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/68/3d0cf169990411532d33a9d0188fd4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/cb5c4b183349561367b746d2c6cdd5/GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/3d0cf169990411532d33a9d0188fd4/.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 GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam --OUTPUT GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam --METRICS_FILE GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:08:29.017 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 08:08:29 GMT 2026] MarkDuplicates --INPUT GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam --OUTPUT GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam --METRICS_FILE GM24385_0001_RNA_0001_23H5VFLT4_s24.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 08:08:29 GMT 2026] Executing as ?@nf-683d0cf169990411532d33a9d0188fd4-1209f-kqlm7 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 08:08:29	MarkDuplicates	Start of doWork freeMemory: 105492576; totalMemory: 134217728; maxMemory: 63585648640
INFO	2026-06-08 08:08:29	MarkDuplicates	Reading input file and constructing read end information.
INFO	2026-06-08 08:08:29	MarkDuplicates	Will retain up to 230382784 data points before spilling to disk.
INFO	2026-06-08 08:08:33	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:02s.  Time for last 1,000,000:    2s.  Last read position: chr1:1,319,354
INFO	2026-06-08 08:08:33	MarkDuplicates	Tracking 1701 as yet unmatched pairs. 245 records in RAM.
INFO	2026-06-08 08:08:36	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    2s.  Last read position: chr1:2,518,100
INFO	2026-06-08 08:08:36	MarkDuplicates	Tracking 3126 as yet unmatched pairs. 101 records in RAM.
INFO	2026-06-08 08:08:38	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    2s.  Last read position: chr1:8,364,746
INFO	2026-06-08 08:08:38	MarkDuplicates	Tracking 4759 as yet unmatched pairs. 345 records in RAM.
INFO	2026-06-08 08:08:41	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    2s.  Last read position: chr1:11,243,146
INFO	2026-06-08 08:08:41	MarkDuplicates	Tracking 6098 as yet unmatched pairs. 316 records in RAM.
INFO	2026-06-08 08:08:44	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    3s.  Last read position: chr1:15,848,025
INFO	2026-06-08 08:08:44	MarkDuplicates	Tracking 7209 as yet unmatched pairs. 153 records in RAM.
INFO	2026-06-08 08:08:46	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    2s.  Last read position: chr1:19,114,928
INFO	2026-06-08 08:08:46	MarkDuplicates	Tracking 8626 as yet unmatched pairs. 560 records in RAM.
INFO	2026-06-08 08:08:49	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    2s.  Last read position: chr1:21,736,479
INFO	2026-06-08 08:08:49	MarkDuplicates	Tracking 9418 as yet unmatched pairs. 190 records in RAM.
INFO	2026-06-08 08:08:52	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    2s.  Last read position: chr1:24,929,655
INFO	2026-06-08 08:08:52	MarkDuplicates	Tracking 11177 as yet unmatched pairs. 708 records in RAM.
INFO	2026-06-08 08:08:54	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    1s.  Last read position: chr1:27,282,258
INFO	2026-06-08 08:08:54	MarkDuplicates	Tracking 12127 as yet unmatched pairs. 290 records in RAM.
INFO	2026-06-08 08:08:56	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    2s.  Last read position: chr1:28,773,030
INFO	2026-06-08 08:08:56	MarkDuplicates	Tracking 13197 as yet unmatched pairs. 67 records in RAM.
INFO	2026-06-08 08:08:58	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    2s.  Last read position: chr1:32,334,776
INFO	2026-06-08 08:08:58	MarkDuplicates	Tracking 14788 as yet unmatched pairs. 376 records in RAM.
INFO	2026-06-08 08:09:00	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    1s.  Last read position: chr1:35,559,111
INFO	2026-06-08 08:09:00	MarkDuplicates	Tracking 15820 as yet unmatched pairs. 239 records in RAM.
INFO	2026-06-08 08:09:02	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    2s.  Last read position: chr1:39,333,878
INFO	2026-06-08 08:09:02	MarkDuplicates	Tracking 17162 as yet unmatched pairs. 316 records in RAM.
INFO	2026-06-08 08:09:05	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    2s.  Last read position: chr1:41,037,444
INFO	2026-06-08 08:09:05	MarkDuplicates	Tracking 18219 as yet unmatched pairs. 213 records in RAM.
INFO	2026-06-08 08:09:08	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    2s.  Last read position: chr1:44,232,221
INFO	2026-06-08 08:09:08	MarkDuplicates	Tracking 19477 as yet unmatched pairs. 283 records in RAM.
INFO	2026-06-08 08:09:09	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    1s.  Last read position: chr1:46,716,327
INFO	2026-06-08 08:09:09	MarkDuplicates	Tracking 20809 as yet unmatched pairs. 470 records in RAM.
INFO	2026-06-08 08:09:12	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    2s.  Last read position: chr1:54,174,538
INFO	2026-06-08 08:09:12	MarkDuplicates	Tracking 21600 as yet unmatched pairs. 146 records in RAM.
INFO	2026-06-08 08:09:14	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    1s.  Last read position: chr1:71,066,794
INFO	2026-06-08 08:09:14	MarkDuplicates	Tracking 22964 as yet unmatched pairs. 437 records in RAM.
INFO	2026-06-08 08:09:16	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    1s.  Last read position: chr1:86,704,682
INFO	2026-06-08 08:09:16	MarkDuplicates	Tracking 23577 as yet unmatched pairs. 109 records in RAM.
INFO	2026-06-08 08:09:18	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    2s.  Last read position: chr1:99,993,586
INFO	2026-06-08 08:09:18	MarkDuplicates	Tracking 24654 as yet unmatched pairs. 265 records in RAM.
INFO	2026-06-08 08:09:20	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    1s.  Last read position: chr1:110,891,437
INFO	2026-06-08 08:09:20	MarkDuplicates	Tracking 26430 as yet unmatched pairs. 925 records in RAM.
INFO	2026-06-08 08:09:22	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    1s.  Last read position: chr1:113,940,454
INFO	2026-06-08 08:09:22	MarkDuplicates	Tracking 26575 as yet unmatched pairs. 119 records in RAM.
INFO	2026-06-08 08:09:24	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    2s.  Last read position: chr1:119,727,070
INFO	2026-06-08 08:09:24	MarkDuplicates	Tracking 28633 as yet unmatched pairs. 1072 records in RAM.
INFO	2026-06-08 08:09:26	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    1s.  Last read position: chr1:146,127,040
INFO	2026-06-08 08:09:26	MarkDuplicates	Tracking 28400 as yet unmatched pairs. 99 records in RAM.
INFO	2026-06-08 08:09:28	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    1s.  Last read position: chr1:149,832,829
INFO	2026-06-08 08:09:28	MarkDuplicates	Tracking 29753 as yet unmatched pairs. 911 records in RAM.
INFO	2026-06-08 08:09:29	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    1s.  Last read position: chr1:150,578,397
INFO	2026-06-08 08:09:29	MarkDuplicates	Tracking 30880 as yet unmatched pairs. 1140 records in RAM.
INFO	2026-06-08 08:09:31	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    2s.  Last read position: chr1:151,763,102
INFO	2026-06-08 08:09:31	MarkDuplicates	Tracking 31037 as yet unmatched pairs. 142 records in RAM.
INFO	2026-06-08 08:09:33	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    2s.  Last read position: chr1:154,170,684
INFO	2026-06-08 08:09:33	MarkDuplicates	Tracking 36590 as yet unmatched pairs. 4635 records in RAM.
INFO	2026-06-08 08:09:35	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    1s.  Last read position: chr1:154,821,929
INFO	2026-06-08 08:09:35	MarkDuplicates	Tracking 33579 as yet unmatched pairs. 441 records in RAM.
INFO	2026-06-08 08:09:37	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    1s.  Last read position: chr1:155,660,456
INFO	2026-06-08 08:09:37	MarkDuplicates	Tracking 34939 as yet unmatched pairs. 665 records in RAM.
INFO	2026-06-08 08:09:39	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    1s.  Last read position: chr1:156,283,046
INFO	2026-06-08 08:09:39	MarkDuplicates	Tracking 35535 as yet unmatched pairs. 96 records in RAM.
INFO	2026-06-08 08:09:41	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    2s.  Last read position: chr1:160,240,210
INFO	2026-06-08 08:09:41	MarkDuplicates	Tracking 36813 as yet unmatched pairs. 307 records in RAM.
INFO	2026-06-08 08:09:43	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    1s.  Last read position: chr1:161,118,425
INFO	2026-06-08 08:09:43	MarkDuplicates	Tracking 37707 as yet unmatched pairs. 251 records in RAM.
INFO	2026-06-08 08:09:45	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    1s.  Last read position: chr1:168,254,589
INFO	2026-06-08 08:09:45	MarkDuplicates	Tracking 38612 as yet unmatched pairs. 86 records in RAM.
INFO	2026-06-08 08:09:47	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    2s.  Last read position: chr1:174,394,048
INFO	2026-06-08 08:09:47	MarkDuplicates	Tracking 39787 as yet unmatched pairs. 401 records in RAM.
INFO	2026-06-08 08:09:50	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    2s.  Last read position: chr1:182,860,071
INFO	2026-06-08 08:09:50	MarkDuplicates	Tracking 40808 as yet unmatched pairs. 119 records in RAM.
INFO	2026-06-08 08:09:52	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    2s.  Last read position: chr1:186,362,339
INFO	2026-06-08 08:09:52	MarkDuplicates	Tracking 42224 as yet unmatched pairs. 660 records in RAM.
INFO	2026-06-08 08:09:54	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    2s.  Last read position: chr1:202,153,780
INFO	2026-06-08 08:09:54	MarkDuplicates	Tracking 43219 as yet unmatched pairs. 382 records in RAM.
INFO	2026-06-08 08:09:56	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    1s.  Last read position: chr1:206,342,954
INFO	2026-06-08 08:09:56	MarkDuplicates	Tracking 43902 as yet unmatched pairs. 92 records in RAM.
INFO	2026-06-08 08:09:58	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    2s.  Last read position: chr1:212,858,571
INFO	2026-06-08 08:09:58	MarkDuplicates	Tracking 46092 as yet unmatched pairs. 1056 records in RAM.
INFO	2026-06-08 08:10:00	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    1s.  Last read position: chr1:225,406,777
INFO	2026-06-08 08:10:00	MarkDuplicates	Tracking 46321 as yet unmatched pairs. 336 records in RAM.
INFO	2026-06-08 08:10:01	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    1s.  Last read position: chr1:228,413,762
INFO	2026-06-08 08:10:01	MarkDuplicates	Tracking 47334 as yet unmatched pairs. 34 records in RAM.
INFO	2026-06-08 08:10:03	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    1s.  Last read position: chr1:235,414,557
INFO	2026-06-08 08:10:03	MarkDuplicates	Tracking 49149 as yet unmatched pairs. 34 records in RAM.
INFO	2026-06-08 08:10:05	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    1s.  Last read position: chr1:246,851,116
INFO	2026-06-08 08:10:05	MarkDuplicates	Tracking 50403 as yet unmatched pairs. 193 records in RAM.
INFO	2026-06-08 08:10:07	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    2s.  Last read position: chr2:10,058,870
INFO	2026-06-08 08:10:07	MarkDuplicates	Tracking 51621 as yet unmatched pairs. 46761 records in RAM.
INFO	2026-06-08 08:10:09	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    2s.  Last read position: chr2:24,252,395
INFO	2026-06-08 08:10:09	MarkDuplicates	Tracking 52522 as yet unmatched pairs. 47520 records in RAM.
INFO	2026-06-08 08:10:11	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:    1s.  Last read position: chr2:27,083,067
INFO	2026-06-08 08:10:11	MarkDuplicates	Tracking 53695 as yet unmatched pairs. 48575 records in RAM.
INFO	2026-06-08 08:10:13	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    1s.  Last read position: chr2:32,089,595
INFO	2026-06-08 08:10:13	MarkDuplicates	Tracking 54774 as yet unmatched pairs. 49530 records in RAM.
INFO	2026-06-08 08:10:15	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    1s.  Last read position: chr2:32,916,264
INFO	2026-06-08 08:10:15	MarkDuplicates	Tracking 190522 as yet unmatched pairs. 42761 records in RAM.
INFO	2026-06-08 08:10:17	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    1s.  Last read position: chr2:32,916,406
INFO	2026-06-08 08:10:17	MarkDuplicates	Tracking 497207 as yet unmatched pairs. 26608 records in RAM.
INFO	2026-06-08 08:10:18	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    1s.  Last read position: chr2:37,105,472
INFO	2026-06-08 08:10:18	MarkDuplicates	Tracking 534386 as yet unmatched pairs. 24111 records in RAM.
INFO	2026-06-08 08:10:20	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    1s.  Last read position: chr2:43,934,190
INFO	2026-06-08 08:10:20	MarkDuplicates	Tracking 533976 as yet unmatched pairs. 23593 records in RAM.
INFO	2026-06-08 08:10:22	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    2s.  Last read position: chr2:54,625,998
INFO	2026-06-08 08:10:22	MarkDuplicates	Tracking 532567 as yet unmatched pairs. 22076 records in RAM.
INFO	2026-06-08 08:10:24	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    2s.  Last read position: chr2:58,134,679
INFO	2026-06-08 08:10:24	MarkDuplicates	Tracking 532030 as yet unmatched pairs. 21455 records in RAM.
INFO	2026-06-08 08:10:26	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    1s.  Last read position: chr2:64,961,924
INFO	2026-06-08 08:10:26	MarkDuplicates	Tracking 530794 as yet unmatched pairs. 20083 records in RAM.
INFO	2026-06-08 08:10:28	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    2s.  Last read position: chr2:71,365,430
INFO	2026-06-08 08:10:28	MarkDuplicates	Tracking 530123 as yet unmatched pairs. 19265 records in RAM.
INFO	2026-06-08 08:10:32	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    3s.  Last read position: chr2:74,462,703
INFO	2026-06-08 08:10:32	MarkDuplicates	Tracking 529461 as yet unmatched pairs. 18474 records in RAM.
INFO	2026-06-08 08:10:35	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    3s.  Last read position: chr2:86,147,656
INFO	2026-06-08 08:10:35	MarkDuplicates	Tracking 528114 as yet unmatched pairs. 17052 records in RAM.
