: chr10:88,941,311
INFO	2026-06-08 09:07:46	MarkDuplicates	Tracking 922586 as yet unmatched pairs. 21479 records in RAM.
INFO	2026-06-08 09:07:48	MarkDuplicates	Read   311,000,000 records.  Elapsed time: 00:10:14s.  Time for last 1,000,000:    1s.  Last read position: chr10:95,867,010
INFO	2026-06-08 09:07:48	MarkDuplicates	Tracking 919146 as yet unmatched pairs. 18033 records in RAM.
INFO	2026-06-08 09:07:50	MarkDuplicates	Read   312,000,000 records.  Elapsed time: 00:10:16s.  Time for last 1,000,000:    1s.  Last read position: chr10:100,529,420
INFO	2026-06-08 09:07:50	MarkDuplicates	Tracking 917458 as yet unmatched pairs. 16337 records in RAM.
INFO	2026-06-08 09:07:51	MarkDuplicates	Read   313,000,000 records.  Elapsed time: 00:10:17s.  Time for last 1,000,000:    1s.  Last read position: chr10:102,656,853
INFO	2026-06-08 09:07:51	MarkDuplicates	Tracking 914478 as yet unmatched pairs. 13334 records in RAM.
INFO	2026-06-08 09:07:53	MarkDuplicates	Read   314,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:    1s.  Last read position: chr10:113,777,549
INFO	2026-06-08 09:07:53	MarkDuplicates	Tracking 910286 as yet unmatched pairs. 9128 records in RAM.
INFO	2026-06-08 09:07:55	MarkDuplicates	Read   315,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:    1s.  Last read position: chr10:121,960,365
INFO	2026-06-08 09:07:55	MarkDuplicates	Tracking 907713 as yet unmatched pairs. 6538 records in RAM.
INFO	2026-06-08 09:07:56	MarkDuplicates	Read   316,000,000 records.  Elapsed time: 00:10:22s.  Time for last 1,000,000:    1s.  Last read position: chr10:122,606,040
INFO	2026-06-08 09:07:56	MarkDuplicates	Tracking 907318 as yet unmatched pairs. 6139 records in RAM.
INFO	2026-06-08 09:07:57	MarkDuplicates	Read   317,000,000 records.  Elapsed time: 00:10:24s.  Time for last 1,000,000:    1s.  Last read position: chr10:128,056,160
INFO	2026-06-08 09:07:57	MarkDuplicates	Tracking 904128 as yet unmatched pairs. 2928 records in RAM.
INFO	2026-06-08 09:08:00	MarkDuplicates	Read   318,000,000 records.  Elapsed time: 00:10:26s.  Time for last 1,000,000:    2s.  Last read position: chr11:290,935
INFO	2026-06-08 09:08:00	MarkDuplicates	Tracking 903452 as yet unmatched pairs. 138756 records in RAM.
INFO	2026-06-08 09:08:02	MarkDuplicates	Read   319,000,000 records.  Elapsed time: 00:10:28s.  Time for last 1,000,000:    1s.  Last read position: chr11:320,566
INFO	2026-06-08 09:08:02	MarkDuplicates	Tracking 912889 as yet unmatched pairs. 148189 records in RAM.
INFO	2026-06-08 09:08:04	MarkDuplicates	Read   320,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    1s.  Last read position: chr11:721,952
INFO	2026-06-08 09:08:04	MarkDuplicates	Tracking 894823 as yet unmatched pairs. 130114 records in RAM.
INFO	2026-06-08 09:08:05	MarkDuplicates	Read   321,000,000 records.  Elapsed time: 00:10:31s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,223,160
INFO	2026-06-08 09:08:05	MarkDuplicates	Tracking 903246 as yet unmatched pairs. 138527 records in RAM.
INFO	2026-06-08 09:08:07	MarkDuplicates	Read   322,000,000 records.  Elapsed time: 00:10:33s.  Time for last 1,000,000:    2s.  Last read position: chr11:1,241,047
INFO	2026-06-08 09:08:07	MarkDuplicates	Tracking 894872 as yet unmatched pairs. 130146 records in RAM.
INFO	2026-06-08 09:08:09	MarkDuplicates	Read   323,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,243,207
INFO	2026-06-08 09:08:09	MarkDuplicates	Tracking 889665 as yet unmatched pairs. 124934 records in RAM.
INFO	2026-06-08 09:08:10	MarkDuplicates	Read   324,000,000 records.  Elapsed time: 00:10:36s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,244,060
INFO	2026-06-08 09:08:10	MarkDuplicates	Tracking 892069 as yet unmatched pairs. 127333 records in RAM.
INFO	2026-06-08 09:08:12	MarkDuplicates	Read   325,000,000 records.  Elapsed time: 00:10:38s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,245,047
INFO	2026-06-08 09:08:12	MarkDuplicates	Tracking 887451 as yet unmatched pairs. 122715 records in RAM.
INFO	2026-06-08 09:08:13	MarkDuplicates	Read   326,000,000 records.  Elapsed time: 00:10:40s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,245,888
INFO	2026-06-08 09:08:13	MarkDuplicates	Tracking 890467 as yet unmatched pairs. 125724 records in RAM.
INFO	2026-06-08 09:08:15	MarkDuplicates	Read   327,000,000 records.  Elapsed time: 00:10:41s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,247,223
INFO	2026-06-08 09:08:15	MarkDuplicates	Tracking 899883 as yet unmatched pairs. 135138 records in RAM.
INFO	2026-06-08 09:08:16	MarkDuplicates	Read   328,000,000 records.  Elapsed time: 00:10:43s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,248,105
INFO	2026-06-08 09:08:16	MarkDuplicates	Tracking 883969 as yet unmatched pairs. 119224 records in RAM.
INFO	2026-06-08 09:08:18	MarkDuplicates	Read   329,000,000 records.  Elapsed time: 00:10:44s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,249,037
INFO	2026-06-08 09:08:18	MarkDuplicates	Tracking 883763 as yet unmatched pairs. 119009 records in RAM.
INFO	2026-06-08 09:08:19	MarkDuplicates	Read   330,000,000 records.  Elapsed time: 00:10:46s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,250,289
INFO	2026-06-08 09:08:19	MarkDuplicates	Tracking 882633 as yet unmatched pairs. 117879 records in RAM.
INFO	2026-06-08 09:08:21	MarkDuplicates	Read   331,000,000 records.  Elapsed time: 00:10:47s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,254,282
INFO	2026-06-08 09:08:21	MarkDuplicates	Tracking 878380 as yet unmatched pairs. 113624 records in RAM.
INFO	2026-06-08 09:08:23	MarkDuplicates	Read   332,000,000 records.  Elapsed time: 00:10:49s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,753,865
INFO	2026-06-08 09:08:23	MarkDuplicates	Tracking 882275 as yet unmatched pairs. 117507 records in RAM.
INFO	2026-06-08 09:08:24	MarkDuplicates	Read   333,000,000 records.  Elapsed time: 00:10:50s.  Time for last 1,000,000:    1s.  Last read position: chr11:1,880,185
INFO	2026-06-08 09:08:24	MarkDuplicates	Tracking 868107 as yet unmatched pairs. 103332 records in RAM.
INFO	2026-06-08 09:08:26	MarkDuplicates	Read   334,000,000 records.  Elapsed time: 00:10:52s.  Time for last 1,000,000:    1s.  Last read position: chr11:3,967,593
INFO	2026-06-08 09:08:26	MarkDuplicates	Tracking 865157 as yet unmatched pairs. 100372 records in RAM.
INFO	2026-06-08 09:08:28	MarkDuplicates	Read   335,000,000 records.  Elapsed time: 00:10:54s.  Time for last 1,000,000:    1s.  Last read position: chr11:7,987,628
INFO	2026-06-08 09:08:28	MarkDuplicates	Tracking 862987 as yet unmatched pairs. 98193 records in RAM.
INFO	2026-06-08 09:08:30	MarkDuplicates	Read   336,000,000 records.  Elapsed time: 00:10:56s.  Time for last 1,000,000:    1s.  Last read position: chr11:10,778,683
INFO	2026-06-08 09:08:30	MarkDuplicates	Tracking 858135 as yet unmatched pairs. 93333 records in RAM.
INFO	2026-06-08 09:08:31	MarkDuplicates	Read   337,000,000 records.  Elapsed time: 00:10:57s.  Time for last 1,000,000:    1s.  Last read position: chr11:16,791,160
INFO	2026-06-08 09:08:31	MarkDuplicates	Tracking 855582 as yet unmatched pairs. 90752 records in RAM.
INFO	2026-06-08 09:08:33	MarkDuplicates	Read   338,000,000 records.  Elapsed time: 00:10:59s.  Time for last 1,000,000:    1s.  Last read position: chr11:28,330,359
INFO	2026-06-08 09:08:33	MarkDuplicates	Tracking 852594 as yet unmatched pairs. 87752 records in RAM.
INFO	2026-06-08 09:08:35	MarkDuplicates	Read   339,000,000 records.  Elapsed time: 00:11:01s.  Time for last 1,000,000:    1s.  Last read position: chr11:35,180,383
INFO	2026-06-08 09:08:35	MarkDuplicates	Tracking 850504 as yet unmatched pairs. 85656 records in RAM.
INFO	2026-06-08 09:08:36	MarkDuplicates	Read   340,000,000 records.  Elapsed time: 00:11:03s.  Time for last 1,000,000:    1s.  Last read position: chr11:46,382,311
INFO	2026-06-08 09:08:36	MarkDuplicates	Tracking 848969 as yet unmatched pairs. 84112 records in RAM.
INFO	2026-06-08 09:08:38	MarkDuplicates	Read   341,000,000 records.  Elapsed time: 00:11:04s.  Time for last 1,000,000:    1s.  Last read position: chr11:47,724,040
INFO	2026-06-08 09:08:38	MarkDuplicates	Tracking 844220 as yet unmatched pairs. 79356 records in RAM.
INFO	2026-06-08 09:08:40	MarkDuplicates	Read   342,000,000 records.  Elapsed time: 00:11:06s.  Time for last 1,000,000:    2s.  Last read position: chr11:57,554,488
INFO	2026-06-08 09:08:40	MarkDuplicates	Tracking 841253 as yet unmatched pairs. 76387 records in RAM.
INFO	2026-06-08 09:08:42	MarkDuplicates	Read   343,000,000 records.  Elapsed time: 00:11:08s.  Time for last 1,000,000:    1s.  Last read position: chr11:59,657,677
INFO	2026-06-08 09:08:42	MarkDuplicates	Tracking 838533 as yet unmatched pairs. 73652 records in RAM.
INFO	2026-06-08 09:08:44	MarkDuplicates	Read   344,000,000 records.  Elapsed time: 00:11:10s.  Time for last 1,000,000:    1s.  Last read position: chr11:61,876,111
INFO	2026-06-08 09:08:44	MarkDuplicates	Tracking 835838 as yet unmatched pairs. 70940 records in RAM.
INFO	2026-06-08 09:08:45	MarkDuplicates	Read   345,000,000 records.  Elapsed time: 00:11:11s.  Time for last 1,000,000:    1s.  Last read position: chr11:62,524,763
INFO	2026-06-08 09:08:45	MarkDuplicates	Tracking 834220 as yet unmatched pairs. 69311 records in RAM.
INFO	2026-06-08 09:08:47	MarkDuplicates	Read   346,000,000 records.  Elapsed time: 00:11:13s.  Time for last 1,000,000:    1s.  Last read position: chr11:62,566,893
INFO	2026-06-08 09:08:47	MarkDuplicates	Tracking 831609 as yet unmatched pairs. 66697 records in RAM.
INFO	2026-06-08 09:08:49	MarkDuplicates	Read   347,000,000 records.  Elapsed time: 00:11:15s.  Time for last 1,000,000:    1s.  Last read position: chr11:62,789,823
INFO	2026-06-08 09:08:49	MarkDuplicates	Tracking 828082 as yet unmatched pairs. 63166 records in RAM.
INFO	2026-06-08 09:08:50	MarkDuplicates	Read   348,000,000 records.  Elapsed time: 00:11:16s.  Time for last 1,000,000:    1s.  Last read position: chr11:64,244,942
INFO	2026-06-08 09:08:50	MarkDuplicates	Tracking 826903 as yet unmatched pairs. 61985 records in RAM.
INFO	2026-06-08 09:08:52	MarkDuplicates	Read   349,000,000 records.  Elapsed time: 00:11:18s.  Time for last 1,000,000:    1s.  Last read position: chr11:64,925,784
INFO	2026-06-08 09:08:52	MarkDuplicates	Tracking 821093 as yet unmatched pairs. 56151 records in RAM.
INFO	2026-06-08 09:08:53	MarkDuplicates	Read   350,000,000 records.  Elapsed time: 00:11:20s.  Time for last 1,000,000:    1s.  Last read position: chr11:65,537,824
INFO	2026-06-08 09:08:53	MarkDuplicates	Tracking 818436 as yet unmatched pairs. 53429 records in RAM.
INFO	2026-06-08 09:08:55	MarkDuplicates	Read   351,000,000 records.  Elapsed time: 00:11:21s.  Time for last 1,000,000:    1s.  Last read position: chr11:65,654,759
INFO	2026-06-08 09:08:55	MarkDuplicates	Tracking 817577 as yet unmatched pairs. 52568 records in RAM.
INFO	2026-06-08 09:08:57	MarkDuplicates	Read   352,000,000 records.  Elapsed time: 00:11:23s.  Time for last 1,000,000:    1s.  Last read position: chr11:66,258,527
INFO	2026-06-08 09:08:57	MarkDuplicates	Tracking 811098 as yet unmatched pairs. 46089 records in RAM.
INFO	2026-06-08 09:08:59	MarkDuplicates	Read   353,000,000 records.  Elapsed time: 00:11:25s.  Time for last 1,000,000:    1s.  Last read position: chr11:67,120,008
INFO	2026-06-08 09:08:59	MarkDuplicates	Tracking 807874 as yet unmatched pairs. 42859 records in RAM.
INFO	2026-06-08 09:09:00	MarkDuplicates	Read   354,000,000 records.  Elapsed time: 00:11:26s.  Time for last 1,000,000:    1s.  Last read position: chr11:67,611,455
INFO	2026-06-08 09:09:00	MarkDuplicates	Tracking 805431 as yet unmatched pairs. 40413 records in RAM.
INFO	2026-06-08 09:09:02	MarkDuplicates	Read   355,000,000 records.  Elapsed time: 00:11:29s.  Time for last 1,000,000:    2s.  Last read position: chr11:69,643,050
INFO	2026-06-08 09:09:02	MarkDuplicates	Tracking 808088 as yet unmatched pairs. 43067 records in RAM.
INFO	2026-06-08 09:09:04	MarkDuplicates	Read   356,000,000 records.  Elapsed time: 00:11:30s.  Time for last 1,000,000:    1s.  Last read position: chr11:72,014,508
INFO	2026-06-08 09:09:04	MarkDuplicates	Tracking 798866 as yet unmatched pairs. 33843 records in RAM.
INFO	2026-06-08 09:09:06	MarkDuplicates	Read   357,000,000 records.  Elapsed time: 00:11:32s.  Time for last 1,000,000:    1s.  Last read position: chr11:73,310,210
INFO	2026-06-08 09:09:06	MarkDuplicates	Tracking 795030 as yet unmatched pairs. 30001 records in RAM.
INFO	2026-06-08 09:09:07	MarkDuplicates	Read   358,000,000 records.  Elapsed time: 00:11:33s.  Time for last 1,000,000:    1s.  Last read position: chr11:75,441,267
INFO	2026-06-08 09:09:07	MarkDuplicates	Tracking 791825 as yet unmatched pairs. 26784 records in RAM.