INFO	2026-06-08 08:10:37	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    2s.  Last read position: chr2:96,281,838
INFO	2026-06-08 08:10:37	MarkDuplicates	Tracking 527025 as yet unmatched pairs. 15856 records in RAM.
INFO	2026-06-08 08:10:39	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    1s.  Last read position: chr2:99,404,461
INFO	2026-06-08 08:10:39	MarkDuplicates	Tracking 525828 as yet unmatched pairs. 14522 records in RAM.
INFO	2026-06-08 08:10:41	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    1s.  Last read position: chr2:109,813,568
INFO	2026-06-08 08:10:41	MarkDuplicates	Tracking 525059 as yet unmatched pairs. 13696 records in RAM.
INFO	2026-06-08 08:10:43	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    1s.  Last read position: chr2:119,245,618
INFO	2026-06-08 08:10:43	MarkDuplicates	Tracking 524390 as yet unmatched pairs. 12919 records in RAM.
INFO	2026-06-08 08:10:45	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    1s.  Last read position: chr2:131,443,882
INFO	2026-06-08 08:10:45	MarkDuplicates	Tracking 523311 as yet unmatched pairs. 11715 records in RAM.
INFO	2026-06-08 08:10:47	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    1s.  Last read position: chr2:151,464,266
INFO	2026-06-08 08:10:47	MarkDuplicates	Tracking 522882 as yet unmatched pairs. 11124 records in RAM.
INFO	2026-06-08 08:10:49	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    2s.  Last read position: chr2:164,461,459
INFO	2026-06-08 08:10:49	MarkDuplicates	Tracking 522079 as yet unmatched pairs. 10185 records in RAM.
INFO	2026-06-08 08:10:52	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:02:21s.  Time for last 1,000,000:    3s.  Last read position: chr2:174,572,264
INFO	2026-06-08 08:10:52	MarkDuplicates	Tracking 521572 as yet unmatched pairs. 9466 records in RAM.
INFO	2026-06-08 08:10:54	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    2s.  Last read position: chr2:178,768,886
INFO	2026-06-08 08:10:54	MarkDuplicates	Tracking 520894 as yet unmatched pairs. 8694 records in RAM.
INFO	2026-06-08 08:10:56	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    1s.  Last read position: chr2:190,930,508
INFO	2026-06-08 08:10:56	MarkDuplicates	Tracking 521210 as yet unmatched pairs. 8877 records in RAM.
INFO	2026-06-08 08:10:58	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    2s.  Last read position: chr2:197,706,817
INFO	2026-06-08 08:10:58	MarkDuplicates	Tracking 519284 as yet unmatched pairs. 6800 records in RAM.
INFO	2026-06-08 08:11:00	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    1s.  Last read position: chr2:207,570,177
INFO	2026-06-08 08:11:00	MarkDuplicates	Tracking 519266 as yet unmatched pairs. 6659 records in RAM.
INFO	2026-06-08 08:11:02	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    1s.  Last read position: chr2:218,272,693
INFO	2026-06-08 08:11:02	MarkDuplicates	Tracking 517898 as yet unmatched pairs. 5163 records in RAM.
INFO	2026-06-08 08:11:04	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:02:33s.  Time for last 1,000,000:    2s.  Last read position: chr2:223,882,919
INFO	2026-06-08 08:11:04	MarkDuplicates	Tracking 516641 as yet unmatched pairs. 3722 records in RAM.
INFO	2026-06-08 08:11:06	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    1s.  Last read position: chr2:230,865,062
INFO	2026-06-08 08:11:06	MarkDuplicates	Tracking 516606 as yet unmatched pairs. 3549 records in RAM.
INFO	2026-06-08 08:11:07	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    1s.  Last read position: chr2:233,434,890
INFO	2026-06-08 08:11:07	MarkDuplicates	Tracking 515254 as yet unmatched pairs. 2066 records in RAM.
INFO	2026-06-08 08:11:09	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:    1s.  Last read position: chr2:241,235,569
INFO	2026-06-08 08:11:09	MarkDuplicates	Tracking 514031 as yet unmatched pairs. 708 records in RAM.
INFO	2026-06-08 08:11:12	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    2s.  Last read position: chr3:5,188,087
INFO	2026-06-08 08:11:12	MarkDuplicates	Tracking 516296 as yet unmatched pairs. 27558 records in RAM.
INFO	2026-06-08 08:11:14	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:    2s.  Last read position: chr3:11,558,533
INFO	2026-06-08 08:11:14	MarkDuplicates	Tracking 511704 as yet unmatched pairs. 22881 records in RAM.
INFO	2026-06-08 08:11:16	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:    2s.  Last read position: chr3:15,032,437
INFO	2026-06-08 08:11:16	MarkDuplicates	Tracking 510802 as yet unmatched pairs. 21859 records in RAM.
INFO	2026-06-08 08:11:18	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    1s.  Last read position: chr3:16,897,186
INFO	2026-06-08 08:11:18	MarkDuplicates	Tracking 510182 as yet unmatched pairs. 21142 records in RAM.
INFO	2026-06-08 08:11:20	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:02:50s.  Time for last 1,000,000:    2s.  Last read position: chr3:33,132,587
INFO	2026-06-08 08:11:20	MarkDuplicates	Tracking 509410 as yet unmatched pairs. 20184 records in RAM.
INFO	2026-06-08 08:11:23	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    2s.  Last read position: chr3:40,311,489
INFO	2026-06-08 08:11:23	MarkDuplicates	Tracking 508604 as yet unmatched pairs. 19285 records in RAM.
INFO	2026-06-08 08:11:25	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    1s.  Last read position: chr3:46,786,056
INFO	2026-06-08 08:11:25	MarkDuplicates	Tracking 507559 as yet unmatched pairs. 18165 records in RAM.
INFO	2026-06-08 08:11:27	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    1s.  Last read position: chr3:47,676,665
INFO	2026-06-08 08:11:27	MarkDuplicates	Tracking 506516 as yet unmatched pairs. 17006 records in RAM.
INFO	2026-06-08 08:11:29	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    1s.  Last read position: chr3:49,013,400
INFO	2026-06-08 08:11:29	MarkDuplicates	Tracking 506478 as yet unmatched pairs. 16831 records in RAM.
INFO	2026-06-08 08:11:31	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    1s.  Last read position: chr3:49,723,598
INFO	2026-06-08 08:11:31	MarkDuplicates	Tracking 504521 as yet unmatched pairs. 14798 records in RAM.
INFO	2026-06-08 08:11:33	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    1s.  Last read position: chr3:51,993,838
INFO	2026-06-08 08:11:33	MarkDuplicates	Tracking 504035 as yet unmatched pairs. 14220 records in RAM.
INFO	2026-06-08 08:11:35	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:03:04s.  Time for last 1,000,000:    1s.  Last read position: chr3:53,189,047
INFO	2026-06-08 08:11:35	MarkDuplicates	Tracking 502611 as yet unmatched pairs. 12691 records in RAM.
INFO	2026-06-08 08:11:36	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    1s.  Last read position: chr3:64,736,203
INFO	2026-06-08 08:11:36	MarkDuplicates	Tracking 501398 as yet unmatched pairs. 11350 records in RAM.
INFO	2026-06-08 08:11:38	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    1s.  Last read position: chr3:101,671,272
INFO	2026-06-08 08:11:38	MarkDuplicates	Tracking 500683 as yet unmatched pairs. 10472 records in RAM.
INFO	2026-06-08 08:11:40	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    1s.  Last read position: chr3:119,390,848
INFO	2026-06-08 08:11:40	MarkDuplicates	Tracking 500151 as yet unmatched pairs. 9824 records in RAM.
INFO	2026-06-08 08:11:42	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    1s.  Last read position: chr3:122,680,927
INFO	2026-06-08 08:11:42	MarkDuplicates	Tracking 499493 as yet unmatched pairs. 9090 records in RAM.
INFO	2026-06-08 08:11:43	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    1s.  Last read position: chr3:128,052,480
INFO	2026-06-08 08:11:43	MarkDuplicates	Tracking 498873 as yet unmatched pairs. 8405 records in RAM.
INFO	2026-06-08 08:11:45	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    1s.  Last read position: chr3:132,639,563
INFO	2026-06-08 08:11:45	MarkDuplicates	Tracking 497295 as yet unmatched pairs. 6709 records in RAM.
INFO	2026-06-08 08:11:47	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    1s.  Last read position: chr3:142,365,340
INFO	2026-06-08 08:11:47	MarkDuplicates	Tracking 496461 as yet unmatched pairs. 5719 records in RAM.
INFO	2026-06-08 08:11:49	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    1s.  Last read position: chr3:156,529,737
INFO	2026-06-08 08:11:49	MarkDuplicates	Tracking 495535 as yet unmatched pairs. 4618 records in RAM.
INFO	2026-06-08 08:11:51	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    1s.  Last read position: chr3:172,106,121
INFO	2026-06-08 08:11:51	MarkDuplicates	Tracking 495173 as yet unmatched pairs. 4095 records in RAM.
INFO	2026-06-08 08:11:53	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    1s.  Last read position: chr3:183,790,836
INFO	2026-06-08 08:11:53	MarkDuplicates	Tracking 494073 as yet unmatched pairs. 2892 records in RAM.
INFO	2026-06-08 08:11:55	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    2s.  Last read position: chr3:187,001,750
INFO	2026-06-08 08:11:55	MarkDuplicates	Tracking 493078 as yet unmatched pairs. 1831 records in RAM.
INFO	2026-06-08 08:11:57	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    2s.  Last read position: chr3:196,461,240
INFO	2026-06-08 08:11:57	MarkDuplicates	Tracking 491980 as yet unmatched pairs. 642 records in RAM.
INFO	2026-06-08 08:12:00	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    2s.  Last read position: chr4:957,851
INFO	2026-06-08 08:12:00	MarkDuplicates	Tracking 491286 as yet unmatched pairs. 13823 records in RAM.
INFO	2026-06-08 08:12:01	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    1s.  Last read position: chr4:2,513,748
INFO	2026-06-08 08:12:01	MarkDuplicates	Tracking 489785 as yet unmatched pairs. 12231 records in RAM.
INFO	2026-06-08 08:12:03	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    1s.  Last read position: chr4:6,642,350
INFO	2026-06-08 08:12:03	MarkDuplicates	Tracking 488516 as yet unmatched pairs. 10845 records in RAM.
INFO	2026-06-08 08:12:05	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    1s.  Last read position: chr4:17,824,968
INFO	2026-06-08 08:12:05	MarkDuplicates	Tracking 487520 as yet unmatched pairs. 9741 records in RAM.
INFO	2026-06-08 08:12:06	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    1s.  Last read position: chr4:39,844,678
INFO	2026-06-08 08:12:06	MarkDuplicates	Tracking 486609 as yet unmatched pairs. 8717 records in RAM.
INFO	2026-06-08 08:12:08	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    1s.  Last read position: chr4:48,839,452
INFO	2026-06-08 08:12:08	MarkDuplicates	Tracking 486282 as yet unmatched pairs. 8202 records in RAM.
INFO	2026-06-08 08:12:10	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    1s.  Last read position: chr4:73,091,608
INFO	2026-06-08 08:12:10	MarkDuplicates	Tracking 484853 as yet unmatched pairs. 6688 records in RAM.
INFO	2026-06-08 08:12:12	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    1s.  Last read position: chr4:83,010,498
INFO	2026-06-08 08:12:12	MarkDuplicates	Tracking 483915 as yet unmatched pairs. 5660 records in RAM.
INFO	2026-06-08 08:12:13	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    1s.  Last read position: chr4:99,949,670
INFO	2026-06-08 08:12:13	MarkDuplicates	Tracking 483202 as yet unmatched pairs. 4844 records in RAM.
INFO	2026-06-08 08:12:15	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:    1s.  Last read position: chr4:112,553,915
INFO	2026-06-08 08:12:15	MarkDuplicates	Tracking 482204 as yet unmatched pairs. 3759 records in RAM.
INFO	2026-06-08 08:12:17	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    1s.  Last read position: chr4:139,698,176
INFO	2026-06-08 08:12:17	MarkDuplicates	Tracking 481501 as yet unmatched pairs. 2958 records in RAM.
INFO	2026-06-08 08:12:19	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    1s.  Last read position: chr4:151,103,016
INFO	2026-06-08 08:12:19	MarkDuplicates	Tracking 483385 as yet unmatched pairs. 4749 records in RAM.
INFO	2026-06-08 08:12:20	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    1s.  Last read position: chr4:168,384,304
INFO	2026-06-08 08:12:20	MarkDuplicates	Tracking 479948 as yet unmatched pairs. 1194 records in RAM.
INFO	2026-06-08 08:12:22	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    1s.  Last read position: chr5:271,762
INFO	2026-06-08 08:12:22	MarkDuplicates	Tracking 479026 as yet unmatched pairs. 23626 records in RAM.
INFO	2026-06-08 08:12:24	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:03:53s.  Time for last 1,000,000:    1s.  Last read position: chr5:10,397,307
INFO	2026-06-08 08:12:24	MarkDuplicates	Tracking 477877 as yet unmatched pairs. 22381 records in RAM.
INFO	2026-06-08 08:12:25	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    1s.  Last read position: chr5:14,419,909
INFO	2026-06-08 08:12:25	MarkDuplicates	Tracking 478425 as yet unmatched pairs. 22790 records in RAM.
INFO	2026-06-08 08:12:27	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    2s.  Last read position: chr5:33,162,177
INFO	2026-06-08 08:12:27	MarkDuplicates	Tracking 475185 as yet unmatched pairs. 19450 records in RAM.
INFO	2026-06-08 08:12:29	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    1s.  Last read position: chr5:44,809,130
INFO	2026-06-08 08:12:29	MarkDuplicates	Tracking 474724 as yet unmatched pairs. 18872 records in RAM.
INFO	2026-06-08 08:12:31	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    1s.  Last read position: chr5:66,164,736
INFO	2026-06-08 08:12:31	MarkDuplicates	Tracking 473827 as yet unmatched pairs. 17889 records in RAM.
INFO	2026-06-08 08:12:34	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    2s.  Last read position: chr5:72,305,322
INFO	2026-06-08 08:12:34	MarkDuplicates	Tracking 473444 as yet unmatched pairs. 17457 records in RAM.