INFO	2026-06-08 09:09:09	MarkDuplicates	Read   359,000,000 records.  Elapsed time: 00:11:35s.  Time for last 1,000,000:    1s.  Last read position: chr11:85,983,949
INFO	2026-06-08 09:09:09	MarkDuplicates	Tracking 789997 as yet unmatched pairs. 24941 records in RAM.
INFO	2026-06-08 09:09:11	MarkDuplicates	Read   360,000,000 records.  Elapsed time: 00:11:37s.  Time for last 1,000,000:    1s.  Last read position: chr11:96,341,609
INFO	2026-06-08 09:09:11	MarkDuplicates	Tracking 787215 as yet unmatched pairs. 22147 records in RAM.
INFO	2026-06-08 09:09:12	MarkDuplicates	Read   361,000,000 records.  Elapsed time: 00:11:38s.  Time for last 1,000,000:    1s.  Last read position: chr11:108,474,797
INFO	2026-06-08 09:09:12	MarkDuplicates	Tracking 783290 as yet unmatched pairs. 18204 records in RAM.
INFO	2026-06-08 09:09:14	MarkDuplicates	Read   362,000,000 records.  Elapsed time: 00:11:40s.  Time for last 1,000,000:    1s.  Last read position: chr11:114,253,544
INFO	2026-06-08 09:09:14	MarkDuplicates	Tracking 781377 as yet unmatched pairs. 16288 records in RAM.
INFO	2026-06-08 09:09:16	MarkDuplicates	Read   363,000,000 records.  Elapsed time: 00:11:42s.  Time for last 1,000,000:    2s.  Last read position: chr11:118,407,011
INFO	2026-06-08 09:09:16	MarkDuplicates	Tracking 783251 as yet unmatched pairs. 18160 records in RAM.
INFO	2026-06-08 09:09:18	MarkDuplicates	Read   364,000,000 records.  Elapsed time: 00:11:44s.  Time for last 1,000,000:    1s.  Last read position: chr11:118,908,640
INFO	2026-06-08 09:09:18	MarkDuplicates	Tracking 775239 as yet unmatched pairs. 10143 records in RAM.
INFO	2026-06-08 09:09:20	MarkDuplicates	Read   365,000,000 records.  Elapsed time: 00:11:46s.  Time for last 1,000,000:    1s.  Last read position: chr11:121,590,145
INFO	2026-06-08 09:09:20	MarkDuplicates	Tracking 772806 as yet unmatched pairs. 7686 records in RAM.
INFO	2026-06-08 09:09:22	MarkDuplicates	Read   366,000,000 records.  Elapsed time: 00:11:48s.  Time for last 1,000,000:    1s.  Last read position: chr11:126,266,586
INFO	2026-06-08 09:09:22	MarkDuplicates	Tracking 769720 as yet unmatched pairs. 4596 records in RAM.
INFO	2026-06-08 09:09:23	MarkDuplicates	Read   367,000,000 records.  Elapsed time: 00:11:49s.  Time for last 1,000,000:    1s.  Last read position: chr11:130,878,481
INFO	2026-06-08 09:09:23	MarkDuplicates	Tracking 766899 as yet unmatched pairs. 1762 records in RAM.
INFO	2026-06-08 09:09:26	MarkDuplicates	Read   368,000,000 records.  Elapsed time: 00:11:52s.  Time for last 1,000,000:    2s.  Last read position: chr12:885,634
INFO	2026-06-08 09:09:26	MarkDuplicates	Tracking 764901 as yet unmatched pairs. 101075 records in RAM.
INFO	2026-06-08 09:09:27	MarkDuplicates	Read   369,000,000 records.  Elapsed time: 00:11:53s.  Time for last 1,000,000:    1s.  Last read position: chr12:6,019,337
INFO	2026-06-08 09:09:27	MarkDuplicates	Tracking 763047 as yet unmatched pairs. 99201 records in RAM.
INFO	2026-06-08 09:09:29	MarkDuplicates	Read   370,000,000 records.  Elapsed time: 00:11:55s.  Time for last 1,000,000:    1s.  Last read position: chr12:6,537,101
INFO	2026-06-08 09:09:29	MarkDuplicates	Tracking 759851 as yet unmatched pairs. 95998 records in RAM.
INFO	2026-06-08 09:09:31	MarkDuplicates	Read   371,000,000 records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:    1s.  Last read position: chr12:6,936,508
INFO	2026-06-08 09:09:31	MarkDuplicates	Tracking 756090 as yet unmatched pairs. 92223 records in RAM.
INFO	2026-06-08 09:09:32	MarkDuplicates	Read   372,000,000 records.  Elapsed time: 00:11:58s.  Time for last 1,000,000:    1s.  Last read position: chr12:7,097,119
INFO	2026-06-08 09:09:32	MarkDuplicates	Tracking 752779 as yet unmatched pairs. 88907 records in RAM.
INFO	2026-06-08 09:09:34	MarkDuplicates	Read   373,000,000 records.  Elapsed time: 00:12:00s.  Time for last 1,000,000:    1s.  Last read position: chr12:9,089,946
INFO	2026-06-08 09:09:34	MarkDuplicates	Tracking 753006 as yet unmatched pairs. 89127 records in RAM.
INFO	2026-06-08 09:09:36	MarkDuplicates	Read   374,000,000 records.  Elapsed time: 00:12:02s.  Time for last 1,000,000:    1s.  Last read position: chr12:11,869,694
INFO	2026-06-08 09:09:36	MarkDuplicates	Tracking 750270 as yet unmatched pairs. 86387 records in RAM.
INFO	2026-06-08 09:09:37	MarkDuplicates	Read   375,000,000 records.  Elapsed time: 00:12:03s.  Time for last 1,000,000:    1s.  Last read position: chr12:15,647,127
INFO	2026-06-08 09:09:37	MarkDuplicates	Tracking 745722 as yet unmatched pairs. 81825 records in RAM.
INFO	2026-06-08 09:09:39	MarkDuplicates	Read   376,000,000 records.  Elapsed time: 00:12:05s.  Time for last 1,000,000:    1s.  Last read position: chr12:26,995,252
INFO	2026-06-08 09:09:39	MarkDuplicates	Tracking 743128 as yet unmatched pairs. 79212 records in RAM.
INFO	2026-06-08 09:09:41	MarkDuplicates	Read   377,000,000 records.  Elapsed time: 00:12:07s.  Time for last 1,000,000:    1s.  Last read position: chr12:40,322,043
INFO	2026-06-08 09:09:41	MarkDuplicates	Tracking 742425 as yet unmatched pairs. 78496 records in RAM.
INFO	2026-06-08 09:09:42	MarkDuplicates	Read   378,000,000 records.  Elapsed time: 00:12:08s.  Time for last 1,000,000:    1s.  Last read position: chr12:47,855,689
INFO	2026-06-08 09:09:42	MarkDuplicates	Tracking 736896 as yet unmatched pairs. 72962 records in RAM.
INFO	2026-06-08 09:09:44	MarkDuplicates	Read   379,000,000 records.  Elapsed time: 00:12:10s.  Time for last 1,000,000:    1s.  Last read position: chr12:49,051,208
INFO	2026-06-08 09:09:44	MarkDuplicates	Tracking 734911 as yet unmatched pairs. 70970 records in RAM.
INFO	2026-06-08 09:09:45	MarkDuplicates	Read   380,000,000 records.  Elapsed time: 00:12:11s.  Time for last 1,000,000:    1s.  Last read position: chr12:49,762,871
INFO	2026-06-08 09:09:45	MarkDuplicates	Tracking 732175 as yet unmatched pairs. 68231 records in RAM.
INFO	2026-06-08 09:09:47	MarkDuplicates	Read   381,000,000 records.  Elapsed time: 00:12:13s.  Time for last 1,000,000:    1s.  Last read position: chr12:52,054,410
INFO	2026-06-08 09:09:47	MarkDuplicates	Tracking 734432 as yet unmatched pairs. 70485 records in RAM.
INFO	2026-06-08 09:09:49	MarkDuplicates	Read   382,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:    1s.  Last read position: chr12:53,037,574
INFO	2026-06-08 09:09:49	MarkDuplicates	Tracking 727505 as yet unmatched pairs. 63553 records in RAM.
INFO	2026-06-08 09:09:51	MarkDuplicates	Read   383,000,000 records.  Elapsed time: 00:12:17s.  Time for last 1,000,000:    1s.  Last read position: chr12:53,461,036
INFO	2026-06-08 09:09:51	MarkDuplicates	Tracking 727314 as yet unmatched pairs. 63355 records in RAM.
INFO	2026-06-08 09:09:52	MarkDuplicates	Read   384,000,000 records.  Elapsed time: 00:12:19s.  Time for last 1,000,000:    1s.  Last read position: chr12:54,283,093
INFO	2026-06-08 09:09:52	MarkDuplicates	Tracking 723229 as yet unmatched pairs. 59260 records in RAM.
INFO	2026-06-08 09:09:54	MarkDuplicates	Read   385,000,000 records.  Elapsed time: 00:12:20s.  Time for last 1,000,000:    1s.  Last read position: chr12:55,986,937
INFO	2026-06-08 09:09:54	MarkDuplicates	Tracking 718252 as yet unmatched pairs. 54282 records in RAM.
INFO	2026-06-08 09:09:56	MarkDuplicates	Read   386,000,000 records.  Elapsed time: 00:12:22s.  Time for last 1,000,000:    1s.  Last read position: chr12:56,244,700
INFO	2026-06-08 09:09:56	MarkDuplicates	Tracking 714751 as yet unmatched pairs. 50768 records in RAM.
INFO	2026-06-08 09:09:58	MarkDuplicates	Read   387,000,000 records.  Elapsed time: 00:12:24s.  Time for last 1,000,000:    2s.  Last read position: chr12:56,714,383
INFO	2026-06-08 09:09:58	MarkDuplicates	Tracking 725871 as yet unmatched pairs. 61887 records in RAM.
INFO	2026-06-08 09:10:00	MarkDuplicates	Read   388,000,000 records.  Elapsed time: 00:12:26s.  Time for last 1,000,000:    2s.  Last read position: chr12:57,099,882
INFO	2026-06-08 09:10:00	MarkDuplicates	Tracking 716521 as yet unmatched pairs. 52535 records in RAM.
INFO	2026-06-08 09:10:03	MarkDuplicates	Read   389,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:    2s.  Last read position: chr12:57,185,658
INFO	2026-06-08 09:10:03	MarkDuplicates	Tracking 707725 as yet unmatched pairs. 43739 records in RAM.
INFO	2026-06-08 09:10:04	MarkDuplicates	Read   390,000,000 records.  Elapsed time: 00:12:30s.  Time for last 1,000,000:    1s.  Last read position: chr12:57,535,821
INFO	2026-06-08 09:10:04	MarkDuplicates	Tracking 705236 as yet unmatched pairs. 41240 records in RAM.
INFO	2026-06-08 09:10:06	MarkDuplicates	Read   391,000,000 records.  Elapsed time: 00:12:32s.  Time for last 1,000,000:    1s.  Last read position: chr12:64,723,089
INFO	2026-06-08 09:10:06	MarkDuplicates	Tracking 701747 as yet unmatched pairs. 37722 records in RAM.
INFO	2026-06-08 09:10:08	MarkDuplicates	Read   392,000,000 records.  Elapsed time: 00:12:34s.  Time for last 1,000,000:    1s.  Last read position: chr12:70,534,892
INFO	2026-06-08 09:10:08	MarkDuplicates	Tracking 698672 as yet unmatched pairs. 34635 records in RAM.
INFO	2026-06-08 09:10:09	MarkDuplicates	Read   393,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:    1s.  Last read position: chr12:91,108,361
INFO	2026-06-08 09:10:09	MarkDuplicates	Tracking 697392 as yet unmatched pairs. 33345 records in RAM.
INFO	2026-06-08 09:10:11	MarkDuplicates	Read   394,000,000 records.  Elapsed time: 00:12:37s.  Time for last 1,000,000:    1s.  Last read position: chr12:96,029,112
INFO	2026-06-08 09:10:11	MarkDuplicates	Tracking 695328 as yet unmatched pairs. 31274 records in RAM.
INFO	2026-06-08 09:10:13	MarkDuplicates	Read   395,000,000 records.  Elapsed time: 00:12:39s.  Time for last 1,000,000:    1s.  Last read position: chr12:104,265,740
INFO	2026-06-08 09:10:13	MarkDuplicates	Tracking 690350 as yet unmatched pairs. 26288 records in RAM.
INFO	2026-06-08 09:10:14	MarkDuplicates	Read   396,000,000 records.  Elapsed time: 00:12:40s.  Time for last 1,000,000:    1s.  Last read position: chr12:109,246,213
INFO	2026-06-08 09:10:14	MarkDuplicates	Tracking 687611 as yet unmatched pairs. 23547 records in RAM.
INFO	2026-06-08 09:10:16	MarkDuplicates	Read   397,000,000 records.  Elapsed time: 00:12:42s.  Time for last 1,000,000:    1s.  Last read position: chr12:111,790,558
INFO	2026-06-08 09:10:16	MarkDuplicates	Tracking 687383 as yet unmatched pairs. 23314 records in RAM.
INFO	2026-06-08 09:10:18	MarkDuplicates	Read   398,000,000 records.  Elapsed time: 00:12:44s.  Time for last 1,000,000:    1s.  Last read position: chr12:113,191,456
INFO	2026-06-08 09:10:18	MarkDuplicates	Tracking 682190 as yet unmatched pairs. 18115 records in RAM.
INFO	2026-06-08 09:10:19	MarkDuplicates	Read   399,000,000 records.  Elapsed time: 00:12:45s.  Time for last 1,000,000:    1s.  Last read position: chr12:119,822,833
INFO	2026-06-08 09:10:19	MarkDuplicates	Tracking 678629 as yet unmatched pairs. 14499 records in RAM.
INFO	2026-06-08 09:10:21	MarkDuplicates	Read   400,000,000 records.  Elapsed time: 00:12:47s.  Time for last 1,000,000:    1s.  Last read position: chr12:121,020,755
INFO	2026-06-08 09:10:21	MarkDuplicates	Tracking 675704 as yet unmatched pairs. 11561 records in RAM.
INFO	2026-06-08 09:10:23	MarkDuplicates	Read   401,000,000 records.  Elapsed time: 00:12:49s.  Time for last 1,000,000:    1s.  Last read position: chr12:122,981,989
INFO	2026-06-08 09:10:23	MarkDuplicates	Tracking 674581 as yet unmatched pairs. 10435 records in RAM.
INFO	2026-06-08 09:10:25	MarkDuplicates	Read   402,000,000 records.  Elapsed time: 00:12:51s.  Time for last 1,000,000:    2s.  Last read position: chr12:124,355,569
INFO	2026-06-08 09:10:25	MarkDuplicates	Tracking 670944 as yet unmatched pairs. 6791 records in RAM.
INFO	2026-06-08 09:10:27	MarkDuplicates	Read   403,000,000 records.  Elapsed time: 00:12:53s.  Time for last 1,000,000:    1s.  Last read position: chr12:132,053,587
INFO	2026-06-08 09:10:27	MarkDuplicates	Tracking 666989 as yet unmatched pairs. 2820 records in RAM.
INFO	2026-06-08 09:10:28	MarkDuplicates	Read   404,000,000 records.  Elapsed time: 00:12:55s.  Time for last 1,000,000:    1s.  Last read position: chr13:20,066,891
INFO	2026-06-08 09:10:28	MarkDuplicates	Tracking 665091 as yet unmatched pairs. 24070 records in RAM.
INFO	2026-06-08 09:10:30	MarkDuplicates	Read   405,000,000 records.  Elapsed time: 00:12:56s.  Time for last 1,000,000:    1s.  Last read position: chr13:30,461,462
INFO	2026-06-08 09:10:30	MarkDuplicates	Tracking 661115 as yet unmatched pairs. 20087 records in RAM.
INFO	2026-06-08 09:10:31	MarkDuplicates	Read   406,000,000 records.  Elapsed time: 00:12:57s.  Time for last 1,000,000:    1s.  Last read position: chr13:41,466,831
INFO	2026-06-08 09:10:31	MarkDuplicates	Tracking 659432 as yet unmatched pairs. 18390 records in RAM.
INFO	2026-06-08 09:10:33	MarkDuplicates	Read   407,000,000 records.  Elapsed time: 00:12:59s.  Time for last 1,000,000:    1s.  Last read position: chr13:48,253,848
INFO	2026-06-08 09:10:33	MarkDuplicates	Tracking 664164 as yet unmatched pairs. 23110 records in RAM.
INFO	2026-06-08 09:10:35	MarkDuplicates	Read   408,000,000 records.  Elapsed time: 00:13:01s.  Time for last 1,000,000:    1s.  Last read position: chr13:76,885,166
INFO	2026-06-08 09:10:35	MarkDuplicates	Tracking 654180 as yet unmatched pairs. 13113 records in RAM.
INFO	2026-06-08 09:10:36	MarkDuplicates	Read   409,000,000 records.  Elapsed time: 00:13:02s.  Time for last 1,000,000:    1s.  Last read position: chr13:98,831,698
INFO	2026-06-08 09:10:36	MarkDuplicates	Tracking 650630 as yet unmatched pairs. 9553 records in RAM.
INFO	2026-06-08 09:10:38	MarkDuplicates	Read   410,000,000 records.  Elapsed time: 00:13:04s.  Time for last 1,000,000:    1s.  Last read position: chr13:110,198,584
INFO	2026-06-08 09:10:38	MarkDuplicates	Tracking 647949 as yet unmatched pairs. 6859 records in RAM.
INFO	2026-06-08 09:10:40	MarkDuplicates	Read   411,000,000 records.  Elapsed time: 00:13:06s.  Time for last 1,000,000:    1s.  Last read position: chr13:112,825,530
INFO	2026-06-08 09:10:40	MarkDuplicates	Tracking 645368 as yet unmatched pairs. 4269 records in RAM.
INFO	2026-06-08 09:10:42	MarkDuplicates	Read   412,000,000 records.  Elapsed time: 00:13:08s.  Time for last 1,000,000:    2s.  Last read position: chr14:20,456,786
INFO	2026-06-08 09:10:42	MarkDuplicates	Tracking 641463 as yet unmatched pairs. 53714 records in RAM.
INFO	2026-06-08 09:10:43	MarkDuplicates	Read   413,000,000 records.  Elapsed time: 00:13:09s.  Time for last 1,000,000:    1s.  Last read position: chr14:22,771,039
INFO	2026-06-08 09:10:43	MarkDuplicates	Tracking 638330 as yet unmatched pairs. 50576 records in RAM.
INFO	2026-06-08 09:10:45	MarkDuplicates	Read   414,000,000 records.  Elapsed time: 00:13:11s.  Time for last 1,000,000:    1s.  Last read position: chr14:23,566,103
INFO	2026-06-08 09:10:45	MarkDuplicates	Tracking 635255 as yet unmatched pairs. 47487 records in RAM.
INFO	2026-06-08 09:10:46	MarkDuplicates	Read   415,000,000 records.  Elapsed time: 00:13:13s.  Time for last 1,000,000:    1s.  Last read position: chr14:24,430,847
INFO	2026-06-08 09:10:46	MarkDuplicates	Tracking 632134 as yet unmatched pairs. 44363 records in RAM.
INFO	2026-06-08 09:10:48	MarkDuplicates	Read   416,000,000 records.  Elapsed time: 00:13:14s.  Time for last 1,000,000:    1s.  Last read position: chr14:35,748,805
INFO	2026-06-08 09:10:48	MarkDuplicates	Tracking 629187 as yet unmatched pairs. 41411 records in RAM.
INFO	2026-06-08 09:10:50	MarkDuplicates	Read   417,000,000 records.  Elapsed time: 00:13:16s.  Time for last 1,000,000:    1s.  Last read position: chr14:49,893,959
INFO	2026-06-08 09:10:50	MarkDuplicates	Tracking 627823 as yet unmatched pairs. 39975 records in RAM.
INFO	2026-06-08 09:10:51	MarkDuplicates	Read   418,000,000 records.  Elapsed time: 00:13:17s.  Time for last 1,000,000:    1s.  Last read position: chr14:57,246,828
INFO	2026-06-08 09:10:51	MarkDuplicates	Tracking 623869 as yet unmatched pairs. 36016 records in RAM.
INFO	2026-06-08 09:10:53	MarkDuplicates	Read   419,000,000 records.  Elapsed time: 00:13:19s.  Time for last 1,000,000:    1s.  Last read position: chr14:64,209,551
INFO	2026-06-08 09:10:53	MarkDuplicates	Tracking 621034 as yet unmatched pairs. 33176 records in RAM.
INFO	2026-06-08 09:10:55	MarkDuplicates	Read   420,000,000 records.  Elapsed time: 00:13:21s.  Time for last 1,000,000:    1s.  Last read position: chr14:68,790,212
INFO	2026-06-08 09:10:55	MarkDuplicates	Tracking 621607 as yet unmatched pairs. 33741 records in RAM.
INFO	2026-06-08 09:10:56	MarkDuplicates	Read   421,000,000 records.  Elapsed time: 00:13:22s.  Time for last 1,000,000:    1s.  Last read position: chr14:73,237,580
INFO	2026-06-08 09:10:56	MarkDuplicates	Tracking 615972 as yet unmatched pairs. 28102 records in RAM.
INFO	2026-06-08 09:10:57	MarkDuplicates	Read   422,000,000 records.  Elapsed time: 00:13:24s.  Time for last 1,000,000:    1s.  Last read position: chr14:74,508,938
INFO	2026-06-08 09:10:57	MarkDuplicates	Tracking 615226 as yet unmatched pairs. 27345 records in RAM.
INFO	2026-06-08 09:10:59	MarkDuplicates	Read   423,000,000 records.  Elapsed time: 00:13:25s.  Time for last 1,000,000:    1s.  Last read position: chr14:75,280,860
INFO	2026-06-08 09:10:59	MarkDuplicates	Tracking 613156 as yet unmatched pairs. 25274 records in RAM.
INFO	2026-06-08 09:11:01	MarkDuplicates	Read   424,000,000 records.  Elapsed time: 00:13:27s.  Time for last 1,000,000:    1s.  Last read position: chr14:90,259,194
INFO	2026-06-08 09:11:01	MarkDuplicates	Tracking 606369 as yet unmatched pairs. 18486 records in RAM.
INFO	2026-06-08 09:11:02	MarkDuplicates	Read   425,000,000 records.  Elapsed time: 00:13:28s.  Time for last 1,000,000:    1s.  Last read position: chr14:94,115,903
INFO	2026-06-08 09:11:02	MarkDuplicates	Tracking 605082 as yet unmatched pairs. 17193 records in RAM.
INFO	2026-06-08 09:11:04	MarkDuplicates	Read   426,000,000 records.  Elapsed time: 00:13:30s.  Time for last 1,000,000:    1s.  Last read position: chr14:100,298,856
INFO	2026-06-08 09:11:04	MarkDuplicates	Tracking 600654 as yet unmatched pairs. 12758 records in RAM.
INFO	2026-06-08 09:11:05	MarkDuplicates	Read   427,000,000 records.  Elapsed time: 00:13:31s.  Time for last 1,000,000:    1s.  Last read position: chr14:102,938,169
INFO	2026-06-08 09:11:05	MarkDuplicates	Tracking 597810 as yet unmatched pairs. 9907 records in RAM.
INFO	2026-06-08 09:11:07	MarkDuplicates	Read   428,000,000 records.  Elapsed time: 00:13:33s.  Time for last 1,000,000:    1s.  Last read position: chr14:104,775,128
INFO	2026-06-08 09:11:07	MarkDuplicates	Tracking 594518 as yet unmatched pairs. 6603 records in RAM.
INFO	2026-06-08 09:11:09	MarkDuplicates	Read   429,000,000 records.  Elapsed time: 00:13:35s.  Time for last 1,000,000:    1s.  Last read position: chr14:105,211,171
INFO	2026-06-08 09:11:09	MarkDuplicates	Tracking 591483 as yet unmatched pairs. 3568 records in RAM.
INFO	2026-06-08 09:11:10	MarkDuplicates	Read   430,000,000 records.  Elapsed time: 00:13:36s.  Time for last 1,000,000:    1s.  Last read position: chr14:105,854,525
INFO	2026-06-08 09:11:10	MarkDuplicates	Tracking 591954 as yet unmatched pairs. 4025 records in RAM.
INFO	2026-06-08 09:11:12	MarkDuplicates	Read   431,000,000 records.  Elapsed time: 00:13:38s.  Time for last 1,000,000:    1s.  Last read position: chr15:29,733,237
INFO	2026-06-08 09:11:12	MarkDuplicates	Tracking 586372 as yet unmatched pairs. 44079 records in RAM.
INFO	2026-06-08 09:11:14	MarkDuplicates	Read   432,000,000 records.  Elapsed time: 00:13:40s.  Time for last 1,000,000:    1s.  Last read position: chr15:39,589,860
INFO	2026-06-08 09:11:14	MarkDuplicates	Tracking 584346 as yet unmatched pairs. 42041 records in RAM.
INFO	2026-06-08 09:11:16	MarkDuplicates	Read   433,000,000 records.  Elapsed time: 00:13:42s.  Time for last 1,000,000:    1s.  Last read position: chr15:41,710,820
INFO	2026-06-08 09:11:16	MarkDuplicates	Tracking 580724 as yet unmatched pairs. 38418 records in RAM.
INFO	2026-06-08 09:11:17	MarkDuplicates	Read   434,000,000 records.  Elapsed time: 00:13:43s.  Time for last 1,000,000:    1s.  Last read position: chr15:43,528,445
INFO	2026-06-08 09:11:17	MarkDuplicates	Tracking 577607 as yet unmatched pairs. 35300 records in RAM.
INFO	2026-06-08 09:11:19	MarkDuplicates	Read   435,000,000 records.  Elapsed time: 00:13:45s.  Time for last 1,000,000:    1s.  Last read position: chr15:45,676,194
INFO	2026-06-08 09:11:19	MarkDuplicates	Tracking 575178 as yet unmatched pairs. 32865 records in RAM.
INFO	2026-06-08 09:11:21	MarkDuplicates	Read   436,000,000 records.  Elapsed time: 00:13:47s.  Time for last 1,000,000:    1s.  Last read position: chr15:52,610,293
INFO	2026-06-08 09:11:21	MarkDuplicates	Tracking 572808 as yet unmatched pairs. 30483 records in RAM.
INFO	2026-06-08 09:11:22	MarkDuplicates	Read   437,000,000 records.  Elapsed time: 00:13:49s.  Time for last 1,000,000:    1s.  Last read position: chr15:60,364,492
INFO	2026-06-08 09:11:22	MarkDuplicates	Tracking 571921 as yet unmatched pairs. 29592 records in RAM.
INFO	2026-06-08 09:11:24	MarkDuplicates	Read   438,000,000 records.  Elapsed time: 00:13:50s.  Time for last 1,000,000:    1s.  Last read position: chr15:64,675,678
INFO	2026-06-08 09:11:24	MarkDuplicates	Tracking 567248 as yet unmatched pairs. 24915 records in RAM.
INFO	2026-06-08 09:11:26	MarkDuplicates	Read   439,000,000 records.  Elapsed time: 00:13:52s.  Time for last 1,000,000:    1s.  Last read position: chr15:68,320,326
INFO	2026-06-08 09:11:26	MarkDuplicates	Tracking 564566 as yet unmatched pairs. 22226 records in RAM.
INFO	2026-06-08 09:11:28	MarkDuplicates	Read   440,000,000 records.  Elapsed time: 00:13:54s.  Time for last 1,000,000:    1s.  Last read position: chr15:73,298,397
INFO	2026-06-08 09:11:28	MarkDuplicates	Tracking 561733 as yet unmatched pairs. 19382 records in RAM.
INFO	2026-06-08 09:11:29	MarkDuplicates	Read   441,000,000 records.  Elapsed time: 00:13:56s.  Time for last 1,000,000:    1s.  Last read position: chr15:74,448,531
INFO	2026-06-08 09:11:29	MarkDuplicates	Tracking 558203 as yet unmatched pairs. 15852 records in RAM.
INFO	2026-06-08 09:11:31	MarkDuplicates	Read   442,000,000 records.  Elapsed time: 00:13:57s.  Time for last 1,000,000:    1s.  Last read position: chr15:77,054,190
INFO	2026-06-08 09:11:31	MarkDuplicates	Tracking 556377 as yet unmatched pairs. 14019 records in RAM.
INFO	2026-06-08 09:11:33	MarkDuplicates	Read   443,000,000 records.  Elapsed time: 00:13:59s.  Time for last 1,000,000:    1s.  Last read position: chr15:82,372,432
INFO	2026-06-08 09:11:33	MarkDuplicates	Tracking 554925 as yet unmatched pairs. 12561 records in RAM.
INFO	2026-06-08 09:11:34	MarkDuplicates	Read   444,000,000 records.  Elapsed time: 00:14:00s.  Time for last 1,000,000:    1s.  Last read position: chr15:85,693,437
INFO	2026-06-08 09:11:34	MarkDuplicates	Tracking 551500 as yet unmatched pairs. 9133 records in RAM.
INFO	2026-06-08 09:11:36	MarkDuplicates	Read   445,000,000 records.  Elapsed time: 00:14:02s.  Time for last 1,000,000:    1s.  Last read position: chr15:90,084,269
INFO	2026-06-08 09:11:36	MarkDuplicates	Tracking 547686 as yet unmatched pairs. 5313 records in RAM.
INFO	2026-06-08 09:11:37	MarkDuplicates	Read   446,000,000 records.  Elapsed time: 00:14:03s.  Time for last 1,000,000:    1s.  Last read position: chr15:93,072,901
INFO	2026-06-08 09:11:37	MarkDuplicates	Tracking 544159 as yet unmatched pairs. 1783 records in RAM.
INFO	2026-06-08 09:11:40	MarkDuplicates	Read   447,000,000 records.  Elapsed time: 00:14:06s.  Time for last 1,000,000:    2s.  Last read position: chr16:400,249
INFO	2026-06-08 09:11:40	MarkDuplicates	Tracking 542509 as yet unmatched pairs. 79681 records in RAM.
INFO	2026-06-08 09:11:41	MarkDuplicates	Read   448,000,000 records.  Elapsed time: 00:14:07s.  Time for last 1,000,000:    1s.  Last read position: chr16:1,241,267
INFO	2026-06-08 09:11:41	MarkDuplicates	Tracking 539009 as yet unmatched pairs. 76179 records in RAM.
INFO	2026-06-08 09:11:43	MarkDuplicates	Read   449,000,000 records.  Elapsed time: 00:14:09s.  Time for last 1,000,000:    1s.  Last read position: chr16:1,977,364
INFO	2026-06-08 09:11:43	MarkDuplicates	Tracking 534023 as yet unmatched pairs. 71185 records in RAM.