INFO	2026-06-08 08:12:35	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    1s.  Last read position: chr5:81,706,664
INFO	2026-06-08 08:12:35	MarkDuplicates	Tracking 472605 as yet unmatched pairs. 16492 records in RAM.
INFO	2026-06-08 08:12:37	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    2s.  Last read position: chr5:96,803,523
INFO	2026-06-08 08:12:37	MarkDuplicates	Tracking 472174 as yet unmatched pairs. 15951 records in RAM.
INFO	2026-06-08 08:12:40	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    2s.  Last read position: chr5:115,616,339
INFO	2026-06-08 08:12:40	MarkDuplicates	Tracking 471250 as yet unmatched pairs. 14884 records in RAM.
INFO	2026-06-08 08:12:41	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    1s.  Last read position: chr5:132,589,822
INFO	2026-06-08 08:12:41	MarkDuplicates	Tracking 470565 as yet unmatched pairs. 14081 records in RAM.
INFO	2026-06-08 08:12:43	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    1s.  Last read position: chr5:138,352,860
INFO	2026-06-08 08:12:43	MarkDuplicates	Tracking 470025 as yet unmatched pairs. 13449 records in RAM.
INFO	2026-06-08 08:12:45	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    1s.  Last read position: chr5:140,552,073
INFO	2026-06-08 08:12:45	MarkDuplicates	Tracking 469125 as yet unmatched pairs. 12309 records in RAM.
INFO	2026-06-08 08:12:46	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:    1s.  Last read position: chr5:146,237,316
INFO	2026-06-08 08:12:46	MarkDuplicates	Tracking 467714 as yet unmatched pairs. 10831 records in RAM.
INFO	2026-06-08 08:12:48	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,402,241
INFO	2026-06-08 08:12:48	MarkDuplicates	Tracking 498113 as yet unmatched pairs. 41132 records in RAM.
INFO	2026-06-08 08:12:50	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,405,152
INFO	2026-06-08 08:12:50	MarkDuplicates	Tracking 493394 as yet unmatched pairs. 36378 records in RAM.
INFO	2026-06-08 08:12:52	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    1s.  Last read position: chr5:150,649,686
INFO	2026-06-08 08:12:52	MarkDuplicates	Tracking 464765 as yet unmatched pairs. 7689 records in RAM.
INFO	2026-06-08 08:12:53	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    1s.  Last read position: chr5:154,803,598
INFO	2026-06-08 08:12:53	MarkDuplicates	Tracking 463619 as yet unmatched pairs. 6447 records in RAM.
INFO	2026-06-08 08:12:55	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    1s.  Last read position: chr5:169,874,495
INFO	2026-06-08 08:12:55	MarkDuplicates	Tracking 462949 as yet unmatched pairs. 5663 records in RAM.
INFO	2026-06-08 08:12:57	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:04:26s.  Time for last 1,000,000:    1s.  Last read position: chr5:171,939,093
INFO	2026-06-08 08:12:57	MarkDuplicates	Tracking 462112 as yet unmatched pairs. 4736 records in RAM.
INFO	2026-06-08 08:12:58	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    1s.  Last read position: chr5:177,303,861
INFO	2026-06-08 08:12:58	MarkDuplicates	Tracking 461306 as yet unmatched pairs. 3846 records in RAM.
INFO	2026-06-08 08:13:00	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    1s.  Last read position: chr5:178,712,780
INFO	2026-06-08 08:13:00	MarkDuplicates	Tracking 459697 as yet unmatched pairs. 2153 records in RAM.
INFO	2026-06-08 08:13:02	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    1s.  Last read position: chr5:179,836,641
INFO	2026-06-08 08:13:02	MarkDuplicates	Tracking 458618 as yet unmatched pairs. 941 records in RAM.
INFO	2026-06-08 08:13:04	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    1s.  Last read position: chr6:673,810
INFO	2026-06-08 08:13:04	MarkDuplicates	Tracking 457385 as yet unmatched pairs. 28412 records in RAM.
INFO	2026-06-08 08:13:05	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:    1s.  Last read position: chr6:7,297,986
INFO	2026-06-08 08:13:05	MarkDuplicates	Tracking 456529 as yet unmatched pairs. 27432 records in RAM.
INFO	2026-06-08 08:13:07	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    1s.  Last read position: chr6:16,328,171
INFO	2026-06-08 08:13:07	MarkDuplicates	Tracking 455259 as yet unmatched pairs. 26022 records in RAM.
INFO	2026-06-08 08:13:09	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:    1s.  Last read position: chr6:26,124,326
INFO	2026-06-08 08:13:09	MarkDuplicates	Tracking 455536 as yet unmatched pairs. 26176 records in RAM.
INFO	2026-06-08 08:13:11	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    2s.  Last read position: chr6:27,810,269
INFO	2026-06-08 08:13:11	MarkDuplicates	Tracking 454490 as yet unmatched pairs. 25033 records in RAM.
INFO	2026-06-08 08:13:13	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    2s.  Last read position: chr6:30,007,569
INFO	2026-06-08 08:13:13	MarkDuplicates	Tracking 452363 as yet unmatched pairs. 22859 records in RAM.
INFO	2026-06-08 08:13:16	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    2s.  Last read position: chr6:30,922,929
INFO	2026-06-08 08:13:16	MarkDuplicates	Tracking 451407 as yet unmatched pairs. 21845 records in RAM.
INFO	2026-06-08 08:13:18	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:04:47s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,628,116
INFO	2026-06-08 08:13:18	MarkDuplicates	Tracking 450691 as yet unmatched pairs. 21058 records in RAM.
INFO	2026-06-08 08:13:19	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    1s.  Last read position: chr6:31,896,874
INFO	2026-06-08 08:13:19	MarkDuplicates	Tracking 449283 as yet unmatched pairs. 19595 records in RAM.
INFO	2026-06-08 08:13:21	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    1s.  Last read position: chr6:32,835,311
INFO	2026-06-08 08:13:21	MarkDuplicates	Tracking 448736 as yet unmatched pairs. 18983 records in RAM.
INFO	2026-06-08 08:13:23	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    1s.  Last read position: chr6:33,086,605
INFO	2026-06-08 08:13:23	MarkDuplicates	Tracking 447792 as yet unmatched pairs. 17972 records in RAM.
INFO	2026-06-08 08:13:25	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    1s.  Last read position: chr6:33,443,263
INFO	2026-06-08 08:13:25	MarkDuplicates	Tracking 446263 as yet unmatched pairs. 16405 records in RAM.
INFO	2026-06-08 08:13:27	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    1s.  Last read position: chr6:36,596,948
INFO	2026-06-08 08:13:27	MarkDuplicates	Tracking 445284 as yet unmatched pairs. 15300 records in RAM.
INFO	2026-06-08 08:13:29	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    1s.  Last read position: chr6:42,051,454
INFO	2026-06-08 08:13:29	MarkDuplicates	Tracking 443984 as yet unmatched pairs. 13907 records in RAM.
INFO	2026-06-08 08:13:31	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:05:00s.  Time for last 1,000,000:    2s.  Last read position: chr6:43,369,206
INFO	2026-06-08 08:13:31	MarkDuplicates	Tracking 444110 as yet unmatched pairs. 13994 records in RAM.
INFO	2026-06-08 08:13:33	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    1s.  Last read position: chr6:52,269,158
INFO	2026-06-08 08:13:33	MarkDuplicates	Tracking 441342 as yet unmatched pairs. 11159 records in RAM.
INFO	2026-06-08 08:13:34	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    1s.  Last read position: chr6:56,633,013
INFO	2026-06-08 08:13:34	MarkDuplicates	Tracking 441060 as yet unmatched pairs. 10749 records in RAM.
INFO	2026-06-08 08:13:36	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    1s.  Last read position: chr6:73,518,392
INFO	2026-06-08 08:13:36	MarkDuplicates	Tracking 440972 as yet unmatched pairs. 10516 records in RAM.
INFO	2026-06-08 08:13:38	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    1s.  Last read position: chr6:87,256,184
INFO	2026-06-08 08:13:38	MarkDuplicates	Tracking 439441 as yet unmatched pairs. 8900 records in RAM.
INFO	2026-06-08 08:13:40	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    1s.  Last read position: chr6:100,540,237
INFO	2026-06-08 08:13:40	MarkDuplicates	Tracking 438257 as yet unmatched pairs. 7647 records in RAM.
INFO	2026-06-08 08:13:42	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:    1s.  Last read position: chr6:111,367,622
INFO	2026-06-08 08:13:42	MarkDuplicates	Tracking 437467 as yet unmatched pairs. 6757 records in RAM.
INFO	2026-06-08 08:13:43	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    1s.  Last read position: chr6:125,956,972
INFO	2026-06-08 08:13:43	MarkDuplicates	Tracking 436280 as yet unmatched pairs. 5440 records in RAM.
INFO	2026-06-08 08:13:46	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    2s.  Last read position: chr6:138,424,325
INFO	2026-06-08 08:13:46	MarkDuplicates	Tracking 435421 as yet unmatched pairs. 4509 records in RAM.
INFO	2026-06-08 08:13:48	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    2s.  Last read position: chr6:149,473,542
INFO	2026-06-08 08:13:48	MarkDuplicates	Tracking 434656 as yet unmatched pairs. 3675 records in RAM.
INFO	2026-06-08 08:13:50	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:05:19s.  Time for last 1,000,000:    2s.  Last read position: chr6:157,190,174
INFO	2026-06-08 08:13:50	MarkDuplicates	Tracking 433237 as yet unmatched pairs. 2192 records in RAM.
INFO	2026-06-08 08:13:52	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:05:21s.  Time for last 1,000,000:    1s.  Last read position: chr6:160,089,974
INFO	2026-06-08 08:13:52	MarkDuplicates	Tracking 432281 as yet unmatched pairs. 1131 records in RAM.
INFO	2026-06-08 08:13:54	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    1s.  Last read position: chr7:886,024
INFO	2026-06-08 08:13:54	MarkDuplicates	Tracking 431383 as yet unmatched pairs. 28056 records in RAM.
INFO	2026-06-08 08:13:56	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:05:25s.  Time for last 1,000,000:    1s.  Last read position: chr7:2,731,415
INFO	2026-06-08 08:13:56	MarkDuplicates	Tracking 429711 as yet unmatched pairs. 26329 records in RAM.
INFO	2026-06-08 08:13:58	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:05:27s.  Time for last 1,000,000:    1s.  Last read position: chr7:5,390,493
INFO	2026-06-08 08:13:58	MarkDuplicates	Tracking 428123 as yet unmatched pairs. 24702 records in RAM.
INFO	2026-06-08 08:14:00	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    1s.  Last read position: chr7:5,529,545
INFO	2026-06-08 08:14:00	MarkDuplicates	Tracking 431897 as yet unmatched pairs. 28389 records in RAM.
INFO	2026-06-08 08:14:01	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    1s.  Last read position: chr7:17,339,476
INFO	2026-06-08 08:14:01	MarkDuplicates	Tracking 425663 as yet unmatched pairs. 22051 records in RAM.
INFO	2026-06-08 08:14:03	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    1s.  Last read position: chr7:27,458,199
INFO	2026-06-08 08:14:03	MarkDuplicates	Tracking 424664 as yet unmatched pairs. 20941 records in RAM.
INFO	2026-06-08 08:14:05	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    1s.  Last read position: chr7:39,951,201
INFO	2026-06-08 08:14:05	MarkDuplicates	Tracking 424513 as yet unmatched pairs. 20636 records in RAM.
INFO	2026-06-08 08:14:07	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    1s.  Last read position: chr7:44,761,793
INFO	2026-06-08 08:14:07	MarkDuplicates	Tracking 423365 as yet unmatched pairs. 19361 records in RAM.
INFO	2026-06-08 08:14:09	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    1s.  Last read position: chr7:56,104,407
INFO	2026-06-08 08:14:09	MarkDuplicates	Tracking 422482 as yet unmatched pairs. 18397 records in RAM.
INFO	2026-06-08 08:14:10	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    1s.  Last read position: chr7:73,063,864
INFO	2026-06-08 08:14:10	MarkDuplicates	Tracking 420988 as yet unmatched pairs. 16799 records in RAM.
INFO	2026-06-08 08:14:12	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    1s.  Last read position: chr7:74,403,850
INFO	2026-06-08 08:14:12	MarkDuplicates	Tracking 420337 as yet unmatched pairs. 16090 records in RAM.
INFO	2026-06-08 08:14:14	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:    1s.  Last read position: chr7:75,494,081
INFO	2026-06-08 08:14:14	MarkDuplicates	Tracking 419680 as yet unmatched pairs. 15378 records in RAM.
INFO	2026-06-08 08:14:16	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    2s.  Last read position: chr7:87,907,387
INFO	2026-06-08 08:14:16	MarkDuplicates	Tracking 418733 as yet unmatched pairs. 14346 records in RAM.
INFO	2026-06-08 08:14:20	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:05:49s.  Time for last 1,000,000:    3s.  Last read position: chr7:93,276,270
INFO	2026-06-08 08:14:20	MarkDuplicates	Tracking 417957 as yet unmatched pairs. 13480 records in RAM.
INFO	2026-06-08 08:14:22	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    2s.  Last read position: chr7:99,531,642
INFO	2026-06-08 08:14:22	MarkDuplicates	Tracking 416920 as yet unmatched pairs. 12382 records in RAM.
INFO	2026-06-08 08:14:24	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    1s.  Last read position: chr7:100,477,946
INFO	2026-06-08 08:14:24	MarkDuplicates	Tracking 416193 as yet unmatched pairs. 11580 records in RAM.
INFO	2026-06-08 08:14:26	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    1s.  Last read position: chr7:102,342,178
INFO	2026-06-08 08:14:26	MarkDuplicates	Tracking 414329 as yet unmatched pairs. 9656 records in RAM.
INFO	2026-06-08 08:14:27	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    1s.  Last read position: chr7:104,671,136
INFO	2026-06-08 08:14:27	MarkDuplicates	Tracking 413751 as yet unmatched pairs. 9031 records in RAM.
INFO	2026-06-08 08:14:29	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    1s.  Last read position: chr7:120,438,208
INFO	2026-06-08 08:14:29	MarkDuplicates	Tracking 412997 as yet unmatched pairs. 8110 records in RAM.
INFO	2026-06-08 08:14:31	MarkDuplicates	Read   181,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    1s.  Last read position: chr7:128,087,000
INFO	2026-06-08 08:14:31	MarkDuplicates	Tracking 414141 as yet unmatched pairs. 9133 records in RAM.
INFO	2026-06-08 08:14:33	MarkDuplicates	Read   182,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    1s.  Last read position: chr7:134,646,972
INFO	2026-06-08 08:14:33	MarkDuplicates	Tracking 411332 as yet unmatched pairs. 6170 records in RAM.
INFO	2026-06-08 08:14:34	MarkDuplicates	Read   183,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    1s.  Last read position: chr7:138,867,984
INFO	2026-06-08 08:14:34	MarkDuplicates	Tracking 410376 as yet unmatched pairs. 5113 records in RAM.
INFO	2026-06-08 08:14:36	MarkDuplicates	Read   184,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    1s.  Last read position: chr7:141,652,803
INFO	2026-06-08 08:14:36	MarkDuplicates	Tracking 409571 as yet unmatched pairs. 4237 records in RAM.
INFO	2026-06-08 08:14:38	MarkDuplicates	Read   185,000,000 records.  Elapsed time: 00:06:07s.  Time for last 1,000,000:    1s.  Last read position: chr7:149,874,129
INFO	2026-06-08 08:14:38	MarkDuplicates	Tracking 408418 as yet unmatched pairs. 3011 records in RAM.
INFO	2026-06-08 08:14:40	MarkDuplicates	Read   186,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    1s.  Last read position: chr7:152,152,908
INFO	2026-06-08 08:14:40	MarkDuplicates	Tracking 406661 as yet unmatched pairs. 1190 records in RAM.
INFO	2026-06-08 08:14:42	MarkDuplicates	Read   187,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    2s.  Last read position: chr8:6,508,624
INFO	2026-06-08 08:14:42	MarkDuplicates	Tracking 405676 as yet unmatched pairs. 18604 records in RAM.
INFO	2026-06-08 08:14:44	MarkDuplicates	Read   188,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    1s.  Last read position: chr8:17,969,732
INFO	2026-06-08 08:14:44	MarkDuplicates	Tracking 404519 as yet unmatched pairs. 17351 records in RAM.
INFO	2026-06-08 08:14:46	MarkDuplicates	Read   189,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    1s.  Last read position: chr8:23,260,584
INFO	2026-06-08 08:14:46	MarkDuplicates	Tracking 403247 as yet unmatched pairs. 15940 records in RAM.
INFO	2026-06-08 08:14:48	MarkDuplicates	Read   190,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    1s.  Last read position: chr8:30,703,185
INFO	2026-06-08 08:14:48	MarkDuplicates	Tracking 402360 as yet unmatched pairs. 14985 records in RAM.
INFO	2026-06-08 08:14:50	MarkDuplicates	Read   191,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    1s.  Last read position: chr8:38,820,046
INFO	2026-06-08 08:14:50	MarkDuplicates	Tracking 402676 as yet unmatched pairs. 15236 records in RAM.
INFO	2026-06-08 08:14:52	MarkDuplicates	Read   192,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    2s.  Last read position: chr8:47,778,753
INFO	2026-06-08 08:14:52	MarkDuplicates	Tracking 400344 as yet unmatched pairs. 12812 records in RAM.
INFO	2026-06-08 08:14:54	MarkDuplicates	Read   193,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    1s.  Last read position: chr8:60,781,226
INFO	2026-06-08 08:14:54	MarkDuplicates	Tracking 399381 as yet unmatched pairs. 11744 records in RAM.
INFO	2026-06-08 08:14:57	MarkDuplicates	Read   194,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    3s.  Last read position: chr8:70,187,151
INFO	2026-06-08 08:14:57	MarkDuplicates	Tracking 398555 as yet unmatched pairs. 10843 records in RAM.
INFO	2026-06-08 08:14:59	MarkDuplicates	Read   195,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    2s.  Last read position: chr8:91,134,365
INFO	2026-06-08 08:14:59	MarkDuplicates	Tracking 397529 as yet unmatched pairs. 9717 records in RAM.
INFO	2026-06-08 08:15:01	MarkDuplicates	Read   196,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    1s.  Last read position: chr8:100,263,979
INFO	2026-06-08 08:15:01	MarkDuplicates	Tracking 397016 as yet unmatched pairs. 9115 records in RAM.
INFO	2026-06-08 08:15:03	MarkDuplicates	Read   197,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    1s.  Last read position: chr8:102,323,461
INFO	2026-06-08 08:15:03	MarkDuplicates	Tracking 395777 as yet unmatched pairs. 7824 records in RAM.
INFO	2026-06-08 08:15:05	MarkDuplicates	Read   198,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    1s.  Last read position: chr8:123,161,780
INFO	2026-06-08 08:15:05	MarkDuplicates	Tracking 394893 as yet unmatched pairs. 6845 records in RAM.
INFO	2026-06-08 08:15:07	MarkDuplicates	Read   199,000,000 records.  Elapsed time: 00:06:36s.  Time for last 1,000,000:    1s.  Last read position: chr8:131,944,821
INFO	2026-06-08 08:15:07	MarkDuplicates	Tracking 394279 as yet unmatched pairs. 6140 records in RAM.
INFO	2026-06-08 08:15:09	MarkDuplicates	Read   200,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    1s.  Last read position: chr8:143,581,060
INFO	2026-06-08 08:15:09	MarkDuplicates	Tracking 394187 as yet unmatched pairs. 5967 records in RAM.
INFO	2026-06-08 08:15:11	MarkDuplicates	Read   201,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    2s.  Last read position: chr8:143,984,878
INFO	2026-06-08 08:15:11	MarkDuplicates	Tracking 391660 as yet unmatched pairs. 3371 records in RAM.
INFO	2026-06-08 08:15:13	MarkDuplicates	Read   202,000,000 records.  Elapsed time: 00:06:42s.  Time for last 1,000,000:    2s.  Last read position: chr8:144,462,242
INFO	2026-06-08 08:15:13	MarkDuplicates	Tracking 389216 as yet unmatched pairs. 862 records in RAM.
INFO	2026-06-08 08:15:15	MarkDuplicates	Read   203,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:    2s.  Last read position: chr9:3,483,820
INFO	2026-06-08 08:15:15	MarkDuplicates	Tracking 387933 as yet unmatched pairs. 22821 records in RAM.
INFO	2026-06-08 08:15:17	MarkDuplicates	Read   204,000,000 records.  Elapsed time: 00:06:46s.  Time for last 1,000,000:    1s.  Last read position: chr9:9,442,096
INFO	2026-06-08 08:15:17	MarkDuplicates	Tracking 393332 as yet unmatched pairs. 28034 records in RAM.
INFO	2026-06-08 08:15:19	MarkDuplicates	Read   205,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    1s.  Last read position: chr9:19,276,199
INFO	2026-06-08 08:15:19	MarkDuplicates	Tracking 386020 as yet unmatched pairs. 20623 records in RAM.
INFO	2026-06-08 08:15:20	MarkDuplicates	Read   206,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:    1s.  Last read position: chr9:33,318,767
INFO	2026-06-08 08:15:20	MarkDuplicates	Tracking 384935 as yet unmatched pairs. 19452 records in RAM.
INFO	2026-06-08 08:15:22	MarkDuplicates	Read   207,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:    1s.  Last read position: chr9:35,714,301
INFO	2026-06-08 08:15:22	MarkDuplicates	Tracking 383940 as yet unmatched pairs. 18387 records in RAM.
INFO	2026-06-08 08:15:24	MarkDuplicates	Read   208,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    1s.  Last read position: chr9:36,839,659
INFO	2026-06-08 08:15:24	MarkDuplicates	Tracking 383236 as yet unmatched pairs. 17609 records in RAM.
INFO	2026-06-08 08:15:26	MarkDuplicates	Read   209,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    1s.  Last read position: chr9:66,281,188
INFO	2026-06-08 08:15:26	MarkDuplicates	Tracking 381701 as yet unmatched pairs. 15986 records in RAM.
INFO	2026-06-08 08:15:28	MarkDuplicates	Read   210,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    1s.  Last read position: chr9:85,692,768
INFO	2026-06-08 08:15:28	MarkDuplicates	Tracking 381135 as yet unmatched pairs. 15364 records in RAM.
INFO	2026-06-08 08:15:30	MarkDuplicates	Read   211,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    1s.  Last read position: chr9:92,976,232
INFO	2026-06-08 08:15:30	MarkDuplicates	Tracking 380419 as yet unmatched pairs. 14563 records in RAM.
INFO	2026-06-08 08:15:32	MarkDuplicates	Read   212,000,000 records.  Elapsed time: 00:07:01s.  Time for last 1,000,000:    2s.  Last read position: chr9:100,226,089
INFO	2026-06-08 08:15:32	MarkDuplicates	Tracking 378968 as yet unmatched pairs. 13007 records in RAM.
INFO	2026-06-08 08:15:34	MarkDuplicates	Read   213,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    2s.  Last read position: chr9:113,166,538
INFO	2026-06-08 08:15:34	MarkDuplicates	Tracking 378332 as yet unmatched pairs. 12311 records in RAM.
INFO	2026-06-08 08:15:37	MarkDuplicates	Read   214,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    2s.  Last read position: chr9:121,135,827
INFO	2026-06-08 08:15:37	MarkDuplicates	Tracking 378056 as yet unmatched pairs. 11972 records in RAM.
INFO	2026-06-08 08:15:39	MarkDuplicates	Read   215,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    2s.  Last read position: chr9:124,923,134
INFO	2026-06-08 08:15:39	MarkDuplicates	Tracking 375928 as yet unmatched pairs. 9768 records in RAM.
INFO	2026-06-08 08:15:41	MarkDuplicates	Read   216,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    2s.  Last read position: chr9:128,068,343
INFO	2026-06-08 08:15:41	MarkDuplicates	Tracking 374728 as yet unmatched pairs. 8470 records in RAM.
INFO	2026-06-08 08:15:43	MarkDuplicates	Read   217,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    1s.  Last read position: chr9:129,009,090
INFO	2026-06-08 08:15:43	MarkDuplicates	Tracking 373979 as yet unmatched pairs. 7680 records in RAM.
INFO	2026-06-08 08:15:45	MarkDuplicates	Read   218,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    1s.  Last read position: chr9:131,146,151
INFO	2026-06-08 08:15:45	MarkDuplicates	Tracking 372497 as yet unmatched pairs. 6103 records in RAM.
INFO	2026-06-08 08:15:47	MarkDuplicates	Read   219,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    1s.  Last read position: chr9:132,896,258
INFO	2026-06-08 08:15:47	MarkDuplicates	Tracking 371549 as yet unmatched pairs. 5088 records in RAM.
INFO	2026-06-08 08:15:49	MarkDuplicates	Read   220,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    1s.  Last read position: chr9:135,938,275
INFO	2026-06-08 08:15:49	MarkDuplicates	Tracking 370513 as yet unmatched pairs. 3939 records in RAM.
INFO	2026-06-08 08:15:51	MarkDuplicates	Read   221,000,000 records.  Elapsed time: 00:07:20s.  Time for last 1,000,000:    1s.  Last read position: chr9:136,831,823
INFO	2026-06-08 08:15:51	MarkDuplicates	Tracking 369134 as yet unmatched pairs. 2496 records in RAM.
INFO	2026-06-08 08:15:53	MarkDuplicates	Read   222,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    2s.  Last read position: chr9:137,457,449
INFO	2026-06-08 08:15:53	MarkDuplicates	Tracking 367733 as yet unmatched pairs. 1038 records in RAM.
INFO	2026-06-08 08:15:55	MarkDuplicates	Read   223,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    2s.  Last read position: chr10:5,925,347
INFO	2026-06-08 08:15:55	MarkDuplicates	Tracking 366169 as yet unmatched pairs. 15962 records in RAM.
INFO	2026-06-08 08:15:57	MarkDuplicates	Read   224,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    1s.  Last read position: chr10:15,140,915
INFO	2026-06-08 08:15:57	MarkDuplicates	Tracking 365062 as yet unmatched pairs. 14712 records in RAM.
INFO	2026-06-08 08:15:59	MarkDuplicates	Read   225,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:    2s.  Last read position: chr10:28,583,473
INFO	2026-06-08 08:15:59	MarkDuplicates	Tracking 364584 as yet unmatched pairs. 14182 records in RAM.
INFO	2026-06-08 08:16:01	MarkDuplicates	Read   226,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    2s.  Last read position: chr10:42,632,347
INFO	2026-06-08 08:16:01	MarkDuplicates	Tracking 363334 as yet unmatched pairs. 12880 records in RAM.
INFO	2026-06-08 08:16:03	MarkDuplicates	Read   227,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:    1s.  Last read position: chr10:48,743,208
INFO	2026-06-08 08:16:03	MarkDuplicates	Tracking 363924 as yet unmatched pairs. 13433 records in RAM.
INFO	2026-06-08 08:16:05	MarkDuplicates	Read   228,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    1s.  Last read position: chr10:62,814,030
INFO	2026-06-08 08:16:05	MarkDuplicates	Tracking 361986 as yet unmatched pairs. 11451 records in RAM.
INFO	2026-06-08 08:16:07	MarkDuplicates	Read   229,000,000 records.  Elapsed time: 00:07:36s.  Time for last 1,000,000:    1s.  Last read position: chr10:72,274,255
INFO	2026-06-08 08:16:07	MarkDuplicates	Tracking 361738 as yet unmatched pairs. 11120 records in RAM.
INFO	2026-06-08 08:16:09	MarkDuplicates	Read   230,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    1s.  Last read position: chr10:75,030,388
INFO	2026-06-08 08:16:09	MarkDuplicates	Tracking 359759 as yet unmatched pairs. 9071 records in RAM.
INFO	2026-06-08 08:16:11	MarkDuplicates	Read   231,000,000 records.  Elapsed time: 00:07:40s.  Time for last 1,000,000:    1s.  Last read position: chr10:87,062,795
INFO	2026-06-08 08:16:11	MarkDuplicates	Tracking 359398 as yet unmatched pairs. 8649 records in RAM.
INFO	2026-06-08 08:16:12	MarkDuplicates	Read   232,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:    1s.  Last read position: chr10:91,817,190
INFO	2026-06-08 08:16:12	MarkDuplicates	Tracking 358130 as yet unmatched pairs. 7301 records in RAM.