INFO	2026-06-08 09:11:45	MarkDuplicates	Read   450,000,000 records.  Elapsed time: 00:14:11s.  Time for last 1,000,000:    1s.  Last read position: chr16:2,514,112
INFO	2026-06-08 09:11:45	MarkDuplicates	Tracking 533762 as yet unmatched pairs. 70924 records in RAM.
INFO	2026-06-08 09:11:46	MarkDuplicates	Read   451,000,000 records.  Elapsed time: 00:14:12s.  Time for last 1,000,000:    1s.  Last read position: chr16:3,023,285
INFO	2026-06-08 09:11:46	MarkDuplicates	Tracking 528661 as yet unmatched pairs. 65821 records in RAM.
INFO	2026-06-08 09:11:48	MarkDuplicates	Read   452,000,000 records.  Elapsed time: 00:14:14s.  Time for last 1,000,000:    1s.  Last read position: chr16:4,657,298
INFO	2026-06-08 09:11:48	MarkDuplicates	Tracking 524884 as yet unmatched pairs. 62042 records in RAM.
INFO	2026-06-08 09:11:49	MarkDuplicates	Read   453,000,000 records.  Elapsed time: 00:14:16s.  Time for last 1,000,000:    1s.  Last read position: chr16:11,126,073
INFO	2026-06-08 09:11:49	MarkDuplicates	Tracking 521300 as yet unmatched pairs. 58447 records in RAM.
INFO	2026-06-08 09:11:51	MarkDuplicates	Read   454,000,000 records.  Elapsed time: 00:14:17s.  Time for last 1,000,000:    1s.  Last read position: chr16:14,922,113
INFO	2026-06-08 09:11:51	MarkDuplicates	Tracking 518554 as yet unmatched pairs. 55693 records in RAM.
INFO	2026-06-08 09:11:53	MarkDuplicates	Read   455,000,000 records.  Elapsed time: 00:14:19s.  Time for last 1,000,000:    1s.  Last read position: chr16:16,243,174
INFO	2026-06-08 09:11:53	MarkDuplicates	Tracking 516203 as yet unmatched pairs. 53339 records in RAM.
INFO	2026-06-08 09:11:54	MarkDuplicates	Read   456,000,000 records.  Elapsed time: 00:14:20s.  Time for last 1,000,000:    1s.  Last read position: chr16:18,351,910
INFO	2026-06-08 09:11:54	MarkDuplicates	Tracking 515638 as yet unmatched pairs. 52772 records in RAM.
INFO	2026-06-08 09:11:55	MarkDuplicates	Read   457,000,000 records.  Elapsed time: 00:14:21s.  Time for last 1,000,000:    1s.  Last read position: chr16:19,637,619
INFO	2026-06-08 09:11:55	MarkDuplicates	Tracking 513565 as yet unmatched pairs. 50699 records in RAM.
INFO	2026-06-08 09:11:57	MarkDuplicates	Read   458,000,000 records.  Elapsed time: 00:14:23s.  Time for last 1,000,000:    1s.  Last read position: chr16:21,879,444
INFO	2026-06-08 09:11:57	MarkDuplicates	Tracking 511836 as yet unmatched pairs. 48970 records in RAM.
INFO	2026-06-08 09:11:59	MarkDuplicates	Read   459,000,000 records.  Elapsed time: 00:14:25s.  Time for last 1,000,000:    2s.  Last read position: chr16:23,679,101
INFO	2026-06-08 09:11:59	MarkDuplicates	Tracking 510263 as yet unmatched pairs. 47397 records in RAM.
INFO	2026-06-08 09:12:00	MarkDuplicates	Read   460,000,000 records.  Elapsed time: 00:14:26s.  Time for last 1,000,000:    1s.  Last read position: chr16:28,714,347
INFO	2026-06-08 09:12:00	MarkDuplicates	Tracking 507778 as yet unmatched pairs. 44905 records in RAM.
INFO	2026-06-08 09:12:02	MarkDuplicates	Read   461,000,000 records.  Elapsed time: 00:14:28s.  Time for last 1,000,000:    1s.  Last read position: chr16:29,483,919
INFO	2026-06-08 09:12:02	MarkDuplicates	Tracking 507219 as yet unmatched pairs. 44346 records in RAM.
INFO	2026-06-08 09:12:03	MarkDuplicates	Read   462,000,000 records.  Elapsed time: 00:14:29s.  Time for last 1,000,000:    1s.  Last read position: chr16:30,000,927
INFO	2026-06-08 09:12:03	MarkDuplicates	Tracking 503542 as yet unmatched pairs. 40661 records in RAM.
INFO	2026-06-08 09:12:04	MarkDuplicates	Read   463,000,000 records.  Elapsed time: 00:14:31s.  Time for last 1,000,000:    1s.  Last read position: chr16:30,445,393
INFO	2026-06-08 09:12:04	MarkDuplicates	Tracking 501619 as yet unmatched pairs. 38733 records in RAM.
INFO	2026-06-08 09:12:06	MarkDuplicates	Read   464,000,000 records.  Elapsed time: 00:14:32s.  Time for last 1,000,000:    1s.  Last read position: chr16:31,081,246
INFO	2026-06-08 09:12:06	MarkDuplicates	Tracking 497612 as yet unmatched pairs. 34725 records in RAM.
INFO	2026-06-08 09:12:08	MarkDuplicates	Read   465,000,000 records.  Elapsed time: 00:14:34s.  Time for last 1,000,000:    1s.  Last read position: chr16:31,492,035
INFO	2026-06-08 09:12:08	MarkDuplicates	Tracking 494679 as yet unmatched pairs. 31785 records in RAM.
INFO	2026-06-08 09:12:09	MarkDuplicates	Read   466,000,000 records.  Elapsed time: 00:14:35s.  Time for last 1,000,000:    1s.  Last read position: chr16:54,932,849
INFO	2026-06-08 09:12:09	MarkDuplicates	Tracking 491983 as yet unmatched pairs. 29084 records in RAM.
INFO	2026-06-08 09:12:11	MarkDuplicates	Read   467,000,000 records.  Elapsed time: 00:14:37s.  Time for last 1,000,000:    1s.  Last read position: chr16:56,943,250
INFO	2026-06-08 09:12:11	MarkDuplicates	Tracking 488916 as yet unmatched pairs. 26017 records in RAM.
INFO	2026-06-08 09:12:13	MarkDuplicates	Read   468,000,000 records.  Elapsed time: 00:14:39s.  Time for last 1,000,000:    1s.  Last read position: chr16:64,948,020
INFO	2026-06-08 09:12:13	MarkDuplicates	Tracking 487643 as yet unmatched pairs. 24741 records in RAM.
INFO	2026-06-08 09:12:14	MarkDuplicates	Read   469,000,000 records.  Elapsed time: 00:14:40s.  Time for last 1,000,000:    1s.  Last read position: chr16:67,438,647
INFO	2026-06-08 09:12:14	MarkDuplicates	Tracking 482352 as yet unmatched pairs. 19448 records in RAM.
INFO	2026-06-08 09:12:16	MarkDuplicates	Read   470,000,000 records.  Elapsed time: 00:14:42s.  Time for last 1,000,000:    1s.  Last read position: chr16:69,114,556
INFO	2026-06-08 09:12:16	MarkDuplicates	Tracking 479262 as yet unmatched pairs. 16356 records in RAM.
INFO	2026-06-08 09:12:17	MarkDuplicates	Read   471,000,000 records.  Elapsed time: 00:14:43s.  Time for last 1,000,000:    1s.  Last read position: chr16:70,664,638
INFO	2026-06-08 09:12:17	MarkDuplicates	Tracking 476898 as yet unmatched pairs. 13987 records in RAM.
INFO	2026-06-08 09:12:19	MarkDuplicates	Read   472,000,000 records.  Elapsed time: 00:14:45s.  Time for last 1,000,000:    2s.  Last read position: chr16:72,958,107
INFO	2026-06-08 09:12:19	MarkDuplicates	Tracking 474200 as yet unmatched pairs. 11280 records in RAM.
INFO	2026-06-08 09:12:21	MarkDuplicates	Read   473,000,000 records.  Elapsed time: 00:14:47s.  Time for last 1,000,000:    1s.  Last read position: chr16:84,054,596
INFO	2026-06-08 09:12:21	MarkDuplicates	Tracking 471458 as yet unmatched pairs. 8532 records in RAM.
INFO	2026-06-08 09:12:23	MarkDuplicates	Read   474,000,000 records.  Elapsed time: 00:14:49s.  Time for last 1,000,000:    1s.  Last read position: chr16:88,643,300
INFO	2026-06-08 09:12:23	MarkDuplicates	Tracking 469809 as yet unmatched pairs. 6881 records in RAM.
INFO	2026-06-08 09:12:25	MarkDuplicates	Read   475,000,000 records.  Elapsed time: 00:14:51s.  Time for last 1,000,000:    2s.  Last read position: chr16:89,561,599
INFO	2026-06-08 09:12:25	MarkDuplicates	Tracking 472169 as yet unmatched pairs. 9237 records in RAM.
INFO	2026-06-08 09:12:28	MarkDuplicates	Read   476,000,000 records.  Elapsed time: 00:14:54s.  Time for last 1,000,000:    3s.  Last read position: chr17:1,361,995
INFO	2026-06-08 09:12:28	MarkDuplicates	Tracking 468609 as yet unmatched pairs. 158217 records in RAM.
INFO	2026-06-08 09:12:30	MarkDuplicates	Read   477,000,000 records.  Elapsed time: 00:14:56s.  Time for last 1,000,000:    1s.  Last read position: chr17:1,728,060
INFO	2026-06-08 09:12:30	MarkDuplicates	Tracking 459026 as yet unmatched pairs. 148631 records in RAM.
INFO	2026-06-08 09:12:31	MarkDuplicates	Read   478,000,000 records.  Elapsed time: 00:14:57s.  Time for last 1,000,000:    1s.  Last read position: chr17:4,076,926
INFO	2026-06-08 09:12:31	MarkDuplicates	Tracking 455541 as yet unmatched pairs. 145139 records in RAM.
INFO	2026-06-08 09:12:33	MarkDuplicates	Read   479,000,000 records.  Elapsed time: 00:14:59s.  Time for last 1,000,000:    1s.  Last read position: chr17:5,020,587
INFO	2026-06-08 09:12:33	MarkDuplicates	Tracking 452507 as yet unmatched pairs. 142104 records in RAM.
INFO	2026-06-08 09:12:35	MarkDuplicates	Read   480,000,000 records.  Elapsed time: 00:15:01s.  Time for last 1,000,000:    1s.  Last read position: chr17:7,311,110
INFO	2026-06-08 09:12:35	MarkDuplicates	Tracking 450745 as yet unmatched pairs. 140341 records in RAM.
INFO	2026-06-08 09:12:36	MarkDuplicates	Read   481,000,000 records.  Elapsed time: 00:15:02s.  Time for last 1,000,000:    1s.  Last read position: chr17:7,566,957
INFO	2026-06-08 09:12:36	MarkDuplicates	Tracking 446755 as yet unmatched pairs. 136351 records in RAM.
INFO	2026-06-08 09:12:38	MarkDuplicates	Read   482,000,000 records.  Elapsed time: 00:15:04s.  Time for last 1,000,000:    1s.  Last read position: chr17:8,039,225
INFO	2026-06-08 09:12:38	MarkDuplicates	Tracking 444507 as yet unmatched pairs. 134103 records in RAM.
INFO	2026-06-08 09:12:40	MarkDuplicates	Read   483,000,000 records.  Elapsed time: 00:15:06s.  Time for last 1,000,000:    1s.  Last read position: chr17:8,888,293
INFO	2026-06-08 09:12:40	MarkDuplicates	Tracking 440914 as yet unmatched pairs. 130506 records in RAM.
INFO	2026-06-08 09:12:41	MarkDuplicates	Read   484,000,000 records.  Elapsed time: 00:15:07s.  Time for last 1,000,000:    1s.  Last read position: chr17:17,142,722
INFO	2026-06-08 09:12:41	MarkDuplicates	Tracking 438805 as yet unmatched pairs. 128387 records in RAM.
INFO	2026-06-08 09:12:43	MarkDuplicates	Read   485,000,000 records.  Elapsed time: 00:15:09s.  Time for last 1,000,000:    1s.  Last read position: chr17:18,246,970
INFO	2026-06-08 09:12:43	MarkDuplicates	Tracking 434830 as yet unmatched pairs. 124408 records in RAM.
INFO	2026-06-08 09:12:45	MarkDuplicates	Read   486,000,000 records.  Elapsed time: 00:15:11s.  Time for last 1,000,000:    1s.  Last read position: chr17:27,640,617
INFO	2026-06-08 09:12:45	MarkDuplicates	Tracking 433511 as yet unmatched pairs. 123089 records in RAM.
INFO	2026-06-08 09:12:46	MarkDuplicates	Read   487,000,000 records.  Elapsed time: 00:15:12s.  Time for last 1,000,000:    1s.  Last read position: chr17:28,912,955
INFO	2026-06-08 09:12:46	MarkDuplicates	Tracking 429122 as yet unmatched pairs. 118695 records in RAM.
INFO	2026-06-08 09:12:48	MarkDuplicates	Read   488,000,000 records.  Elapsed time: 00:15:14s.  Time for last 1,000,000:    1s.  Last read position: chr17:31,937,467
INFO	2026-06-08 09:12:48	MarkDuplicates	Tracking 426881 as yet unmatched pairs. 116450 records in RAM.
INFO	2026-06-08 09:12:50	MarkDuplicates	Read   489,000,000 records.  Elapsed time: 00:15:16s.  Time for last 1,000,000:    2s.  Last read position: chr17:35,844,934
INFO	2026-06-08 09:12:50	MarkDuplicates	Tracking 423859 as yet unmatched pairs. 113421 records in RAM.
INFO	2026-06-08 09:12:52	MarkDuplicates	Read   490,000,000 records.  Elapsed time: 00:15:18s.  Time for last 1,000,000:    1s.  Last read position: chr17:38,715,899
INFO	2026-06-08 09:12:52	MarkDuplicates	Tracking 421662 as yet unmatched pairs. 111223 records in RAM.
INFO	2026-06-08 09:12:53	MarkDuplicates	Read   491,000,000 records.  Elapsed time: 00:15:19s.  Time for last 1,000,000:    1s.  Last read position: chr17:39,661,054
INFO	2026-06-08 09:12:53	MarkDuplicates	Tracking 418807 as yet unmatched pairs. 108365 records in RAM.
INFO	2026-06-08 09:12:55	MarkDuplicates	Read   492,000,000 records.  Elapsed time: 00:15:21s.  Time for last 1,000,000:    1s.  Last read position: chr17:39,904,792
INFO	2026-06-08 09:12:55	MarkDuplicates	Tracking 415299 as yet unmatched pairs. 104847 records in RAM.
INFO	2026-06-08 09:12:56	MarkDuplicates	Read   493,000,000 records.  Elapsed time: 00:15:22s.  Time for last 1,000,000:    1s.  Last read position: chr17:41,769,037
INFO	2026-06-08 09:12:56	MarkDuplicates	Tracking 412515 as yet unmatched pairs. 102061 records in RAM.
INFO	2026-06-08 09:12:58	MarkDuplicates	Read   494,000,000 records.  Elapsed time: 00:15:24s.  Time for last 1,000,000:    2s.  Last read position: chr17:42,592,056
INFO	2026-06-08 09:12:58	MarkDuplicates	Tracking 409792 as yet unmatched pairs. 99333 records in RAM.