INFO	2026-06-08 08:16:14	MarkDuplicates	Read   233,000,000 records.  Elapsed time: 00:07:44s.  Time for last 1,000,000:    2s.  Last read position: chr10:95,874,048
INFO	2026-06-08 08:16:14	MarkDuplicates	Tracking 357202 as yet unmatched pairs. 6279 records in RAM.
INFO	2026-06-08 08:16:16	MarkDuplicates	Read   234,000,000 records.  Elapsed time: 00:07:45s.  Time for last 1,000,000:    1s.  Last read position: chr10:99,743,327
INFO	2026-06-08 08:16:16	MarkDuplicates	Tracking 356030 as yet unmatched pairs. 5039 records in RAM.
INFO	2026-06-08 08:16:18	MarkDuplicates	Read   235,000,000 records.  Elapsed time: 00:07:47s.  Time for last 1,000,000:    1s.  Last read position: chr10:102,380,272
INFO	2026-06-08 08:16:18	MarkDuplicates	Tracking 355114 as yet unmatched pairs. 4047 records in RAM.
INFO	2026-06-08 08:16:20	MarkDuplicates	Read   236,000,000 records.  Elapsed time: 00:07:49s.  Time for last 1,000,000:    1s.  Last read position: chr10:110,890,659
INFO	2026-06-08 08:16:20	MarkDuplicates	Tracking 354441 as yet unmatched pairs. 3311 records in RAM.
INFO	2026-06-08 08:16:23	MarkDuplicates	Read   237,000,000 records.  Elapsed time: 00:07:52s.  Time for last 1,000,000:    2s.  Last read position: chr10:121,974,953
INFO	2026-06-08 08:16:23	MarkDuplicates	Tracking 353188 as yet unmatched pairs. 1998 records in RAM.
INFO	2026-06-08 08:16:26	MarkDuplicates	Read   238,000,000 records.  Elapsed time: 00:07:55s.  Time for last 1,000,000:    2s.  Last read position: chr10:133,308,976
INFO	2026-06-08 08:16:26	MarkDuplicates	Tracking 351945 as yet unmatched pairs. 695 records in RAM.
INFO	2026-06-08 08:16:28	MarkDuplicates	Read   239,000,000 records.  Elapsed time: 00:07:57s.  Time for last 1,000,000:    2s.  Last read position: chr11:562,551
INFO	2026-06-08 08:16:28	MarkDuplicates	Tracking 350383 as yet unmatched pairs. 31211 records in RAM.
INFO	2026-06-08 08:16:30	MarkDuplicates	Read   240,000,000 records.  Elapsed time: 00:07:59s.  Time for last 1,000,000:    2s.  Last read position: chr11:1,761,371
INFO	2026-06-08 08:16:30	MarkDuplicates	Tracking 350118 as yet unmatched pairs. 30897 records in RAM.
INFO	2026-06-08 08:16:32	MarkDuplicates	Read   241,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    2s.  Last read position: chr11:5,709,583
INFO	2026-06-08 08:16:32	MarkDuplicates	Tracking 348263 as yet unmatched pairs. 28974 records in RAM.
INFO	2026-06-08 08:16:35	MarkDuplicates	Read   242,000,000 records.  Elapsed time: 00:08:04s.  Time for last 1,000,000:    2s.  Last read position: chr11:9,853,558
INFO	2026-06-08 08:16:35	MarkDuplicates	Tracking 346378 as yet unmatched pairs. 27016 records in RAM.
INFO	2026-06-08 08:16:37	MarkDuplicates	Read   243,000,000 records.  Elapsed time: 00:08:06s.  Time for last 1,000,000:    2s.  Last read position: chr11:19,170,542
INFO	2026-06-08 08:16:37	MarkDuplicates	Tracking 345595 as yet unmatched pairs. 26160 records in RAM.
INFO	2026-06-08 08:16:39	MarkDuplicates	Read   244,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:    2s.  Last read position: chr11:36,487,827
INFO	2026-06-08 08:16:39	MarkDuplicates	Tracking 344605 as yet unmatched pairs. 25119 records in RAM.
INFO	2026-06-08 08:16:41	MarkDuplicates	Read   245,000,000 records.  Elapsed time: 00:08:11s.  Time for last 1,000,000:    2s.  Last read position: chr11:47,232,283
INFO	2026-06-08 08:16:41	MarkDuplicates	Tracking 343741 as yet unmatched pairs. 24174 records in RAM.
INFO	2026-06-08 08:16:44	MarkDuplicates	Read   246,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    2s.  Last read position: chr11:57,796,477
INFO	2026-06-08 08:16:44	MarkDuplicates	Tracking 342672 as yet unmatched pairs. 23043 records in RAM.
INFO	2026-06-08 08:16:46	MarkDuplicates	Read   247,000,000 records.  Elapsed time: 00:08:15s.  Time for last 1,000,000:    2s.  Last read position: chr11:60,931,755
INFO	2026-06-08 08:16:46	MarkDuplicates	Tracking 341843 as yet unmatched pairs. 22183 records in RAM.
INFO	2026-06-08 08:17:51	MarkDuplicates	Read   248,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:   65s.  Last read position: chr11:62,532,420
INFO	2026-06-08 08:17:51	MarkDuplicates	Tracking 340564 as yet unmatched pairs. 20837 records in RAM.
INFO	2026-06-08 08:17:54	MarkDuplicates	Read   249,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    2s.  Last read position: chr11:62,885,203
INFO	2026-06-08 08:17:54	MarkDuplicates	Tracking 339851 as yet unmatched pairs. 20068 records in RAM.
INFO	2026-06-08 08:17:55	MarkDuplicates	Read   250,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    1s.  Last read position: chr11:64,343,180
INFO	2026-06-08 08:17:55	MarkDuplicates	Tracking 338565 as yet unmatched pairs. 18711 records in RAM.
INFO	2026-06-08 08:17:57	MarkDuplicates	Read   251,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    1s.  Last read position: chr11:65,108,677
INFO	2026-06-08 08:17:57	MarkDuplicates	Tracking 336906 as yet unmatched pairs. 17027 records in RAM.
INFO	2026-06-08 08:17:59	MarkDuplicates	Read   252,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    1s.  Last read position: chr11:65,501,354
INFO	2026-06-08 08:17:59	MarkDuplicates	Tracking 335979 as yet unmatched pairs. 15981 records in RAM.
INFO	2026-06-08 08:18:01	MarkDuplicates	Read   253,000,000 records.  Elapsed time: 00:09:30s.  Time for last 1,000,000:    1s.  Last read position: chr11:65,641,171
INFO	2026-06-08 08:18:01	MarkDuplicates	Tracking 334728 as yet unmatched pairs. 14662 records in RAM.
INFO	2026-06-08 08:18:03	MarkDuplicates	Read   254,000,000 records.  Elapsed time: 00:09:32s.  Time for last 1,000,000:    1s.  Last read position: chr11:66,232,966
INFO	2026-06-08 08:18:03	MarkDuplicates	Tracking 332929 as yet unmatched pairs. 12799 records in RAM.
INFO	2026-06-08 08:18:05	MarkDuplicates	Read   255,000,000 records.  Elapsed time: 00:09:34s.  Time for last 1,000,000:    2s.  Last read position: chr11:67,391,983
INFO	2026-06-08 08:18:05	MarkDuplicates	Tracking 331188 as yet unmatched pairs. 11025 records in RAM.
INFO	2026-06-08 08:18:07	MarkDuplicates	Read   256,000,000 records.  Elapsed time: 00:09:36s.  Time for last 1,000,000:    1s.  Last read position: chr11:68,043,853
INFO	2026-06-08 08:18:07	MarkDuplicates	Tracking 330220 as yet unmatched pairs. 10032 records in RAM.
INFO	2026-06-08 08:18:09	MarkDuplicates	Read   257,000,000 records.  Elapsed time: 00:09:38s.  Time for last 1,000,000:    1s.  Last read position: chr11:72,013,278
INFO	2026-06-08 08:18:09	MarkDuplicates	Tracking 329088 as yet unmatched pairs. 8842 records in RAM.
INFO	2026-06-08 08:18:11	MarkDuplicates	Read   258,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    1s.  Last read position: chr11:73,720,888
INFO	2026-06-08 08:18:11	MarkDuplicates	Tracking 327024 as yet unmatched pairs. 6693 records in RAM.
INFO	2026-06-08 08:18:13	MarkDuplicates	Read   259,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:    1s.  Last read position: chr11:82,931,738
INFO	2026-06-08 08:18:13	MarkDuplicates	Tracking 325984 as yet unmatched pairs. 5557 records in RAM.
INFO	2026-06-08 08:18:15	MarkDuplicates	Read   260,000,000 records.  Elapsed time: 00:09:44s.  Time for last 1,000,000:    1s.  Last read position: chr11:96,147,104
INFO	2026-06-08 08:18:15	MarkDuplicates	Tracking 325202 as yet unmatched pairs. 4673 records in RAM.
INFO	2026-06-08 08:18:17	MarkDuplicates	Read   261,000,000 records.  Elapsed time: 00:09:46s.  Time for last 1,000,000:    1s.  Last read position: chr11:111,357,806
INFO	2026-06-08 08:18:17	MarkDuplicates	Tracking 324720 as yet unmatched pairs. 4114 records in RAM.
INFO	2026-06-08 08:18:18	MarkDuplicates	Read   262,000,000 records.  Elapsed time: 00:09:47s.  Time for last 1,000,000:    1s.  Last read position: chr11:118,489,831
INFO	2026-06-08 08:18:18	MarkDuplicates	Tracking 323178 as yet unmatched pairs. 2524 records in RAM.
INFO	2026-06-08 08:18:20	MarkDuplicates	Read   263,000,000 records.  Elapsed time: 00:09:49s.  Time for last 1,000,000:    1s.  Last read position: chr11:121,531,370
INFO	2026-06-08 08:18:20	MarkDuplicates	Tracking 322116 as yet unmatched pairs. 1434 records in RAM.
INFO	2026-06-08 08:18:22	MarkDuplicates	Read   264,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:    2s.  Last read position: chr11:129,865,085
INFO	2026-06-08 08:18:22	MarkDuplicates	Tracking 321180 as yet unmatched pairs. 446 records in RAM.
INFO	2026-06-08 08:18:24	MarkDuplicates	Read   265,000,000 records.  Elapsed time: 00:09:53s.  Time for last 1,000,000:    2s.  Last read position: chr12:2,858,725
INFO	2026-06-08 08:18:24	MarkDuplicates	Tracking 320129 as yet unmatched pairs. 28342 records in RAM.
INFO	2026-06-08 08:18:26	MarkDuplicates	Read   266,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    1s.  Last read position: chr12:6,601,433
INFO	2026-06-08 08:18:26	MarkDuplicates	Tracking 318983 as yet unmatched pairs. 27141 records in RAM.
INFO	2026-06-08 08:18:28	MarkDuplicates	Read   267,000,000 records.  Elapsed time: 00:09:57s.  Time for last 1,000,000:    1s.  Last read position: chr12:7,136,873
INFO	2026-06-08 08:18:28	MarkDuplicates	Tracking 318267 as yet unmatched pairs. 26398 records in RAM.
INFO	2026-06-08 08:18:30	MarkDuplicates	Read   268,000,000 records.  Elapsed time: 00:09:59s.  Time for last 1,000,000:    2s.  Last read position: chr12:11,824,004
INFO	2026-06-08 08:18:30	MarkDuplicates	Tracking 317604 as yet unmatched pairs. 25659 records in RAM.
INFO	2026-06-08 08:18:33	MarkDuplicates	Read   269,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    2s.  Last read position: chr12:22,625,254
INFO	2026-06-08 08:18:33	MarkDuplicates	Tracking 318226 as yet unmatched pairs. 26213 records in RAM.
INFO	2026-06-08 08:18:35	MarkDuplicates	Read   270,000,000 records.  Elapsed time: 00:10:04s.  Time for last 1,000,000:    1s.  Last read position: chr12:27,317,972
INFO	2026-06-08 08:18:35	MarkDuplicates	Tracking 315292 as yet unmatched pairs. 23219 records in RAM.
INFO	2026-06-08 08:18:37	MarkDuplicates	Read   271,000,000 records.  Elapsed time: 00:10:06s.  Time for last 1,000,000:    1s.  Last read position: chr12:42,464,925
INFO	2026-06-08 08:18:37	MarkDuplicates	Tracking 314358 as yet unmatched pairs. 22196 records in RAM.
INFO	2026-06-08 08:18:38	MarkDuplicates	Read   272,000,000 records.  Elapsed time: 00:10:07s.  Time for last 1,000,000:    1s.  Last read position: chr12:49,026,491
INFO	2026-06-08 08:18:38	MarkDuplicates	Tracking 313746 as yet unmatched pairs. 21516 records in RAM.
INFO	2026-06-08 08:18:40	MarkDuplicates	Read   273,000,000 records.  Elapsed time: 00:10:09s.  Time for last 1,000,000:    1s.  Last read position: chr12:49,646,637
INFO	2026-06-08 08:18:40	MarkDuplicates	Tracking 312661 as yet unmatched pairs. 20382 records in RAM.
INFO	2026-06-08 08:18:42	MarkDuplicates	Read   274,000,000 records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:    1s.  Last read position: chr12:53,195,423
INFO	2026-06-08 08:18:42	MarkDuplicates	Tracking 311828 as yet unmatched pairs. 19493 records in RAM.
INFO	2026-06-08 08:18:44	MarkDuplicates	Read   275,000,000 records.  Elapsed time: 00:10:13s.  Time for last 1,000,000:    1s.  Last read position: chr12:54,281,486
INFO	2026-06-08 08:18:44	MarkDuplicates	Tracking 312499 as yet unmatched pairs. 20101 records in RAM.
INFO	2026-06-08 08:18:46	MarkDuplicates	Read   276,000,000 records.  Elapsed time: 00:10:15s.  Time for last 1,000,000:    1s.  Last read position: chr12:56,159,709
INFO	2026-06-08 08:18:46	MarkDuplicates	Tracking 310128 as yet unmatched pairs. 17690 records in RAM.
INFO	2026-06-08 08:18:48	MarkDuplicates	Read   277,000,000 records.  Elapsed time: 00:10:17s.  Time for last 1,000,000:    1s.  Last read position: chr12:56,670,278
INFO	2026-06-08 08:18:48	MarkDuplicates	Tracking 309393 as yet unmatched pairs. 16929 records in RAM.
INFO	2026-06-08 08:18:49	MarkDuplicates	Read   278,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:    1s.  Last read position: chr12:57,105,476
INFO	2026-06-08 08:18:49	MarkDuplicates	Tracking 308378 as yet unmatched pairs. 15878 records in RAM.
INFO	2026-06-08 08:18:51	MarkDuplicates	Read   279,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:    1s.  Last read position: chr12:57,695,795
INFO	2026-06-08 08:18:51	MarkDuplicates	Tracking 307082 as yet unmatched pairs. 14551 records in RAM.
INFO	2026-06-08 08:18:53	MarkDuplicates	Read   280,000,000 records.  Elapsed time: 00:10:22s.  Time for last 1,000,000:    1s.  Last read position: chr12:68,615,503
INFO	2026-06-08 08:18:53	MarkDuplicates	Tracking 306142 as yet unmatched pairs. 13538 records in RAM.
INFO	2026-06-08 08:18:55	MarkDuplicates	Read   281,000,000 records.  Elapsed time: 00:10:24s.  Time for last 1,000,000:    1s.  Last read position: chr12:79,821,460
INFO	2026-06-08 08:18:55	MarkDuplicates	Tracking 304967 as yet unmatched pairs. 12301 records in RAM.
INFO	2026-06-08 08:18:58	MarkDuplicates	Read   282,000,000 records.  Elapsed time: 00:10:27s.  Time for last 1,000,000:    2s.  Last read position: chr12:95,296,094
INFO	2026-06-08 08:18:58	MarkDuplicates	Tracking 303959 as yet unmatched pairs. 11224 records in RAM.
INFO	2026-06-08 08:19:01	MarkDuplicates	Read   283,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    3s.  Last read position: chr12:104,265,637
INFO	2026-06-08 08:19:01	MarkDuplicates	Tracking 303798 as yet unmatched pairs. 11027 records in RAM.
INFO	2026-06-08 08:19:03	MarkDuplicates	Read   284,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:    1s.  Last read position: chr12:109,907,654
INFO	2026-06-08 08:19:03	MarkDuplicates	Tracking 301977 as yet unmatched pairs. 9161 records in RAM.
INFO	2026-06-08 08:19:04	MarkDuplicates	Read   285,000,000 records.  Elapsed time: 00:10:34s.  Time for last 1,000,000:    1s.  Last read position: chr12:112,171,258
INFO	2026-06-08 08:19:04	MarkDuplicates	Tracking 301198 as yet unmatched pairs. 8310 records in RAM.
INFO	2026-06-08 08:19:06	MarkDuplicates	Read   286,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    1s.  Last read position: chr12:113,158,958
INFO	2026-06-08 08:19:06	MarkDuplicates	Tracking 300146 as yet unmatched pairs. 7231 records in RAM.
INFO	2026-06-08 08:19:08	MarkDuplicates	Read   287,000,000 records.  Elapsed time: 00:10:37s.  Time for last 1,000,000:    1s.  Last read position: chr12:120,158,544
INFO	2026-06-08 08:19:08	MarkDuplicates	Tracking 298936 as yet unmatched pairs. 5955 records in RAM.
INFO	2026-06-08 08:19:10	MarkDuplicates	Read   288,000,000 records.  Elapsed time: 00:10:39s.  Time for last 1,000,000:    1s.  Last read position: chr12:121,793,151
INFO	2026-06-08 08:19:10	MarkDuplicates	Tracking 297666 as yet unmatched pairs. 4608 records in RAM.
INFO	2026-06-08 08:19:12	MarkDuplicates	Read   289,000,000 records.  Elapsed time: 00:10:41s.  Time for last 1,000,000:    1s.  Last read position: chr12:124,325,464
INFO	2026-06-08 08:19:12	MarkDuplicates	Tracking 296510 as yet unmatched pairs. 3405 records in RAM.
INFO	2026-06-08 08:19:14	MarkDuplicates	Read   290,000,000 records.  Elapsed time: 00:10:43s.  Time for last 1,000,000:    1s.  Last read position: chr12:130,875,677
INFO	2026-06-08 08:19:14	MarkDuplicates	Tracking 296354 as yet unmatched pairs. 3193 records in RAM.
INFO	2026-06-08 08:19:16	MarkDuplicates	Read   291,000,000 records.  Elapsed time: 00:10:45s.  Time for last 1,000,000:    1s.  Last read position: chr12:132,775,206
INFO	2026-06-08 08:19:16	MarkDuplicates	Tracking 293800 as yet unmatched pairs. 608 records in RAM.
INFO	2026-06-08 08:19:18	MarkDuplicates	Read   292,000,000 records.  Elapsed time: 00:10:47s.  Time for last 1,000,000:    2s.  Last read position: chr13:21,381,447
INFO	2026-06-08 08:19:18	MarkDuplicates	Tracking 292757 as yet unmatched pairs. 6561 records in RAM.
INFO	2026-06-08 08:19:21	MarkDuplicates	Read   293,000,000 records.  Elapsed time: 00:10:50s.  Time for last 1,000,000:    3s.  Last read position: chr13:31,885,848
INFO	2026-06-08 08:19:21	MarkDuplicates	Tracking 291624 as yet unmatched pairs. 5359 records in RAM.
INFO	2026-06-08 08:19:23	MarkDuplicates	Read   294,000,000 records.  Elapsed time: 00:10:52s.  Time for last 1,000,000:    1s.  Last read position: chr13:42,301,108
INFO	2026-06-08 08:19:23	MarkDuplicates	Tracking 290954 as yet unmatched pairs. 4613 records in RAM.
INFO	2026-06-08 08:19:25	MarkDuplicates	Read   295,000,000 records.  Elapsed time: 00:10:54s.  Time for last 1,000,000:    1s.  Last read position: chr13:48,490,072
INFO	2026-06-08 08:19:25	MarkDuplicates	Tracking 290092 as yet unmatched pairs. 3706 records in RAM.
INFO	2026-06-08 08:19:27	MarkDuplicates	Read   296,000,000 records.  Elapsed time: 00:10:56s.  Time for last 1,000,000:    1s.  Last read position: chr13:77,070,657
INFO	2026-06-08 08:19:27	MarkDuplicates	Tracking 289327 as yet unmatched pairs. 2875 records in RAM.
INFO	2026-06-08 08:19:29	MarkDuplicates	Read   297,000,000 records.  Elapsed time: 00:10:58s.  Time for last 1,000,000:    1s.  Last read position: chr13:98,453,152
INFO	2026-06-08 08:19:29	MarkDuplicates	Tracking 288677 as yet unmatched pairs. 2177 records in RAM.
INFO	2026-06-08 08:19:31	MarkDuplicates	Read   298,000,000 records.  Elapsed time: 00:11:00s.  Time for last 1,000,000:    2s.  Last read position: chr13:113,321,711
INFO	2026-06-08 08:19:31	MarkDuplicates	Tracking 287095 as yet unmatched pairs. 548 records in RAM.
INFO	2026-06-08 08:19:33	MarkDuplicates	Read   299,000,000 records.  Elapsed time: 00:11:02s.  Time for last 1,000,000:    2s.  Last read position: chr14:21,428,028
INFO	2026-06-08 08:19:33	MarkDuplicates	Tracking 285949 as yet unmatched pairs. 20395 records in RAM.
INFO	2026-06-08 08:19:36	MarkDuplicates	Read   300,000,000 records.  Elapsed time: 00:11:05s.  Time for last 1,000,000:    3s.  Last read position: chr14:23,566,571
INFO	2026-06-08 08:19:36	MarkDuplicates	Tracking 284842 as yet unmatched pairs. 19249 records in RAM.
INFO	2026-06-08 08:19:38	MarkDuplicates	Read   301,000,000 records.  Elapsed time: 00:11:08s.  Time for last 1,000,000:    2s.  Last read position: chr14:24,300,638
INFO	2026-06-08 08:19:38	MarkDuplicates	Tracking 283487 as yet unmatched pairs. 17860 records in RAM.
INFO	2026-06-08 08:19:40	MarkDuplicates	Read   302,000,000 records.  Elapsed time: 00:11:09s.  Time for last 1,000,000:    1s.  Last read position: chr14:35,292,421
INFO	2026-06-08 08:19:40	MarkDuplicates	Tracking 282552 as yet unmatched pairs. 16884 records in RAM.
INFO	2026-06-08 08:19:42	MarkDuplicates	Read   303,000,000 records.  Elapsed time: 00:11:11s.  Time for last 1,000,000:    1s.  Last read position: chr14:49,586,608
INFO	2026-06-08 08:19:42	MarkDuplicates	Tracking 324734 as yet unmatched pairs. 59005 records in RAM.
INFO	2026-06-08 08:19:44	MarkDuplicates	Read   304,000,000 records.  Elapsed time: 00:11:13s.  Time for last 1,000,000:    1s.  Last read position: chr14:49,586,722
INFO	2026-06-08 08:19:44	MarkDuplicates	Tracking 285373 as yet unmatched pairs. 19545 records in RAM.
INFO	2026-06-08 08:19:45	MarkDuplicates	Read   305,000,000 records.  Elapsed time: 00:11:14s.  Time for last 1,000,000:    1s.  Last read position: chr14:49,862,578
INFO	2026-06-08 08:19:45	MarkDuplicates	Tracking 294700 as yet unmatched pairs. 28817 records in RAM.
INFO	2026-06-08 08:19:47	MarkDuplicates	Read   306,000,000 records.  Elapsed time: 00:11:16s.  Time for last 1,000,000:    1s.  Last read position: chr14:49,862,686
INFO	2026-06-08 08:19:47	MarkDuplicates	Tracking 307910 as yet unmatched pairs. 42003 records in RAM.
INFO	2026-06-08 08:19:49	MarkDuplicates	Read   307,000,000 records.  Elapsed time: 00:11:18s.  Time for last 1,000,000:    1s.  Last read position: chr14:55,138,174
INFO	2026-06-08 08:19:49	MarkDuplicates	Tracking 278638 as yet unmatched pairs. 12668 records in RAM.
INFO	2026-06-08 08:19:51	MarkDuplicates	Read   308,000,000 records.  Elapsed time: 00:11:20s.  Time for last 1,000,000:    2s.  Last read position: chr14:64,002,824
INFO	2026-06-08 08:19:51	MarkDuplicates	Tracking 277852 as yet unmatched pairs. 11839 records in RAM.
INFO	2026-06-08 08:19:53	MarkDuplicates	Read   309,000,000 records.  Elapsed time: 00:11:22s.  Time for last 1,000,000:    2s.  Last read position: chr14:67,279,256
INFO	2026-06-08 08:19:53	MarkDuplicates	Tracking 276515 as yet unmatched pairs. 10481 records in RAM.
INFO	2026-06-08 08:19:56	MarkDuplicates	Read   310,000,000 records.  Elapsed time: 00:11:25s.  Time for last 1,000,000:    2s.  Last read position: chr14:71,105,254
INFO	2026-06-08 08:19:56	MarkDuplicates	Tracking 275748 as yet unmatched pairs. 9679 records in RAM.
INFO	2026-06-08 08:19:58	MarkDuplicates	Read   311,000,000 records.  Elapsed time: 00:11:27s.  Time for last 1,000,000:    1s.  Last read position: chr14:74,493,770
INFO	2026-06-08 08:19:58	MarkDuplicates	Tracking 274413 as yet unmatched pairs. 8292 records in RAM.
INFO	2026-06-08 08:20:00	MarkDuplicates	Read   312,000,000 records.  Elapsed time: 00:11:29s.  Time for last 1,000,000:    1s.  Last read position: chr14:89,162,779
INFO	2026-06-08 08:20:00	MarkDuplicates	Tracking 273563 as yet unmatched pairs. 7386 records in RAM.
INFO	2026-06-08 08:20:02	MarkDuplicates	Read   313,000,000 records.  Elapsed time: 00:11:31s.  Time for last 1,000,000:    1s.  Last read position: chr14:94,079,435
INFO	2026-06-08 08:20:02	MarkDuplicates	Tracking 272389 as yet unmatched pairs. 6183 records in RAM.
INFO	2026-06-08 08:20:03	MarkDuplicates	Read   314,000,000 records.  Elapsed time: 00:11:32s.  Time for last 1,000,000:    1s.  Last read position: chr14:100,361,818
INFO	2026-06-08 08:20:03	MarkDuplicates	Tracking 271947 as yet unmatched pairs. 5655 records in RAM.
INFO	2026-06-08 08:20:05	MarkDuplicates	Read   315,000,000 records.  Elapsed time: 00:11:34s.  Time for last 1,000,000:    1s.  Last read position: chr14:103,685,639
INFO	2026-06-08 08:20:05	MarkDuplicates	Tracking 270679 as yet unmatched pairs. 4350 records in RAM.
INFO	2026-06-08 08:20:07	MarkDuplicates	Read   316,000,000 records.  Elapsed time: 00:11:36s.  Time for last 1,000,000:    1s.  Last read position: chr14:105,765,905
INFO	2026-06-08 08:20:07	MarkDuplicates	Tracking 270985 as yet unmatched pairs. 4623 records in RAM.
INFO	2026-06-08 08:20:09	MarkDuplicates	Read   317,000,000 records.  Elapsed time: 00:11:38s.  Time for last 1,000,000:    1s.  Last read position: chr14:105,854,509
INFO	2026-06-08 08:20:09	MarkDuplicates	Tracking 269375 as yet unmatched pairs. 2972 records in RAM.
INFO	2026-06-08 08:20:12	MarkDuplicates	Read   318,000,000 records.  Elapsed time: 00:11:41s.  Time for last 1,000,000:    3s.  Last read position: chr14:105,931,284
INFO	2026-06-08 08:20:12	MarkDuplicates	Tracking 266902 as yet unmatched pairs. 435 records in RAM.
INFO	2026-06-08 08:20:14	MarkDuplicates	Read   319,000,000 records.  Elapsed time: 00:11:43s.  Time for last 1,000,000:    1s.  Last read position: chr15:31,327,282
INFO	2026-06-08 08:20:14	MarkDuplicates	Tracking 266021 as yet unmatched pairs. 16121 records in RAM.