INFO	2026-06-08 09:15:15	MarkDuplicates	Read   495,000,000 records.  Elapsed time: 00:17:41s.  Time for last 1,000,000:  136s.  Last read position: chr17:44,178,230
INFO	2026-06-08 09:15:15	MarkDuplicates	Tracking 406250 as yet unmatched pairs. 95788 records in RAM.
INFO	2026-06-08 09:15:17	MarkDuplicates	Read   496,000,000 records.  Elapsed time: 00:17:43s.  Time for last 1,000,000:    2s.  Last read position: chr17:45,518,930
INFO	2026-06-08 09:15:17	MarkDuplicates	Tracking 403307 as yet unmatched pairs. 92840 records in RAM.
INFO	2026-06-08 09:15:20	MarkDuplicates	Read   497,000,000 records.  Elapsed time: 00:17:46s.  Time for last 1,000,000:    2s.  Last read position: chr17:48,071,398
INFO	2026-06-08 09:15:20	MarkDuplicates	Tracking 401062 as yet unmatched pairs. 90585 records in RAM.
INFO	2026-06-08 09:15:21	MarkDuplicates	Read   498,000,000 records.  Elapsed time: 00:17:48s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,185,890
INFO	2026-06-08 09:15:21	MarkDuplicates	Tracking 408666 as yet unmatched pairs. 98187 records in RAM.
INFO	2026-06-08 09:15:23	MarkDuplicates	Read   499,000,000 records.  Elapsed time: 00:17:49s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,187,025
INFO	2026-06-08 09:15:23	MarkDuplicates	Tracking 458989 as yet unmatched pairs. 148510 records in RAM.
INFO	2026-06-08 09:15:25	MarkDuplicates	Read   500,000,000 records.  Elapsed time: 00:17:51s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,187,953
INFO	2026-06-08 09:15:25	MarkDuplicates	Tracking 466350 as yet unmatched pairs. 155871 records in RAM.
INFO	2026-06-08 09:15:27	MarkDuplicates	Read   501,000,000 records.  Elapsed time: 00:17:53s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,188,784
INFO	2026-06-08 09:15:27	MarkDuplicates	Tracking 462782 as yet unmatched pairs. 152301 records in RAM.
INFO	2026-06-08 09:15:30	MarkDuplicates	Read   502,000,000 records.  Elapsed time: 00:17:56s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,189,462
INFO	2026-06-08 09:15:30	MarkDuplicates	Tracking 433768 as yet unmatched pairs. 123285 records in RAM.
INFO	2026-06-08 09:15:32	MarkDuplicates	Read   503,000,000 records.  Elapsed time: 00:17:58s.  Time for last 1,000,000:    2s.  Last read position: chr17:50,190,064
INFO	2026-06-08 09:15:32	MarkDuplicates	Tracking 455661 as yet unmatched pairs. 145177 records in RAM.
INFO	2026-06-08 09:15:34	MarkDuplicates	Read   504,000,000 records.  Elapsed time: 00:18:00s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,191,428
INFO	2026-06-08 09:15:34	MarkDuplicates	Tracking 435337 as yet unmatched pairs. 124853 records in RAM.
INFO	2026-06-08 09:15:36	MarkDuplicates	Read   505,000,000 records.  Elapsed time: 00:18:02s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,192,662
INFO	2026-06-08 09:15:36	MarkDuplicates	Tracking 448912 as yet unmatched pairs. 138421 records in RAM.
INFO	2026-06-08 09:15:37	MarkDuplicates	Read   506,000,000 records.  Elapsed time: 00:18:03s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,193,982
INFO	2026-06-08 09:15:37	MarkDuplicates	Tracking 448884 as yet unmatched pairs. 138392 records in RAM.
INFO	2026-06-08 09:15:39	MarkDuplicates	Read   507,000,000 records.  Elapsed time: 00:18:05s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,194,576
INFO	2026-06-08 09:15:39	MarkDuplicates	Tracking 426329 as yet unmatched pairs. 115837 records in RAM.
INFO	2026-06-08 09:15:41	MarkDuplicates	Read   508,000,000 records.  Elapsed time: 00:18:07s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,195,275
INFO	2026-06-08 09:15:41	MarkDuplicates	Tracking 434807 as yet unmatched pairs. 124315 records in RAM.
INFO	2026-06-08 09:15:43	MarkDuplicates	Read   509,000,000 records.  Elapsed time: 00:18:09s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,195,951
INFO	2026-06-08 09:15:43	MarkDuplicates	Tracking 421800 as yet unmatched pairs. 111304 records in RAM.
INFO	2026-06-08 09:15:45	MarkDuplicates	Read   510,000,000 records.  Elapsed time: 00:18:11s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,196,504
INFO	2026-06-08 09:15:45	MarkDuplicates	Tracking 435118 as yet unmatched pairs. 124619 records in RAM.
INFO	2026-06-08 09:15:46	MarkDuplicates	Read   511,000,000 records.  Elapsed time: 00:18:13s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,197,757
INFO	2026-06-08 09:15:46	MarkDuplicates	Tracking 419989 as yet unmatched pairs. 109488 records in RAM.
INFO	2026-06-08 09:15:48	MarkDuplicates	Read   512,000,000 records.  Elapsed time: 00:18:14s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,199,315
INFO	2026-06-08 09:15:48	MarkDuplicates	Tracking 383695 as yet unmatched pairs. 73184 records in RAM.
INFO	2026-06-08 09:15:50	MarkDuplicates	Read   513,000,000 records.  Elapsed time: 00:18:16s.  Time for last 1,000,000:    1s.  Last read position: chr17:50,659,280
INFO	2026-06-08 09:15:50	MarkDuplicates	Tracking 351935 as yet unmatched pairs. 41415 records in RAM.
INFO	2026-06-08 09:15:52	MarkDuplicates	Read   514,000,000 records.  Elapsed time: 00:18:18s.  Time for last 1,000,000:    1s.  Last read position: chr17:58,083,582
INFO	2026-06-08 09:15:52	MarkDuplicates	Tracking 348473 as yet unmatched pairs. 37951 records in RAM.
INFO	2026-06-08 09:15:53	MarkDuplicates	Read   515,000,000 records.  Elapsed time: 00:18:19s.  Time for last 1,000,000:    1s.  Last read position: chr17:59,682,761
INFO	2026-06-08 09:15:53	MarkDuplicates	Tracking 350219 as yet unmatched pairs. 39688 records in RAM.
INFO	2026-06-08 09:15:55	MarkDuplicates	Read   516,000,000 records.  Elapsed time: 00:18:21s.  Time for last 1,000,000:    1s.  Last read position: chr17:63,314,437
INFO	2026-06-08 09:15:55	MarkDuplicates	Tracking 343091 as yet unmatched pairs. 32557 records in RAM.
INFO	2026-06-08 09:15:57	MarkDuplicates	Read   517,000,000 records.  Elapsed time: 00:18:23s.  Time for last 1,000,000:    1s.  Last read position: chr17:64,504,725
INFO	2026-06-08 09:15:57	MarkDuplicates	Tracking 340714 as yet unmatched pairs. 30173 records in RAM.
INFO	2026-06-08 09:15:59	MarkDuplicates	Read   518,000,000 records.  Elapsed time: 00:18:25s.  Time for last 1,000,000:    1s.  Last read position: chr17:68,528,925
INFO	2026-06-08 09:15:59	MarkDuplicates	Tracking 338616 as yet unmatched pairs. 28072 records in RAM.
INFO	2026-06-08 09:16:01	MarkDuplicates	Read   519,000,000 records.  Elapsed time: 00:18:27s.  Time for last 1,000,000:    2s.  Last read position: chr17:75,231,574
INFO	2026-06-08 09:16:01	MarkDuplicates	Tracking 334208 as yet unmatched pairs. 23662 records in RAM.
INFO	2026-06-08 09:16:03	MarkDuplicates	Read   520,000,000 records.  Elapsed time: 00:18:29s.  Time for last 1,000,000:    2s.  Last read position: chr17:75,836,399
INFO	2026-06-08 09:16:03	MarkDuplicates	Tracking 331246 as yet unmatched pairs. 20698 records in RAM.
INFO	2026-06-08 09:16:05	MarkDuplicates	Read   521,000,000 records.  Elapsed time: 00:18:31s.  Time for last 1,000,000:    1s.  Last read position: chr17:77,402,406
INFO	2026-06-08 09:16:05	MarkDuplicates	Tracking 328968 as yet unmatched pairs. 18419 records in RAM.
INFO	2026-06-08 09:16:06	MarkDuplicates	Read   522,000,000 records.  Elapsed time: 00:18:32s.  Time for last 1,000,000:    1s.  Last read position: chr17:78,979,757
INFO	2026-06-08 09:16:06	MarkDuplicates	Tracking 324210 as yet unmatched pairs. 13660 records in RAM.
INFO	2026-06-08 09:16:08	MarkDuplicates	Read   523,000,000 records.  Elapsed time: 00:18:34s.  Time for last 1,000,000:    1s.  Last read position: chr17:81,057,921
INFO	2026-06-08 09:16:08	MarkDuplicates	Tracking 321579 as yet unmatched pairs. 11027 records in RAM.
INFO	2026-06-08 09:16:10	MarkDuplicates	Read   524,000,000 records.  Elapsed time: 00:18:36s.  Time for last 1,000,000:    1s.  Last read position: chr17:81,690,675
INFO	2026-06-08 09:16:10	MarkDuplicates	Tracking 318274 as yet unmatched pairs. 7714 records in RAM.
INFO	2026-06-08 09:16:11	MarkDuplicates	Read   525,000,000 records.  Elapsed time: 00:18:37s.  Time for last 1,000,000:    1s.  Last read position: chr17:82,059,977
INFO	2026-06-08 09:16:11	MarkDuplicates	Tracking 315108 as yet unmatched pairs. 4547 records in RAM.
INFO	2026-06-08 09:16:13	MarkDuplicates	Read   526,000,000 records.  Elapsed time: 00:18:39s.  Time for last 1,000,000:    1s.  Last read position: chr17:82,750,641
INFO	2026-06-08 09:16:13	MarkDuplicates	Tracking 311210 as yet unmatched pairs. 642 records in RAM.
INFO	2026-06-08 09:16:14	MarkDuplicates	Read   527,000,000 records.  Elapsed time: 00:18:40s.  Time for last 1,000,000:    1s.  Last read position: chr18:9,577,067
INFO	2026-06-08 09:16:14	MarkDuplicates	Tracking 308615 as yet unmatched pairs. 10974 records in RAM.
INFO	2026-06-08 09:16:16	MarkDuplicates	Read   528,000,000 records.  Elapsed time: 00:18:42s.  Time for last 1,000,000:    2s.  Last read position: chr18:26,852,332
INFO	2026-06-08 09:16:16	MarkDuplicates	Tracking 305823 as yet unmatched pairs. 8175 records in RAM.
INFO	2026-06-08 09:16:18	MarkDuplicates	Read   529,000,000 records.  Elapsed time: 00:18:44s.  Time for last 1,000,000:    1s.  Last read position: chr18:49,430,289
INFO	2026-06-08 09:16:18	MarkDuplicates	Tracking 303447 as yet unmatched pairs. 5798 records in RAM.
INFO	2026-06-08 09:16:19	MarkDuplicates	Read   530,000,000 records.  Elapsed time: 00:18:45s.  Time for last 1,000,000:    1s.  Last read position: chr18:62,264,040
INFO	2026-06-08 09:16:19	MarkDuplicates	Tracking 300824 as yet unmatched pairs. 3169 records in RAM.
INFO	2026-06-08 09:16:22	MarkDuplicates	Read   531,000,000 records.  Elapsed time: 00:18:48s.  Time for last 1,000,000:    2s.  Last read position: chr19:572,608
INFO	2026-06-08 09:16:22	MarkDuplicates	Tracking 299116 as yet unmatched pairs. 138450 records in RAM.
INFO	2026-06-08 09:16:24	MarkDuplicates	Read   532,000,000 records.  Elapsed time: 00:18:50s.  Time for last 1,000,000:    2s.  Last read position: chr19:1,036,499
INFO	2026-06-08 09:16:24	MarkDuplicates	Tracking 294652 as yet unmatched pairs. 133977 records in RAM.
INFO	2026-06-08 09:16:25	MarkDuplicates	Read   533,000,000 records.  Elapsed time: 00:18:52s.  Time for last 1,000,000:    1s.  Last read position: chr19:1,257,190
INFO	2026-06-08 09:16:25	MarkDuplicates	Tracking 290234 as yet unmatched pairs. 129557 records in RAM.
INFO	2026-06-08 09:16:28	MarkDuplicates	Read   534,000,000 records.  Elapsed time: 00:18:54s.  Time for last 1,000,000:    2s.  Last read position: chr19:1,979,575
INFO	2026-06-08 09:16:28	MarkDuplicates	Tracking 286459 as yet unmatched pairs. 125776 records in RAM.
INFO	2026-06-08 09:16:30	MarkDuplicates	Read   535,000,000 records.  Elapsed time: 00:18:56s.  Time for last 1,000,000:    2s.  Last read position: chr19:3,000,707
INFO	2026-06-08 09:16:30	MarkDuplicates	Tracking 283486 as yet unmatched pairs. 122798 records in RAM.
INFO	2026-06-08 09:16:32	MarkDuplicates	Read   536,000,000 records.  Elapsed time: 00:18:58s.  Time for last 1,000,000:    1s.  Last read position: chr19:4,101,229
INFO	2026-06-08 09:16:32	MarkDuplicates	Tracking 280435 as yet unmatched pairs. 119745 records in RAM.
INFO	2026-06-08 09:16:34	MarkDuplicates	Read   537,000,000 records.  Elapsed time: 00:19:00s.  Time for last 1,000,000:    1s.  Last read position: chr19:5,649,141
INFO	2026-06-08 09:16:34	MarkDuplicates	Tracking 276752 as yet unmatched pairs. 116060 records in RAM.
INFO	2026-06-08 09:16:35	MarkDuplicates	Read   538,000,000 records.  Elapsed time: 00:19:01s.  Time for last 1,000,000:    1s.  Last read position: chr19:6,684,571
INFO	2026-06-08 09:16:35	MarkDuplicates	Tracking 276396 as yet unmatched pairs. 115704 records in RAM.
INFO	2026-06-08 09:16:37	MarkDuplicates	Read   539,000,000 records.  Elapsed time: 00:19:03s.  Time for last 1,000,000:    1s.  Last read position: chr19:7,184,376
INFO	2026-06-08 09:16:37	MarkDuplicates	Tracking 270130 as yet unmatched pairs. 109435 records in RAM.
INFO	2026-06-08 09:16:39	MarkDuplicates	Read   540,000,000 records.  Elapsed time: 00:19:05s.  Time for last 1,000,000:    2s.  Last read position: chr19:8,402,215
INFO	2026-06-08 09:16:39	MarkDuplicates	Tracking 268128 as yet unmatched pairs. 107433 records in RAM.
INFO	2026-06-08 09:16:41	MarkDuplicates	Read   541,000,000 records.  Elapsed time: 00:19:07s.  Time for last 1,000,000:    1s.  Last read position: chr19:10,109,979
INFO	2026-06-08 09:16:41	MarkDuplicates	Tracking 263764 as yet unmatched pairs. 103066 records in RAM.
INFO	2026-06-08 09:16:42	MarkDuplicates	Read   542,000,000 records.  Elapsed time: 00:19:08s.  Time for last 1,000,000:    1s.  Last read position: chr19:10,635,488
INFO	2026-06-08 09:16:42	MarkDuplicates	Tracking 261132 as yet unmatched pairs. 100434 records in RAM.
INFO	2026-06-08 09:16:44	MarkDuplicates	Read   543,000,000 records.  Elapsed time: 00:19:10s.  Time for last 1,000,000:    1s.  Last read position: chr19:11,325,478
INFO	2026-06-08 09:16:44	MarkDuplicates	Tracking 257707 as yet unmatched pairs. 97009 records in RAM.
INFO	2026-06-08 09:16:46	MarkDuplicates	Read   544,000,000 records.  Elapsed time: 00:19:12s.  Time for last 1,000,000:    1s.  Last read position: chr19:12,734,429
INFO	2026-06-08 09:16:46	MarkDuplicates	Tracking 255581 as yet unmatched pairs. 94882 records in RAM.
INFO	2026-06-08 09:16:47	MarkDuplicates	Read   545,000,000 records.  Elapsed time: 00:19:13s.  Time for last 1,000,000:    1s.  Last read position: chr19:13,762,422
INFO	2026-06-08 09:16:47	MarkDuplicates	Tracking 250922 as yet unmatched pairs. 90221 records in RAM.
INFO	2026-06-08 09:16:49	MarkDuplicates	Read   546,000,000 records.  Elapsed time: 00:19:15s.  Time for last 1,000,000:    1s.  Last read position: chr19:14,478,434
INFO	2026-06-08 09:16:49	MarkDuplicates	Tracking 248310 as yet unmatched pairs. 87609 records in RAM.
INFO	2026-06-08 09:16:50	MarkDuplicates	Read   547,000,000 records.  Elapsed time: 00:19:16s.  Time for last 1,000,000:    1s.  Last read position: chr19:15,192,470
INFO	2026-06-08 09:16:50	MarkDuplicates	Tracking 245295 as yet unmatched pairs. 84594 records in RAM.
INFO	2026-06-08 09:16:52	MarkDuplicates	Read   548,000,000 records.  Elapsed time: 00:19:18s.  Time for last 1,000,000:    2s.  Last read position: chr19:16,325,591
INFO	2026-06-08 09:16:52	MarkDuplicates	Tracking 241040 as yet unmatched pairs. 80338 records in RAM.
INFO	2026-06-08 09:16:54	MarkDuplicates	Read   549,000,000 records.  Elapsed time: 00:19:20s.  Time for last 1,000,000:    1s.  Last read position: chr19:17,726,198
INFO	2026-06-08 09:16:54	MarkDuplicates	Tracking 237710 as yet unmatched pairs. 77006 records in RAM.
INFO	2026-06-08 09:16:57	MarkDuplicates	Read   550,000,000 records.  Elapsed time: 00:19:23s.  Time for last 1,000,000:    2s.  Last read position: chr19:18,432,014
INFO	2026-06-08 09:16:57	MarkDuplicates	Tracking 235679 as yet unmatched pairs. 74974 records in RAM.
INFO	2026-06-08 09:16:59	MarkDuplicates	Read   551,000,000 records.  Elapsed time: 00:19:25s.  Time for last 1,000,000:    2s.  Last read position: chr19:19,199,196
INFO	2026-06-08 09:16:59	MarkDuplicates	Tracking 231281 as yet unmatched pairs. 70576 records in RAM.
INFO	2026-06-08 09:17:00	MarkDuplicates	Read   552,000,000 records.  Elapsed time: 00:19:27s.  Time for last 1,000,000:    1s.  Last read position: chr19:34,342,033
INFO	2026-06-08 09:17:00	MarkDuplicates	Tracking 227839 as yet unmatched pairs. 67134 records in RAM.
INFO	2026-06-08 09:17:02	MarkDuplicates	Read   553,000,000 records.  Elapsed time: 00:19:28s.  Time for last 1,000,000:    1s.  Last read position: chr19:35,721,053
INFO	2026-06-08 09:17:02	MarkDuplicates	Tracking 224675 as yet unmatched pairs. 63970 records in RAM.
INFO	2026-06-08 09:17:04	MarkDuplicates	Read   554,000,000 records.  Elapsed time: 00:19:30s.  Time for last 1,000,000:    1s.  Last read position: chr19:38,291,860
INFO	2026-06-08 09:17:04	MarkDuplicates	Tracking 222729 as yet unmatched pairs. 62015 records in RAM.
INFO	2026-06-08 09:17:06	MarkDuplicates	Read   555,000,000 records.  Elapsed time: 00:19:32s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,390,079
INFO	2026-06-08 09:17:06	MarkDuplicates	Tracking 218515 as yet unmatched pairs. 57801 records in RAM.
INFO	2026-06-08 09:17:08	MarkDuplicates	Read   556,000,000 records.  Elapsed time: 00:19:34s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,474,689
INFO	2026-06-08 09:17:08	MarkDuplicates	Tracking 215283 as yet unmatched pairs. 54561 records in RAM.
INFO	2026-06-08 09:17:09	MarkDuplicates	Read   557,000,000 records.  Elapsed time: 00:19:35s.  Time for last 1,000,000:    1s.  Last read position: chr19:40,235,997
INFO	2026-06-08 09:17:09	MarkDuplicates	Tracking 213423 as yet unmatched pairs. 52699 records in RAM.
INFO	2026-06-08 09:17:11	MarkDuplicates	Read   558,000,000 records.  Elapsed time: 00:19:37s.  Time for last 1,000,000:    1s.  Last read position: chr19:40,627,757
INFO	2026-06-08 09:17:11	MarkDuplicates	Tracking 212346 as yet unmatched pairs. 51619 records in RAM.
INFO	2026-06-08 09:17:13	MarkDuplicates	Read   559,000,000 records.  Elapsed time: 00:19:39s.  Time for last 1,000,000:    1s.  Last read position: chr19:41,869,136
INFO	2026-06-08 09:17:13	MarkDuplicates	Tracking 209113 as yet unmatched pairs. 48386 records in RAM.
INFO	2026-06-08 09:17:15	MarkDuplicates	Read   560,000,000 records.  Elapsed time: 00:19:41s.  Time for last 1,000,000:    2s.  Last read position: chr19:42,287,563
INFO	2026-06-08 09:17:15	MarkDuplicates	Tracking 203770 as yet unmatched pairs. 43037 records in RAM.
INFO	2026-06-08 09:17:17	MarkDuplicates	Read   561,000,000 records.  Elapsed time: 00:19:43s.  Time for last 1,000,000:    1s.  Last read position: chr19:43,780,789
INFO	2026-06-08 09:17:17	MarkDuplicates	Tracking 198942 as yet unmatched pairs. 38200 records in RAM.
INFO	2026-06-08 09:17:19	MarkDuplicates	Read   562,000,000 records.  Elapsed time: 00:19:45s.  Time for last 1,000,000:    1s.  Last read position: chr19:44,990,472
INFO	2026-06-08 09:17:19	MarkDuplicates	Tracking 195733 as yet unmatched pairs. 34991 records in RAM.
INFO	2026-06-08 09:17:21	MarkDuplicates	Read   563,000,000 records.  Elapsed time: 00:19:47s.  Time for last 1,000,000:    2s.  Last read position: chr19:45,835,172
INFO	2026-06-08 09:17:21	MarkDuplicates	Tracking 192821 as yet unmatched pairs. 32079 records in RAM.
INFO	2026-06-08 09:17:23	MarkDuplicates	Read   564,000,000 records.  Elapsed time: 00:19:49s.  Time for last 1,000,000:    2s.  Last read position: chr19:47,609,152
INFO	2026-06-08 09:17:23	MarkDuplicates	Tracking 188510 as yet unmatched pairs. 27768 records in RAM.
INFO	2026-06-08 09:17:25	MarkDuplicates	Read   565,000,000 records.  Elapsed time: 00:19:51s.  Time for last 1,000,000:    1s.  Last read position: chr19:48,739,410
INFO	2026-06-08 09:17:25	MarkDuplicates	Tracking 185007 as yet unmatched pairs. 24264 records in RAM.
INFO	2026-06-08 09:17:28	MarkDuplicates	Read   566,000,000 records.  Elapsed time: 00:19:54s.  Time for last 1,000,000:    2s.  Last read position: chr19:49,489,900
INFO	2026-06-08 09:17:28	MarkDuplicates	Tracking 195534 as yet unmatched pairs. 34791 records in RAM.
INFO	2026-06-08 09:17:30	MarkDuplicates	Read   567,000,000 records.  Elapsed time: 00:19:56s.  Time for last 1,000,000:    2s.  Last read position: chr19:49,661,823
INFO	2026-06-08 09:17:30	MarkDuplicates	Tracking 179403 as yet unmatched pairs. 18659 records in RAM.
INFO	2026-06-08 09:17:32	MarkDuplicates	Read   568,000,000 records.  Elapsed time: 00:19:58s.  Time for last 1,000,000:    1s.  Last read position: chr19:50,358,725
INFO	2026-06-08 09:17:32	MarkDuplicates	Tracking 178574 as yet unmatched pairs. 17822 records in RAM.
INFO	2026-06-08 09:17:33	MarkDuplicates	Read   569,000,000 records.  Elapsed time: 00:19:59s.  Time for last 1,000,000:    1s.  Last read position: chr19:51,896,518
INFO	2026-06-08 09:17:33	MarkDuplicates	Tracking 172545 as yet unmatched pairs. 11787 records in RAM.
INFO	2026-06-08 09:17:35	MarkDuplicates	Read   570,000,000 records.  Elapsed time: 00:20:01s.  Time for last 1,000,000:    1s.  Last read position: chr19:54,254,961
INFO	2026-06-08 09:17:35	MarkDuplicates	Tracking 169908 as yet unmatched pairs. 9143 records in RAM.
INFO	2026-06-08 09:17:37	MarkDuplicates	Read   571,000,000 records.  Elapsed time: 00:20:03s.  Time for last 1,000,000:    2s.  Last read position: chr19:55,483,710
INFO	2026-06-08 09:17:37	MarkDuplicates	Tracking 166783 as yet unmatched pairs. 6016 records in RAM.
INFO	2026-06-08 09:17:39	MarkDuplicates	Read   572,000,000 records.  Elapsed time: 00:20:05s.  Time for last 1,000,000:    1s.  Last read position: chr19:57,859,646
INFO	2026-06-08 09:17:39	MarkDuplicates	Tracking 163443 as yet unmatched pairs. 2670 records in RAM.
INFO	2026-06-08 09:17:41	MarkDuplicates	Read   573,000,000 records.  Elapsed time: 00:20:07s.  Time for last 1,000,000:    2s.  Last read position: chr20:1,135,193
INFO	2026-06-08 09:17:41	MarkDuplicates	Tracking 160232 as yet unmatched pairs. 38895 records in RAM.
INFO	2026-06-08 09:17:44	MarkDuplicates	Read   574,000,000 records.  Elapsed time: 00:20:10s.  Time for last 1,000,000:    2s.  Last read position: chr20:3,786,045
INFO	2026-06-08 09:17:44	MarkDuplicates	Tracking 157582 as yet unmatched pairs. 36245 records in RAM.
INFO	2026-06-08 09:17:46	MarkDuplicates	Read   575,000,000 records.  Elapsed time: 00:20:12s.  Time for last 1,000,000:    1s.  Last read position: chr20:17,641,905
INFO	2026-06-08 09:17:46	MarkDuplicates	Tracking 154594 as yet unmatched pairs. 33257 records in RAM.
INFO	2026-06-08 09:17:47	MarkDuplicates	Read   576,000,000 records.  Elapsed time: 00:20:13s.  Time for last 1,000,000:    1s.  Last read position: chr20:23,985,744
INFO	2026-06-08 09:17:47	MarkDuplicates	Tracking 151683 as yet unmatched pairs. 30346 records in RAM.
INFO	2026-06-08 09:17:49	MarkDuplicates	Read   577,000,000 records.  Elapsed time: 00:20:15s.  Time for last 1,000,000:    1s.  Last read position: chr20:34,073,577
INFO	2026-06-08 09:17:49	MarkDuplicates	Tracking 148238 as yet unmatched pairs. 26901 records in RAM.
INFO	2026-06-08 09:17:51	MarkDuplicates	Read   578,000,000 records.  Elapsed time: 00:20:17s.  Time for last 1,000,000:    1s.  Last read position: chr20:35,742,025
INFO	2026-06-08 09:17:51	MarkDuplicates	Tracking 144840 as yet unmatched pairs. 23502 records in RAM.
INFO	2026-06-08 09:17:53	MarkDuplicates	Read   579,000,000 records.  Elapsed time: 00:20:19s.  Time for last 1,000,000:    1s.  Last read position: chr20:38,771,687
INFO	2026-06-08 09:17:53	MarkDuplicates	Tracking 141629 as yet unmatched pairs. 20287 records in RAM.
INFO	2026-06-08 09:17:55	MarkDuplicates	Read   580,000,000 records.  Elapsed time: 00:20:21s.  Time for last 1,000,000:    2s.  Last read position: chr20:45,330,438
INFO	2026-06-08 09:17:55	MarkDuplicates	Tracking 147455 as yet unmatched pairs. 26110 records in RAM.
INFO	2026-06-08 09:17:57	MarkDuplicates	Read   581,000,000 records.  Elapsed time: 00:20:23s.  Time for last 1,000,000:    1s.  Last read position: chr20:46,013,376
INFO	2026-06-08 09:17:57	MarkDuplicates	Tracking 136579 as yet unmatched pairs. 15234 records in RAM.
INFO	2026-06-08 09:17:59	MarkDuplicates	Read   582,000,000 records.  Elapsed time: 00:20:25s.  Time for last 1,000,000:    1s.  Last read position: chr20:50,891,425
INFO	2026-06-08 09:17:59	MarkDuplicates	Tracking 133268 as yet unmatched pairs. 11919 records in RAM.
INFO	2026-06-08 09:18:01	MarkDuplicates	Read   583,000,000 records.  Elapsed time: 00:20:27s.  Time for last 1,000,000:    1s.  Last read position: chr20:58,910,028
INFO	2026-06-08 09:18:01	MarkDuplicates	Tracking 132496 as yet unmatched pairs. 11146 records in RAM.
INFO	2026-06-08 09:18:03	MarkDuplicates	Read   584,000,000 records.  Elapsed time: 00:20:29s.  Time for last 1,000,000:    1s.  Last read position: chr20:62,656,601
INFO	2026-06-08 09:18:03	MarkDuplicates	Tracking 126305 as yet unmatched pairs. 4953 records in RAM.
INFO	2026-06-08 09:18:05	MarkDuplicates	Read   585,000,000 records.  Elapsed time: 00:20:31s.  Time for last 1,000,000:    2s.  Last read position: chr20:63,862,247
INFO	2026-06-08 09:18:05	MarkDuplicates	Tracking 122498 as yet unmatched pairs. 1141 records in RAM.
INFO	2026-06-08 09:18:07	MarkDuplicates	Read   586,000,000 records.  Elapsed time: 00:20:33s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,217,384
INFO	2026-06-08 09:18:07	MarkDuplicates	Tracking 119694 as yet unmatched pairs. 22272 records in RAM.
INFO	2026-06-08 09:18:08	MarkDuplicates	Read   587,000,000 records.  Elapsed time: 00:20:34s.  Time for last 1,000,000:    1s.  Last read position: chr21:21,477,386
INFO	2026-06-08 09:18:08	MarkDuplicates	Tracking 118033 as yet unmatched pairs. 20610 records in RAM.