INFO	2026-06-08 08:20:16	MarkDuplicates	Read   320,000,000 records.  Elapsed time: 00:11:45s.  Time for last 1,000,000:    1s.  Last read position: chr15:40,036,455
INFO	2026-06-08 08:20:16	MarkDuplicates	Tracking 265311 as yet unmatched pairs. 15384 records in RAM.
INFO	2026-06-08 08:20:18	MarkDuplicates	Read   321,000,000 records.  Elapsed time: 00:11:47s.  Time for last 1,000,000:    1s.  Last read position: chr15:41,814,772
INFO	2026-06-08 08:20:18	MarkDuplicates	Tracking 263533 as yet unmatched pairs. 13569 records in RAM.
INFO	2026-06-08 08:20:19	MarkDuplicates	Read   322,000,000 records.  Elapsed time: 00:11:49s.  Time for last 1,000,000:    1s.  Last read position: chr15:43,793,749
INFO	2026-06-08 08:20:19	MarkDuplicates	Tracking 265152 as yet unmatched pairs. 15162 records in RAM.
INFO	2026-06-08 08:20:21	MarkDuplicates	Read   323,000,000 records.  Elapsed time: 00:11:50s.  Time for last 1,000,000:    1s.  Last read position: chr15:50,587,921
INFO	2026-06-08 08:20:21	MarkDuplicates	Tracking 261570 as yet unmatched pairs. 11540 records in RAM.
INFO	2026-06-08 08:20:23	MarkDuplicates	Read   324,000,000 records.  Elapsed time: 00:11:52s.  Time for last 1,000,000:    1s.  Last read position: chr15:57,231,212
INFO	2026-06-08 08:20:23	MarkDuplicates	Tracking 262598 as yet unmatched pairs. 12518 records in RAM.
INFO	2026-06-08 08:20:25	MarkDuplicates	Read   325,000,000 records.  Elapsed time: 00:11:54s.  Time for last 1,000,000:    1s.  Last read position: chr15:63,156,458
INFO	2026-06-08 08:20:25	MarkDuplicates	Tracking 259824 as yet unmatched pairs. 9701 records in RAM.
INFO	2026-06-08 08:20:27	MarkDuplicates	Read   326,000,000 records.  Elapsed time: 00:11:56s.  Time for last 1,000,000:    1s.  Last read position: chr15:65,650,469
INFO	2026-06-08 08:20:27	MarkDuplicates	Tracking 258911 as yet unmatched pairs. 8743 records in RAM.
INFO	2026-06-08 08:20:29	MarkDuplicates	Read   327,000,000 records.  Elapsed time: 00:11:58s.  Time for last 1,000,000:    1s.  Last read position: chr15:70,066,020
INFO	2026-06-08 08:20:29	MarkDuplicates	Tracking 257920 as yet unmatched pairs. 7705 records in RAM.
INFO	2026-06-08 08:20:31	MarkDuplicates	Read   328,000,000 records.  Elapsed time: 00:12:00s.  Time for last 1,000,000:    1s.  Last read position: chr15:74,035,636
INFO	2026-06-08 08:20:31	MarkDuplicates	Tracking 257533 as yet unmatched pairs. 7280 records in RAM.
INFO	2026-06-08 08:20:33	MarkDuplicates	Read   329,000,000 records.  Elapsed time: 00:12:03s.  Time for last 1,000,000:    2s.  Last read position: chr15:75,207,888
INFO	2026-06-08 08:20:33	MarkDuplicates	Tracking 256619 as yet unmatched pairs. 6332 records in RAM.
INFO	2026-06-08 08:20:36	MarkDuplicates	Read   330,000,000 records.  Elapsed time: 00:12:05s.  Time for last 1,000,000:    2s.  Last read position: chr15:78,541,921
INFO	2026-06-08 08:20:36	MarkDuplicates	Tracking 254662 as yet unmatched pairs. 4333 records in RAM.
INFO	2026-06-08 08:20:37	MarkDuplicates	Read   331,000,000 records.  Elapsed time: 00:12:06s.  Time for last 1,000,000:    1s.  Last read position: chr15:85,111,973
INFO	2026-06-08 08:20:37	MarkDuplicates	Tracking 253074 as yet unmatched pairs. 2703 records in RAM.
INFO	2026-06-08 08:20:39	MarkDuplicates	Read   332,000,000 records.  Elapsed time: 00:12:08s.  Time for last 1,000,000:    1s.  Last read position: chr15:90,530,022
INFO	2026-06-08 08:20:39	MarkDuplicates	Tracking 252139 as yet unmatched pairs. 1718 records in RAM.
INFO	2026-06-08 08:20:41	MarkDuplicates	Read   333,000,000 records.  Elapsed time: 00:12:10s.  Time for last 1,000,000:    1s.  Last read position: chr15:101,244,265
INFO	2026-06-08 08:20:41	MarkDuplicates	Tracking 250737 as yet unmatched pairs. 238 records in RAM.
INFO	2026-06-08 08:20:43	MarkDuplicates	Read   334,000,000 records.  Elapsed time: 00:12:12s.  Time for last 1,000,000:    2s.  Last read position: chr16:676,717
INFO	2026-06-08 08:20:43	MarkDuplicates	Tracking 249066 as yet unmatched pairs. 34181 records in RAM.
INFO	2026-06-08 08:20:45	MarkDuplicates	Read   335,000,000 records.  Elapsed time: 00:12:14s.  Time for last 1,000,000:    1s.  Last read position: chr16:1,788,593
INFO	2026-06-08 08:20:45	MarkDuplicates	Tracking 247604 as yet unmatched pairs. 32664 records in RAM.
INFO	2026-06-08 08:20:47	MarkDuplicates	Read   336,000,000 records.  Elapsed time: 00:12:16s.  Time for last 1,000,000:    1s.  Last read position: chr16:2,264,184
INFO	2026-06-08 08:20:47	MarkDuplicates	Tracking 245592 as yet unmatched pairs. 30636 records in RAM.
INFO	2026-06-08 08:20:49	MarkDuplicates	Read   337,000,000 records.  Elapsed time: 00:12:18s.  Time for last 1,000,000:    1s.  Last read position: chr16:2,769,031
INFO	2026-06-08 08:20:49	MarkDuplicates	Tracking 244910 as yet unmatched pairs. 29949 records in RAM.
INFO	2026-06-08 08:20:51	MarkDuplicates	Read   338,000,000 records.  Elapsed time: 00:12:21s.  Time for last 1,000,000:    2s.  Last read position: chr16:4,357,200
INFO	2026-06-08 08:20:51	MarkDuplicates	Tracking 243403 as yet unmatched pairs. 28423 records in RAM.
INFO	2026-06-08 08:20:54	MarkDuplicates	Read   339,000,000 records.  Elapsed time: 00:12:23s.  Time for last 1,000,000:    2s.  Last read position: chr16:10,904,776
INFO	2026-06-08 08:20:54	MarkDuplicates	Tracking 242543 as yet unmatched pairs. 27527 records in RAM.
INFO	2026-06-08 08:20:55	MarkDuplicates	Read   340,000,000 records.  Elapsed time: 00:12:25s.  Time for last 1,000,000:    1s.  Last read position: chr16:12,524,724
INFO	2026-06-08 08:20:55	MarkDuplicates	Tracking 240651 as yet unmatched pairs. 25550 records in RAM.
INFO	2026-06-08 08:20:57	MarkDuplicates	Read   341,000,000 records.  Elapsed time: 00:12:26s.  Time for last 1,000,000:    1s.  Last read position: chr16:15,612,775
INFO	2026-06-08 08:20:57	MarkDuplicates	Tracking 239761 as yet unmatched pairs. 24629 records in RAM.
INFO	2026-06-08 08:20:59	MarkDuplicates	Read   342,000,000 records.  Elapsed time: 00:12:28s.  Time for last 1,000,000:    1s.  Last read position: chr16:18,345,307
INFO	2026-06-08 08:20:59	MarkDuplicates	Tracking 239454 as yet unmatched pairs. 24315 records in RAM.
INFO	2026-06-08 08:21:00	MarkDuplicates	Read   343,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:    1s.  Last read position: chr16:19,608,251
INFO	2026-06-08 08:21:00	MarkDuplicates	Tracking 238699 as yet unmatched pairs. 23512 records in RAM.
INFO	2026-06-08 08:21:02	MarkDuplicates	Read   344,000,000 records.  Elapsed time: 00:12:31s.  Time for last 1,000,000:    1s.  Last read position: chr16:21,424,978
INFO	2026-06-08 08:21:02	MarkDuplicates	Tracking 238985 as yet unmatched pairs. 23776 records in RAM.
INFO	2026-06-08 08:21:03	MarkDuplicates	Read   345,000,000 records.  Elapsed time: 00:12:32s.  Time for last 1,000,000:    1s.  Last read position: chr16:21,837,630
INFO	2026-06-08 08:21:03	MarkDuplicates	Tracking 239157 as yet unmatched pairs. 23938 records in RAM.
INFO	2026-06-08 08:21:05	MarkDuplicates	Read   346,000,000 records.  Elapsed time: 00:12:34s.  Time for last 1,000,000:    1s.  Last read position: chr16:22,492,381
INFO	2026-06-08 08:21:05	MarkDuplicates	Tracking 237370 as yet unmatched pairs. 22137 records in RAM.
INFO	2026-06-08 08:21:06	MarkDuplicates	Read   347,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:    1s.  Last read position: chr16:22,535,932
INFO	2026-06-08 08:21:06	MarkDuplicates	Tracking 237218 as yet unmatched pairs. 21978 records in RAM.
INFO	2026-06-08 08:21:08	MarkDuplicates	Read   348,000,000 records.  Elapsed time: 00:12:38s.  Time for last 1,000,000:    2s.  Last read position: chr16:27,449,179
INFO	2026-06-08 08:21:08	MarkDuplicates	Tracking 237339 as yet unmatched pairs. 22076 records in RAM.
INFO	2026-06-08 08:21:10	MarkDuplicates	Read   349,000,000 records.  Elapsed time: 00:12:39s.  Time for last 1,000,000:    1s.  Last read position: chr16:28,843,132
INFO	2026-06-08 08:21:10	MarkDuplicates	Tracking 235320 as yet unmatched pairs. 20040 records in RAM.
INFO	2026-06-08 08:21:12	MarkDuplicates	Read   350,000,000 records.  Elapsed time: 00:12:41s.  Time for last 1,000,000:    1s.  Last read position: chr16:29,454,022
INFO	2026-06-08 08:21:12	MarkDuplicates	Tracking 236306 as yet unmatched pairs. 21021 records in RAM.
INFO	2026-06-08 08:21:13	MarkDuplicates	Read   351,000,000 records.  Elapsed time: 00:12:42s.  Time for last 1,000,000:    1s.  Last read position: chr16:29,696,693
INFO	2026-06-08 08:21:13	MarkDuplicates	Tracking 234229 as yet unmatched pairs. 18930 records in RAM.
INFO	2026-06-08 08:21:15	MarkDuplicates	Read   352,000,000 records.  Elapsed time: 00:12:44s.  Time for last 1,000,000:    1s.  Last read position: chr16:30,187,739
INFO	2026-06-08 08:21:15	MarkDuplicates	Tracking 232900 as yet unmatched pairs. 17591 records in RAM.
INFO	2026-06-08 08:21:17	MarkDuplicates	Read   353,000,000 records.  Elapsed time: 00:12:46s.  Time for last 1,000,000:    2s.  Last read position: chr16:30,369,758
INFO	2026-06-08 08:21:17	MarkDuplicates	Tracking 232385 as yet unmatched pairs. 17056 records in RAM.
INFO	2026-06-08 08:21:20	MarkDuplicates	Read   354,000,000 records.  Elapsed time: 00:12:49s.  Time for last 1,000,000:    2s.  Last read position: chr16:30,763,180
INFO	2026-06-08 08:21:20	MarkDuplicates	Tracking 230575 as yet unmatched pairs. 15210 records in RAM.
INFO	2026-06-08 08:21:22	MarkDuplicates	Read   355,000,000 records.  Elapsed time: 00:12:51s.  Time for last 1,000,000:    1s.  Last read position: chr16:31,490,509
INFO	2026-06-08 08:21:22	MarkDuplicates	Tracking 229134 as yet unmatched pairs. 13736 records in RAM.
INFO	2026-06-08 08:21:24	MarkDuplicates	Read   356,000,000 records.  Elapsed time: 00:12:53s.  Time for last 1,000,000:    1s.  Last read position: chr16:53,267,338
INFO	2026-06-08 08:21:24	MarkDuplicates	Tracking 228145 as yet unmatched pairs. 12679 records in RAM.
INFO	2026-06-08 08:21:26	MarkDuplicates	Read   357,000,000 records.  Elapsed time: 00:12:55s.  Time for last 1,000,000:    1s.  Last read position: chr16:57,471,068
INFO	2026-06-08 08:21:26	MarkDuplicates	Tracking 226916 as yet unmatched pairs. 11423 records in RAM.
INFO	2026-06-08 08:21:28	MarkDuplicates	Read   358,000,000 records.  Elapsed time: 00:12:57s.  Time for last 1,000,000:    1s.  Last read position: chr16:67,538,480
INFO	2026-06-08 08:21:28	MarkDuplicates	Tracking 226075 as yet unmatched pairs. 10549 records in RAM.
INFO	2026-06-08 08:21:30	MarkDuplicates	Read   359,000,000 records.  Elapsed time: 00:12:59s.  Time for last 1,000,000:    1s.  Last read position: chr16:68,877,441
INFO	2026-06-08 08:21:30	MarkDuplicates	Tracking 224078 as yet unmatched pairs. 8527 records in RAM.
INFO	2026-06-08 08:21:31	MarkDuplicates	Read   360,000,000 records.  Elapsed time: 00:13:01s.  Time for last 1,000,000:    1s.  Last read position: chr16:70,381,699
INFO	2026-06-08 08:21:31	MarkDuplicates	Tracking 223269 as yet unmatched pairs. 7693 records in RAM.