INFO	2026-06-08 09:18:10	MarkDuplicates	Read   588,000,000 records.  Elapsed time: 00:20:36s.  Time for last 1,000,000:    1s.  Last read position: chr21:32,609,841
INFO	2026-06-08 09:18:10	MarkDuplicates	Tracking 115219 as yet unmatched pairs. 17793 records in RAM.
INFO	2026-06-08 09:18:12	MarkDuplicates	Read   589,000,000 records.  Elapsed time: 00:20:38s.  Time for last 1,000,000:    1s.  Last read position: chr21:36,070,376
INFO	2026-06-08 09:18:12	MarkDuplicates	Tracking 112359 as yet unmatched pairs. 14929 records in RAM.
INFO	2026-06-08 09:18:14	MarkDuplicates	Read   590,000,000 records.  Elapsed time: 00:20:40s.  Time for last 1,000,000:    1s.  Last read position: chr21:41,756,620
INFO	2026-06-08 09:18:14	MarkDuplicates	Tracking 109003 as yet unmatched pairs. 11573 records in RAM.
INFO	2026-06-08 09:18:15	MarkDuplicates	Read   591,000,000 records.  Elapsed time: 00:20:41s.  Time for last 1,000,000:    1s.  Last read position: chr21:44,777,344
INFO	2026-06-08 09:18:15	MarkDuplicates	Tracking 107450 as yet unmatched pairs. 10020 records in RAM.
INFO	2026-06-08 09:18:17	MarkDuplicates	Read   592,000,000 records.  Elapsed time: 00:20:43s.  Time for last 1,000,000:    1s.  Last read position: chr21:45,512,238
INFO	2026-06-08 09:18:17	MarkDuplicates	Tracking 104419 as yet unmatched pairs. 6989 records in RAM.
INFO	2026-06-08 09:18:19	MarkDuplicates	Read   593,000,000 records.  Elapsed time: 00:20:45s.  Time for last 1,000,000:    1s.  Last read position: chr21:46,124,696
INFO	2026-06-08 09:18:19	MarkDuplicates	Tracking 102844 as yet unmatched pairs. 5414 records in RAM.
INFO	2026-06-08 09:18:21	MarkDuplicates	Read   594,000,000 records.  Elapsed time: 00:20:47s.  Time for last 1,000,000:    2s.  Last read position: chr22:19,041,067
INFO	2026-06-08 09:18:21	MarkDuplicates	Tracking 96356 as yet unmatched pairs. 44544 records in RAM.
INFO	2026-06-08 09:18:23	MarkDuplicates	Read   595,000,000 records.  Elapsed time: 00:20:49s.  Time for last 1,000,000:    2s.  Last read position: chr22:20,918,182
INFO	2026-06-08 09:18:23	MarkDuplicates	Tracking 93264 as yet unmatched pairs. 41452 records in RAM.
INFO	2026-06-08 09:18:25	MarkDuplicates	Read   596,000,000 records.  Elapsed time: 00:20:51s.  Time for last 1,000,000:    1s.  Last read position: chr22:23,767,431
INFO	2026-06-08 09:18:25	MarkDuplicates	Tracking 90004 as yet unmatched pairs. 38192 records in RAM.
INFO	2026-06-08 09:18:27	MarkDuplicates	Read   597,000,000 records.  Elapsed time: 00:20:53s.  Time for last 1,000,000:    1s.  Last read position: chr22:26,453,385
INFO	2026-06-08 09:18:27	MarkDuplicates	Tracking 86076 as yet unmatched pairs. 34264 records in RAM.
INFO	2026-06-08 09:18:29	MarkDuplicates	Read   598,000,000 records.  Elapsed time: 00:20:55s.  Time for last 1,000,000:    1s.  Last read position: chr22:29,311,506
INFO	2026-06-08 09:18:29	MarkDuplicates	Tracking 83158 as yet unmatched pairs. 31346 records in RAM.
INFO	2026-06-08 09:18:30	MarkDuplicates	Read   599,000,000 records.  Elapsed time: 00:20:57s.  Time for last 1,000,000:    1s.  Last read position: chr22:31,650,699
INFO	2026-06-08 09:18:30	MarkDuplicates	Tracking 79947 as yet unmatched pairs. 28135 records in RAM.
INFO	2026-06-08 09:18:32	MarkDuplicates	Read   600,000,000 records.  Elapsed time: 00:20:58s.  Time for last 1,000,000:    1s.  Last read position: chr22:36,288,724
INFO	2026-06-08 09:18:32	MarkDuplicates	Tracking 78082 as yet unmatched pairs. 26270 records in RAM.
INFO	2026-06-08 09:18:34	MarkDuplicates	Read   601,000,000 records.  Elapsed time: 00:21:00s.  Time for last 1,000,000:    1s.  Last read position: chr22:37,491,809
INFO	2026-06-08 09:18:34	MarkDuplicates	Tracking 74003 as yet unmatched pairs. 22191 records in RAM.
INFO	2026-06-08 09:18:36	MarkDuplicates	Read   602,000,000 records.  Elapsed time: 00:21:02s.  Time for last 1,000,000:    1s.  Last read position: chr22:38,505,953
INFO	2026-06-08 09:18:36	MarkDuplicates	Tracking 72705 as yet unmatched pairs. 20884 records in RAM.
INFO	2026-06-08 09:18:37	MarkDuplicates	Read   603,000,000 records.  Elapsed time: 00:21:04s.  Time for last 1,000,000:    1s.  Last read position: chr22:40,826,576
INFO	2026-06-08 09:18:37	MarkDuplicates	Tracking 68843 as yet unmatched pairs. 17022 records in RAM.
INFO	2026-06-08 09:18:39	MarkDuplicates	Read   604,000,000 records.  Elapsed time: 00:21:05s.  Time for last 1,000,000:    1s.  Last read position: chr22:42,086,236
INFO	2026-06-08 09:18:39	MarkDuplicates	Tracking 66233 as yet unmatched pairs. 14411 records in RAM.
INFO	2026-06-08 09:18:41	MarkDuplicates	Read   605,000,000 records.  Elapsed time: 00:21:07s.  Time for last 1,000,000:    1s.  Last read position: chr22:45,563,210
INFO	2026-06-08 09:18:41	MarkDuplicates	Tracking 63053 as yet unmatched pairs. 11231 records in RAM.
INFO	2026-06-08 09:18:43	MarkDuplicates	Read   606,000,000 records.  Elapsed time: 00:21:09s.  Time for last 1,000,000:    1s.  Last read position: chr22:50,245,699
INFO	2026-06-08 09:18:43	MarkDuplicates	Tracking 58596 as yet unmatched pairs. 6774 records in RAM.
INFO	2026-06-08 09:18:45	MarkDuplicates	Read   607,000,000 records.  Elapsed time: 00:21:11s.  Time for last 1,000,000:    1s.  Last read position: chr22:50,525,758
INFO	2026-06-08 09:18:45	MarkDuplicates	Tracking 57405 as yet unmatched pairs. 5583 records in RAM.
INFO	2026-06-08 09:18:47	MarkDuplicates	Read   608,000,000 records.  Elapsed time: 00:21:13s.  Time for last 1,000,000:    2s.  Last read position: chrX:2,740,778
INFO	2026-06-08 09:18:47	MarkDuplicates	Tracking 53207 as yet unmatched pairs. 48477 records in RAM.
INFO	2026-06-08 09:18:49	MarkDuplicates	Read   609,000,000 records.  Elapsed time: 00:21:15s.  Time for last 1,000,000:    2s.  Last read position: chrX:15,845,917
INFO	2026-06-08 09:18:49	MarkDuplicates	Tracking 47980 as yet unmatched pairs. 43250 records in RAM.
INFO	2026-06-08 09:18:52	MarkDuplicates	Read   610,000,000 records.  Elapsed time: 00:21:18s.  Time for last 1,000,000:    2s.  Last read position: chrX:38,160,171
INFO	2026-06-08 09:18:52	MarkDuplicates	Tracking 45176 as yet unmatched pairs. 40443 records in RAM.
INFO	2026-06-08 09:18:53	MarkDuplicates	Read   611,000,000 records.  Elapsed time: 00:21:19s.  Time for last 1,000,000:    1s.  Last read position: chrX:47,181,780
INFO	2026-06-08 09:18:53	MarkDuplicates	Tracking 42441 as yet unmatched pairs. 37708 records in RAM.
INFO	2026-06-08 09:18:55	MarkDuplicates	Read   612,000,000 records.  Elapsed time: 00:21:21s.  Time for last 1,000,000:    1s.  Last read position: chrX:49,030,201
INFO	2026-06-08 09:18:55	MarkDuplicates	Tracking 41160 as yet unmatched pairs. 36427 records in RAM.
INFO	2026-06-08 09:18:57	MarkDuplicates	Read   613,000,000 records.  Elapsed time: 00:21:23s.  Time for last 1,000,000:    1s.  Last read position: chrX:53,236,395
INFO	2026-06-08 09:18:57	MarkDuplicates	Tracking 36780 as yet unmatched pairs. 32047 records in RAM.
INFO	2026-06-08 09:18:59	MarkDuplicates	Read   614,000,000 records.  Elapsed time: 00:21:25s.  Time for last 1,000,000:    1s.  Last read position: chrX:65,667,830
INFO	2026-06-08 09:18:59	MarkDuplicates	Tracking 37065 as yet unmatched pairs. 32332 records in RAM.
INFO	2026-06-08 09:19:01	MarkDuplicates	Read   615,000,000 records.  Elapsed time: 00:21:27s.  Time for last 1,000,000:    1s.  Last read position: chrX:71,297,410
INFO	2026-06-08 09:19:01	MarkDuplicates	Tracking 33205 as yet unmatched pairs. 28472 records in RAM.
INFO	2026-06-08 09:19:03	MarkDuplicates	Read   616,000,000 records.  Elapsed time: 00:21:29s.  Time for last 1,000,000:    2s.  Last read position: chrX:77,521,423
INFO	2026-06-08 09:19:03	MarkDuplicates	Tracking 31136 as yet unmatched pairs. 26403 records in RAM.
INFO	2026-06-08 09:19:05	MarkDuplicates	Read   617,000,000 records.  Elapsed time: 00:21:31s.  Time for last 1,000,000:    1s.  Last read position: chrX:100,676,175
INFO	2026-06-08 09:19:05	MarkDuplicates	Tracking 26381 as yet unmatched pairs. 21647 records in RAM.
INFO	2026-06-08 09:19:07	MarkDuplicates	Read   618,000,000 records.  Elapsed time: 00:21:33s.  Time for last 1,000,000:    1s.  Last read position: chrX:107,714,689
INFO	2026-06-08 09:19:07	MarkDuplicates	Tracking 28405 as yet unmatched pairs. 23671 records in RAM.
INFO	2026-06-08 09:19:09	MarkDuplicates	Read   619,000,000 records.  Elapsed time: 00:21:35s.  Time for last 1,000,000:    1s.  Last read position: chrX:119,591,262
INFO	2026-06-08 09:19:09	MarkDuplicates	Tracking 21261 as yet unmatched pairs. 16527 records in RAM.
INFO	2026-06-08 09:19:12	MarkDuplicates	Read   620,000,000 records.  Elapsed time: 00:21:38s.  Time for last 1,000,000:    2s.  Last read position: chrX:132,214,350
INFO	2026-06-08 09:19:12	MarkDuplicates	Tracking 18908 as yet unmatched pairs. 14174 records in RAM.
INFO	2026-06-08 09:19:14	MarkDuplicates	Read   621,000,000 records.  Elapsed time: 00:21:40s.  Time for last 1,000,000:    1s.  Last read position: chrX:153,074,052
INFO	2026-06-08 09:19:14	MarkDuplicates	Tracking 16029 as yet unmatched pairs. 11295 records in RAM.
INFO	2026-06-08 09:19:16	MarkDuplicates	Read   622,000,000 records.  Elapsed time: 00:21:42s.  Time for last 1,000,000:    2s.  Last read position: chrX:153,959,455
INFO	2026-06-08 09:19:16	MarkDuplicates	Tracking 13681 as yet unmatched pairs. 8947 records in RAM.
INFO	2026-06-08 09:19:18	MarkDuplicates	Read   623,000,000 records.  Elapsed time: 00:21:44s.  Time for last 1,000,000:    2s.  Last read position: chrX:154,360,356
INFO	2026-06-08 09:19:18	MarkDuplicates	Tracking 14353 as yet unmatched pairs. 9619 records in RAM.
INFO	2026-06-08 09:19:20	MarkDuplicates	Read   624,000,000 records.  Elapsed time: 00:21:46s.  Time for last 1,000,000:    2s.  Last read position: chrX:154,440,076
INFO	2026-06-08 09:19:20	MarkDuplicates	Tracking 7114 as yet unmatched pairs. 2380 records in RAM.
INFO	2026-06-08 09:19:23	MarkDuplicates	Read   625,000,000 records.  Elapsed time: 00:21:49s.  Time for last 1,000,000:    2s.  Last read position: chrY:13,358,500
INFO	2026-06-08 09:19:23	MarkDuplicates	Tracking 4264 as yet unmatched pairs. 542 records in RAM.
INFO	2026-06-08 09:19:24	MarkDuplicates	Read   626,000,000 records.  Elapsed time: 00:21:50s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:132,350
INFO	2026-06-08 09:19:24	MarkDuplicates	Tracking 1209 as yet unmatched pairs. 1122 records in RAM.
INFO	2026-06-08 09:19:25	MarkDuplicates	Read 626518619 records. 0 pairs never matched.
INFO	2026-06-08 09:20:23	MarkDuplicates	After buildSortedReadEndLists freeMemory: 204141928; totalMemory: 234881024; maxMemory: 63585648640
INFO	2026-06-08 09:20:23	MarkDuplicates	Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO	2026-06-08 09:20:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
WARNING	2026-06-08 09:20:27	SortingCollection	There is not enough memory per file for buffering. Reading will be unbuffered.