INFO	2026-06-08 08:21:33	MarkDuplicates	Read   361,000,000 records.  Elapsed time: 00:13:02s.  Time for last 1,000,000:    1s.  Last read position: chr16:74,956,546
INFO	2026-06-08 08:21:33	MarkDuplicates	Tracking 222255 as yet unmatched pairs. 6641 records in RAM.
INFO	2026-06-08 08:21:35	MarkDuplicates	Read   362,000,000 records.  Elapsed time: 00:13:04s.  Time for last 1,000,000:    1s.  Last read position: chr16:84,179,228
INFO	2026-06-08 08:21:35	MarkDuplicates	Tracking 221706 as yet unmatched pairs. 6025 records in RAM.
INFO	2026-06-08 08:21:37	MarkDuplicates	Read   363,000,000 records.  Elapsed time: 00:13:06s.  Time for last 1,000,000:    1s.  Last read position: chr16:87,869,187
INFO	2026-06-08 08:21:37	MarkDuplicates	Tracking 219855 as yet unmatched pairs. 4130 records in RAM.
INFO	2026-06-08 08:21:40	MarkDuplicates	Read   364,000,000 records.  Elapsed time: 00:13:09s.  Time for last 1,000,000:    2s.  Last read position: chr16:88,859,681
INFO	2026-06-08 08:21:40	MarkDuplicates	Tracking 217995 as yet unmatched pairs. 2239 records in RAM.
INFO	2026-06-08 08:21:42	MarkDuplicates	Read   365,000,000 records.  Elapsed time: 00:13:11s.  Time for last 1,000,000:    1s.  Last read position: chr16:89,721,612
INFO	2026-06-08 08:21:42	MarkDuplicates	Tracking 216868 as yet unmatched pairs. 1078 records in RAM.
INFO	2026-06-08 08:21:44	MarkDuplicates	Read   366,000,000 records.  Elapsed time: 00:13:13s.  Time for last 1,000,000:    2s.  Last read position: chr17:1,482,549
INFO	2026-06-08 08:21:44	MarkDuplicates	Tracking 215995 as yet unmatched pairs. 38690 records in RAM.
INFO	2026-06-08 08:21:46	MarkDuplicates	Read   367,000,000 records.  Elapsed time: 00:13:15s.  Time for last 1,000,000:    1s.  Last read position: chr17:2,697,895
INFO	2026-06-08 08:21:46	MarkDuplicates	Tracking 214281 as yet unmatched pairs. 36956 records in RAM.
INFO	2026-06-08 08:21:48	MarkDuplicates	Read   368,000,000 records.  Elapsed time: 00:13:17s.  Time for last 1,000,000:    1s.  Last read position: chr17:4,898,837
INFO	2026-06-08 08:21:48	MarkDuplicates	Tracking 212776 as yet unmatched pairs. 35439 records in RAM.
INFO	2026-06-08 08:21:50	MarkDuplicates	Read   369,000,000 records.  Elapsed time: 00:13:19s.  Time for last 1,000,000:    1s.  Last read position: chr17:7,015,099
INFO	2026-06-08 08:21:50	MarkDuplicates	Tracking 211981 as yet unmatched pairs. 34613 records in RAM.
INFO	2026-06-08 08:21:51	MarkDuplicates	Read   370,000,000 records.  Elapsed time: 00:13:21s.  Time for last 1,000,000:    1s.  Last read position: chr17:7,513,406
INFO	2026-06-08 08:21:51	MarkDuplicates	Tracking 210449 as yet unmatched pairs. 33075 records in RAM.
INFO	2026-06-08 08:21:53	MarkDuplicates	Read   371,000,000 records.  Elapsed time: 00:13:22s.  Time for last 1,000,000:    1s.  Last read position: chr17:8,175,729
INFO	2026-06-08 08:21:53	MarkDuplicates	Tracking 209215 as yet unmatched pairs. 31829 records in RAM.
INFO	2026-06-08 08:21:55	MarkDuplicates	Read   372,000,000 records.  Elapsed time: 00:13:24s.  Time for last 1,000,000:    1s.  Last read position: chr17:16,233,968
INFO	2026-06-08 08:21:55	MarkDuplicates	Tracking 207951 as yet unmatched pairs. 30554 records in RAM.
INFO	2026-06-08 08:21:57	MarkDuplicates	Read   373,000,000 records.  Elapsed time: 00:13:26s.  Time for last 1,000,000:    1s.  Last read position: chr17:18,103,870
INFO	2026-06-08 08:21:57	MarkDuplicates	Tracking 206877 as yet unmatched pairs. 29441 records in RAM.
INFO	2026-06-08 08:21:59	MarkDuplicates	Read   374,000,000 records.  Elapsed time: 00:13:28s.  Time for last 1,000,000:    1s.  Last read position: chr17:22,204,560
INFO	2026-06-08 08:21:59	MarkDuplicates	Tracking 205490 as yet unmatched pairs. 28037 records in RAM.
INFO	2026-06-08 08:22:01	MarkDuplicates	Read   375,000,000 records.  Elapsed time: 00:13:30s.  Time for last 1,000,000:    2s.  Last read position: chr17:28,697,015
INFO	2026-06-08 08:22:01	MarkDuplicates	Tracking 204802 as yet unmatched pairs. 27339 records in RAM.
INFO	2026-06-08 08:22:03	MarkDuplicates	Read   376,000,000 records.  Elapsed time: 00:13:32s.  Time for last 1,000,000:    2s.  Last read position: chr17:30,495,472
INFO	2026-06-08 08:22:03	MarkDuplicates	Tracking 203453 as yet unmatched pairs. 25959 records in RAM.
INFO	2026-06-08 08:22:05	MarkDuplicates	Read   377,000,000 records.  Elapsed time: 00:13:34s.  Time for last 1,000,000:    1s.  Last read position: chr17:35,137,615
INFO	2026-06-08 08:22:05	MarkDuplicates	Tracking 202583 as yet unmatched pairs. 25073 records in RAM.
INFO	2026-06-08 08:22:07	MarkDuplicates	Read   378,000,000 records.  Elapsed time: 00:13:36s.  Time for last 1,000,000:    1s.  Last read position: chr17:36,334,055
INFO	2026-06-08 08:22:07	MarkDuplicates	Tracking 201532 as yet unmatched pairs. 24021 records in RAM.
INFO	2026-06-08 08:22:08	MarkDuplicates	Read   379,000,000 records.  Elapsed time: 00:13:38s.  Time for last 1,000,000:    1s.  Last read position: chr17:38,466,759
INFO	2026-06-08 08:22:08	MarkDuplicates	Tracking 201061 as yet unmatched pairs. 23522 records in RAM.
INFO	2026-06-08 08:22:10	MarkDuplicates	Read   380,000,000 records.  Elapsed time: 00:13:39s.  Time for last 1,000,000:    1s.  Last read position: chr17:39,658,488
INFO	2026-06-08 08:22:10	MarkDuplicates	Tracking 199948 as yet unmatched pairs. 22390 records in RAM.
INFO	2026-06-08 08:22:12	MarkDuplicates	Read   381,000,000 records.  Elapsed time: 00:13:41s.  Time for last 1,000,000:    1s.  Last read position: chr17:41,690,859
INFO	2026-06-08 08:22:12	MarkDuplicates	Tracking 198792 as yet unmatched pairs. 21202 records in RAM.
INFO	2026-06-08 08:22:14	MarkDuplicates	Read   382,000,000 records.  Elapsed time: 00:13:43s.  Time for last 1,000,000:    1s.  Last read position: chr17:42,669,435
INFO	2026-06-08 08:22:14	MarkDuplicates	Tracking 198136 as yet unmatched pairs. 20527 records in RAM.
INFO	2026-06-08 08:22:16	MarkDuplicates	Read   383,000,000 records.  Elapsed time: 00:13:45s.  Time for last 1,000,000:    1s.  Last read position: chr17:44,189,175
INFO	2026-06-08 08:22:16	MarkDuplicates	Tracking 196197 as yet unmatched pairs. 18585 records in RAM.
INFO	2026-06-08 08:22:18	MarkDuplicates	Read   384,000,000 records.  Elapsed time: 00:13:47s.  Time for last 1,000,000:    2s.  Last read position: chr17:45,468,367
INFO	2026-06-08 08:22:18	MarkDuplicates	Tracking 194775 as yet unmatched pairs. 17128 records in RAM.
INFO	2026-06-08 08:22:20	MarkDuplicates	Read   385,000,000 records.  Elapsed time: 00:13:49s.  Time for last 1,000,000:    1s.  Last read position: chr17:47,677,105
INFO	2026-06-08 08:22:20	MarkDuplicates	Tracking 194413 as yet unmatched pairs. 16737 records in RAM.
INFO	2026-06-08 08:22:22	MarkDuplicates	Read   386,000,000 records.  Elapsed time: 00:13:52s.  Time for last 1,000,000:    2s.  Last read position: chr17:49,717,665
INFO	2026-06-08 08:22:22	MarkDuplicates	Tracking 192989 as yet unmatched pairs. 15295 records in RAM.
INFO	2026-06-08 08:22:24	MarkDuplicates	Read   387,000,000 records.  Elapsed time: 00:13:53s.  Time for last 1,000,000:    1s.  Last read position: chr17:57,849,291
INFO	2026-06-08 08:22:24	MarkDuplicates	Tracking 191581 as yet unmatched pairs. 13862 records in RAM.
INFO	2026-06-08 08:22:26	MarkDuplicates	Read   388,000,000 records.  Elapsed time: 00:13:55s.  Time for last 1,000,000:    1s.  Last read position: chr17:59,693,732
INFO	2026-06-08 08:22:26	MarkDuplicates	Tracking 190731 as yet unmatched pairs. 12988 records in RAM.
INFO	2026-06-08 08:22:28	MarkDuplicates	Read   389,000,000 records.  Elapsed time: 00:13:57s.  Time for last 1,000,000:    1s.  Last read position: chr17:63,837,488
INFO	2026-06-08 08:22:28	MarkDuplicates	Tracking 190120 as yet unmatched pairs. 12344 records in RAM.
INFO	2026-06-08 08:22:30	MarkDuplicates	Read   390,000,000 records.  Elapsed time: 00:13:59s.  Time for last 1,000,000:    1s.  Last read position: chr17:68,042,911
INFO	2026-06-08 08:22:30	MarkDuplicates	Tracking 188401 as yet unmatched pairs. 10604 records in RAM.
INFO	2026-06-08 08:22:32	MarkDuplicates	Read   391,000,000 records.  Elapsed time: 00:14:01s.  Time for last 1,000,000:    1s.  Last read position: chr17:75,154,363
INFO	2026-06-08 08:22:32	MarkDuplicates	Tracking 186887 as yet unmatched pairs. 9073 records in RAM.
INFO	2026-06-08 08:22:34	MarkDuplicates	Read   392,000,000 records.  Elapsed time: 00:14:03s.  Time for last 1,000,000:    1s.  Last read position: chr17:76,090,357
INFO	2026-06-08 08:22:34	MarkDuplicates	Tracking 185772 as yet unmatched pairs. 7947 records in RAM.
INFO	2026-06-08 08:22:35	MarkDuplicates	Read   393,000,000 records.  Elapsed time: 00:14:04s.  Time for last 1,000,000:    1s.  Last read position: chr17:78,117,913
INFO	2026-06-08 08:22:35	MarkDuplicates	Tracking 184890 as yet unmatched pairs. 7018 records in RAM.
INFO	2026-06-08 08:22:37	MarkDuplicates	Read   394,000,000 records.  Elapsed time: 00:14:06s.  Time for last 1,000,000:    1s.  Last read position: chr17:78,997,171
INFO	2026-06-08 08:22:37	MarkDuplicates	Tracking 182959 as yet unmatched pairs. 5067 records in RAM.
INFO	2026-06-08 08:22:39	MarkDuplicates	Read   395,000,000 records.  Elapsed time: 00:14:08s.  Time for last 1,000,000:    1s.  Last read position: chr17:80,390,013
INFO	2026-06-08 08:22:39	MarkDuplicates	Tracking 182004 as yet unmatched pairs. 4096 records in RAM.
INFO	2026-06-08 08:22:41	MarkDuplicates	Read   396,000,000 records.  Elapsed time: 00:14:10s.  Time for last 1,000,000:    1s.  Last read position: chr17:81,855,163
INFO	2026-06-08 08:22:41	MarkDuplicates	Tracking 181096 as yet unmatched pairs. 3180 records in RAM.
INFO	2026-06-08 08:22:45	MarkDuplicates	Read   397,000,000 records.  Elapsed time: 00:14:14s.  Time for last 1,000,000:    3s.  Last read position: chr17:82,248,904
INFO	2026-06-08 08:22:45	MarkDuplicates	Tracking 178829 as yet unmatched pairs. 900 records in RAM.
INFO	2026-06-08 08:22:47	MarkDuplicates	Read   398,000,000 records.  Elapsed time: 00:14:16s.  Time for last 1,000,000:    2s.  Last read position: chr18:3,879,363
INFO	2026-06-08 08:22:47	MarkDuplicates	Tracking 177608 as yet unmatched pairs. 7055 records in RAM.
INFO	2026-06-08 08:22:49	MarkDuplicates	Read   399,000,000 records.  Elapsed time: 00:14:18s.  Time for last 1,000,000:    1s.  Last read position: chr18:20,986,953
INFO	2026-06-08 08:22:49	MarkDuplicates	Tracking 176683 as yet unmatched pairs. 6096 records in RAM.
INFO	2026-06-08 08:22:50	MarkDuplicates	Read   400,000,000 records.  Elapsed time: 00:14:19s.  Time for last 1,000,000:    1s.  Last read position: chr18:36,114,454
INFO	2026-06-08 08:22:50	MarkDuplicates	Tracking 175554 as yet unmatched pairs. 4947 records in RAM.
INFO	2026-06-08 08:22:52	MarkDuplicates	Read   401,000,000 records.  Elapsed time: 00:14:21s.  Time for last 1,000,000:    1s.  Last read position: chr18:51,177,072
INFO	2026-06-08 08:22:52	MarkDuplicates	Tracking 174587 as yet unmatched pairs. 3973 records in RAM.
INFO	2026-06-08 08:22:54	MarkDuplicates	Read   402,000,000 records.  Elapsed time: 00:14:23s.  Time for last 1,000,000:    1s.  Last read position: chr18:62,575,149
INFO	2026-06-08 08:22:54	MarkDuplicates	