INFO	2026-06-08 09:20:48	OpticalDuplicateFinder	Large duplicate set. size = 1580
INFO	2026-06-08 09:20:48	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-24,944
INFO	2026-06-08 09:20:48	OpticalDuplicateFinder	Large duplicate set. size = 1588
INFO	2026-06-08 09:20:48	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-29,976
INFO	2026-06-08 09:20:48	OpticalDuplicateFinder	Large duplicate set. size = 1288
INFO	2026-06-08 09:20:48	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-27,702
INFO	2026-06-08 09:20:48	OpticalDuplicateFinder	Large duplicate set. size = 1135
INFO	2026-06-08 09:20:48	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-24,280
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1260
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:5,951
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1244
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:12,027
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1445
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:28,118
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1242
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:22,188
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1218
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:22,366
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1477
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-14,742
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1773
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:31,184
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1914
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-18,035
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1547
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-16,020
INFO	2026-06-08 09:20:49	OpticalDuplicateFinder	Large duplicate set. size = 1328
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:2,343
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	Large duplicate set. size = 2773
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:3,006
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-23,989
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	Large duplicate set. size = 1484
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-30,170
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	Large duplicate set. size = 1772
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:9,527
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	Large duplicate set. size = 1139
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:25,917
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	Large duplicate set. size = 1082
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-20,259
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	Large duplicate set. size = 1269
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,018
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	Large duplicate set. size = 1051
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:9,672
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	Large duplicate set. size = 1218
INFO	2026-06-08 09:20:50	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-29,134
INFO	2026-06-08 09:20:55	OpticalDuplicateFinder	Large duplicate set. size = 1041
INFO	2026-06-08 09:20:55	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,301
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1545
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-21,238
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1221
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:20,934
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1127
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,366
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 3681
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-17,266
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:12,633
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         3,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:11,282
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1636
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-13,876
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 2160
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:19,372
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:11,784
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 2461
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-30,914
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-16,797
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1952
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:4,220
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1133
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-32,047
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1464
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:8,718
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1106
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-26,100
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1606
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:21,290
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1183
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-26,036
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1115
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:26,233
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1255
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,738
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1066
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-26,262
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1445
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-16,368
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1227
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-29,450
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1012
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:6,558
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	Large duplicate set. size = 1072
INFO	2026-06-08 09:20:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:5,878
INFO	2026-06-08 09:21:12	OpticalDuplicateFinder	Large duplicate set. size = 1821
INFO	2026-06-08 09:21:12	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:12,116
INFO	2026-06-08 09:21:57	OpticalDuplicateFinder	Large duplicate set. size = 1036
INFO	2026-06-08 09:21:57	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:1,979
INFO	2026-06-08 09:21:57	OpticalDuplicateFinder	Large duplicate set. size = 1234
INFO	2026-06-08 09:21:57	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-16,312
INFO	2026-06-08 09:21:57	OpticalDuplicateFinder	Large duplicate set. size = 1273
INFO	2026-06-08 09:21:57	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:29,016
INFO	2026-06-08 09:21:57	OpticalDuplicateFinder	Large duplicate set. size = 1721
INFO	2026-06-08 09:21:57	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:11,938
INFO	2026-06-08 09:21:58	OpticalDuplicateFinder	Large duplicate set. size = 1271
INFO	2026-06-08 09:21:58	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-16,125
INFO	2026-06-08 09:21:59	OpticalDuplicateFinder	Large duplicate set. size = 1103
INFO	2026-06-08 09:21:59	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:15,999
INFO	2026-06-08 09:21:59	OpticalDuplicateFinder	Large duplicate set. size = 1308
INFO	2026-06-08 09:21:59	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,326
INFO	2026-06-08 09:21:59	OpticalDuplicateFinder	Large duplicate set. size = 1338
INFO	2026-06-08 09:21:59	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:19,777
INFO	2026-06-08 09:21:59	OpticalDuplicateFinder	Large duplicate set. size = 1916
INFO	2026-06-08 09:21:59	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:5,320
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 1197
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-19,580
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 1042
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:15,530
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 1655
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:5,716
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 1041
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:32,260
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 1006
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-16,619
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 2035
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-25,955
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:30,302
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 1003
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-28,989
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 1104
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:26,977
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	Large duplicate set. size = 1042
INFO	2026-06-08 09:22:00	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-19,475
INFO	2026-06-08 09:22:18	MarkDuplicates	Traversing fragment information and detecting duplicates.
WARNING	2026-06-08 09:22:18	SortingCollection	There is not enough memory per file for buffering. Reading will be unbuffered.
INFO	2026-06-08 09:23:30	MarkDuplicates	Sorting list of duplicate records.
INFO	2026-06-08 09:23:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 203930288; totalMemory: 234881024; maxMemory: 63585648640
INFO	2026-06-08 09:23:35	MarkDuplicates	Marking 344364935 records as duplicates.
INFO	2026-06-08 09:23:35	MarkDuplicates	Found 15799126 optical duplicate clusters.
INFO	2026-06-08 09:23:35	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2026-06-08 09:23:54	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:00:18s.  Time for last 10,000,000:   18s.  Last read position: chr1:23,337,761
INFO	2026-06-08 09:24:11	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:00:36s.  Time for last 10,000,000:   17s.  Last read position: chr1:47,219,011
INFO	2026-06-08 09:24:29	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:00:53s.  Time for last 10,000,000:   17s.  Last read position: chr1:146,156,461
INFO	2026-06-08 09:24:46	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:01:10s.  Time for last 10,000,000:   17s.  Last read position: chr1:155,346,468
INFO	2026-06-08 09:25:03	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:01:28s.  Time for last 10,000,000:   17s.  Last read position: chr1:186,336,568
INFO	2026-06-08 09:25:21	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:01:45s.  Time for last 10,000,000:   17s.  Last read position: chr1:228,743,282
INFO	2026-06-08 09:25:37	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:02:01s.  Time for last 10,000,000:   16s.  Last read position: chr2:32,916,406
INFO	2026-06-08 09:25:53	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:02:17s.  Time for last 10,000,000:   15s.  Last read position: chr2:85,663,706
INFO	2026-06-08 09:26:09	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:02:34s.  Time for last 10,000,000:   16s.  Last read position: chr2:177,219,143
INFO	2026-06-08 09:26:25	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:02:50s.  Time for last 10,000,000:   16s.  Last read position: chr2:215,406,252
INFO	2026-06-08 09:26:41	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:03:05s.  Time for last 10,000,000:   15s.  Last read position: chr3:9,450,254
INFO	2026-06-08 09:26:56	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:03:21s.  Time for last 10,000,000:   15s.  Last read position: chr3:51,993,707
INFO	2026-06-08 09:27:12	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:03:37s.  Time for last 10,000,000:   15s.  Last read position: chr3:143,028,333
INFO	2026-06-08 09:27:28	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:03:52s.  Time for last 10,000,000:   15s.  Last read position: chr4:3,187,815
INFO	2026-06-08 09:27:42	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:04:07s.  Time for last 10,000,000:   14s.  Last read position: chr4:39,103,288
INFO	2026-06-08 09:27:58	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:04:23s.  Time for last 10,000,000:   15s.  Last read position: chr4:151,102,999
INFO	2026-06-08 09:28:14	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:04:38s.  Time for last 10,000,000:   15s.  Last read position: chr5:69,419,437
INFO	2026-06-08 09:28:29	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:04:54s.  Time for last 10,000,000:   15s.  Last read position: chr5:140,647,296
INFO	2026-06-08 09:28:44	MarkDuplicates	Written   190,000,000 records.  Elapsed time: 00:05:09s.  Time for last 10,000,000:   15s.  Last read position: chr5:151,664,225
INFO	2026-06-08 09:29:00	MarkDuplicates	Written   200,000,000 records.  Elapsed time: 00:05:24s.  Time for last 10,000,000:   15s.  Last read position: chr5:181,238,181
INFO	2026-06-08 09:29:15	MarkDuplicates	Written   210,000,000 records.  Elapsed time: 00:05:39s.  Time for last 10,000,000:   15s.  Last read position: chr6:32,056,703
INFO	2026-06-08 09:29:31	MarkDuplicates	Written   220,000,000 records.  Elapsed time: 00:05:56s.  Time for last 10,000,000:   16s.  Last read position: chr6:89,080,838
INFO	2026-06-08 09:29:48	MarkDuplicates	Written   230,000,000 records.  Elapsed time: 00:06:13s.  Time for last 10,000,000:   16s.  Last read position: chr7:5,528,041
INFO	2026-06-08 09:30:04	MarkDuplicates	Written   240,000,000 records.  Elapsed time: 00:06:29s.  Time for last 10,000,000:   16s.  Last read position: chr7:76,302,841
INFO	2026-06-08 09:30:21	MarkDuplicates	Written   250,000,000 records.  Elapsed time: 00:06:45s.  Time for last 10,000,000:   16s.  Last read position: chr7:128,479,176
INFO	2026-06-08 09:30:37	MarkDuplicates	Written   260,000,000 records.  Elapsed time: 00:07:01s.  Time for last 10,000,000:   16s.  Last read position: chr8:28,113,018
INFO	2026-06-08 09:30:55	MarkDuplicates	Written   270,000,000 records.  Elapsed time: 00:07:20s.  Time for last 10,000,000:   18s.  Last read position: chr8:123,253,717
INFO	2026-06-08 09:31:13	MarkDuplicates	Written   280,000,000 records.  Elapsed time: 00:07:37s.  Time for last 10,000,000:   17s.  Last read position: chr9:35,072,337
INFO	2026-06-08 09:31:30	MarkDuplicates	Written   290,000,000 records.  Elapsed time: 00:07:55s.  Time for last 10,000,000:   17s.  Last read position: chr9:127,872,821
INFO	2026-06-08 09:31:47	MarkDuplicates	Written   300,000,000 records.  Elapsed time: 00:08:12s.  Time for last 10,000,000:   17s.  Last read position: chr10:30,027,526
INFO	2026-06-08 09:32:04	MarkDuplicates	Written   310,000,000 records.  Elapsed time: 00:08:29s.  Time for last 10,000,000:   17s.  Last read position: chr10:88,941,311
INFO	2026-06-08 09:32:21	MarkDuplicates	Written   320,000,000 records.  Elapsed time: 00:08:46s.  Time for last 10,000,000:   16s.  Last read position: chr11:721,952
INFO	2026-06-08 09:32:37	MarkDuplicates	Written   330,000,000 records.  Elapsed time: 00:09:02s.  Time for last 10,000,000:   16s.  Last read position: chr11:1,250,289
INFO	2026-06-08 09:32:54	MarkDuplicates	Written   340,000,000 records.  Elapsed time: 00:09:19s.  Time for last 10,000,000:   16s.  Last read position: chr11:46,382,311
INFO	2026-06-08 09:33:10	MarkDuplicates	Written   350,000,000 records.  Elapsed time: 00:09:34s.  Time for last 10,000,000:   15s.  Last read position: chr11:65,537,824
INFO	2026-06-08 09:33:25	MarkDuplicates	Written   360,000,000 records.  Elapsed time: 00:09:50s.  Time for last 10,000,000:   15s.  Last read position: chr11:96,341,609
INFO	2026-06-08 09:33:41	MarkDuplicates	Written   370,000,000 records.  Elapsed time: 00:10:06s.  Time for last 10,000,000:   15s.  Last read position: chr12:6,537,101
INFO	2026-06-08 09:33:57	MarkDuplicates	Written   380,000,000 records.  Elapsed time: 00:10:21s.  Time for last 10,000,000:   15s.  Last read position: chr12:49,762,871
INFO	2026-06-08 09:34:12	MarkDuplicates	Written   390,000,000 records.  Elapsed time: 00:10:37s.  Time for last 10,000,000:   15s.  Last read position: chr12:57,535,821
INFO	2026-06-08 09:34:28	MarkDuplicates	Written   400,000,000 records.  Elapsed time: 00:10:52s.  Time for last 10,000,000:   15s.  Last read position: chr12:121,020,755
INFO	2026-06-08 09:34:43	MarkDuplicates	Written   410,000,000 records.  Elapsed time: 00:11:07s.  Time for last 10,000,000:   15s.  Last read position: chr13:110,198,584
INFO	2026-06-08 09:34:58	MarkDuplicates	Written   420,000,000 records.  Elapsed time: 00:11:23s.  Time for last 10,000,000:   15s.  Last read position: chr14:68,790,212
INFO	2026-06-08 09:35:14	MarkDuplicates	Written   430,000,000 records.  Elapsed time: 00:11:38s.  Time for last 10,000,000:   15s.  Last read position: chr14:105,854,525
INFO	2026-06-08 09:35:30	MarkDuplicates	Written   440,000,000 records.  Elapsed time: 00:11:54s.  Time for last 10,000,000:   15s.  Last read position: chr15:73,298,397
INFO	2026-06-08 09:35:45	MarkDuplicates	Written   450,000,000 records.  Elapsed time: 00:12:09s.  Time for last 10,000,000:   15s.  Last read position: chr16:2,514,112
INFO	2026-06-08 09:36:00	MarkDuplicates	Written   460,000,000 records.  Elapsed time: 00:12:25s.  Time for last 10,000,000:   15s.  Last read position: chr16:28,714,347
INFO	2026-06-08 09:36:16	MarkDuplicates	Written   470,000,000 records.  Elapsed time: 00:12:40s.  Time for last 10,000,000:   15s.  Last read position: chr16:69,114,556
INFO	2026-06-08 09:36:32	MarkDuplicates	Written   480,000,000 records.  Elapsed time: 00:12:56s.  Time for last 10,000,000:   15s.  Last read position: chr17:7,311,110
INFO	2026-06-08 09:36:47	MarkDuplicates	Written   490,000,000 records.  Elapsed time: 00:13:11s.  Time for last 10,000,000:   15s.  Last read position: chr17:38,715,899
INFO	2026-06-08 09:37:03	MarkDuplicates	Written   500,000,000 records.  Elapsed time: 00:13:27s.  Time for last 10,000,000:   15s.  Last read position: chr17:50,187,953
INFO	2026-06-08 09:37:19	MarkDuplicates	Written   510,000,000 records.  Elapsed time: 00:13:43s.  Time for last 10,000,000:   16s.  Last read position: chr17:50,196,504
INFO	2026-06-08 09:37:35	MarkDuplicates	Written   520,000,000 records.  Elapsed time: 00:13:59s.  Time for last 10,000,000:   15s.  Last read position: chr17:75,836,399
INFO	2026-06-08 09:37:51	MarkDuplicates	Written   530,000,000 records.  Elapsed time: 00:14:15s.  Time for last 10,000,000:   16s.  Last read position: chr18:62,264,040
INFO	2026-06-08 09:38:07	MarkDuplicates	Written   540,000,000 records.  Elapsed time: 00:14:31s.  Time for last 10,000,000:   15s.  Last read position: chr19:8,402,215
INFO	2026-06-08 09:38:22	MarkDuplicates	Written   550,000,000 records.  Elapsed time: 00:14:46s.  Time for last 10,000,000:   15s.  Last read position: chr19:18,432,014
INFO	2026-06-08 09:38:37	MarkDuplicates	Written   560,000,000 records.  Elapsed time: 00:15:02s.  Time for last 10,000,000:   15s.  Last read position: chr19:42,287,563
INFO	2026-06-08 09:38:53	MarkDuplicates	Written   570,000,000 records.  Elapsed time: 00:15:18s.  Time for last 10,000,000:   15s.  Last read position: chr19:54,254,961
INFO	2026-06-08 09:39:09	MarkDuplicates	Written   580,000,000 records.  Elapsed time: 00:15:33s.  Time for last 10,000,000:   15s.  Last read position: chr20:45,330,438
INFO	2026-06-08 09:39:24	MarkDuplicates	Written   590,000,000 records.  Elapsed time: 00:15:49s.  Time for last 10,000,000:   15s.  Last read position: chr21:41,756,620
INFO	2026-06-08 09:39:40	MarkDuplicates	Written   600,000,000 records.  Elapsed time: 00:16:04s.  Time for last 10,000,000:   15s.  Last read position: chr22:36,288,724
INFO	2026-06-08 09:39:55	MarkDuplicates	Written   610,000,000 records.  Elapsed time: 00:16:20s.  Time for last 10,000,000:   15s.  Last read position: chrX:38,160,171
INFO	2026-06-08 09:40:11	MarkDuplicates	Written   620,000,000 records.  Elapsed time: 00:16:36s.  Time for last 10,000,000:   16s.  Last read position: chrX:132,214,350
INFO	2026-06-08 09:40:30	MarkDuplicates	Written   630,000,000 records.  Elapsed time: 00:16:55s.  Time for last 10,000,000:   18s.  Last read position: */*
INFO	2026-06-08 09:40:31	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2026-06-08 09:40:31	MarkDuplicates	Duplicate Index cleanup.
INFO	2026-06-08 09:40:31	MarkDuplicates	Getting Memory Stats.
INFO	2026-06-08 09:40:31	MarkDuplicates	Before output close freeMemory: 203875152; totalMemory: 234881024; maxMemory: 63585648640
INFO	2026-06-08 09:40:31	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2026-06-08 09:40:31	MarkDuplicates	After output close freeMemory: 104128952; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 09:40:31 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 42.98 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory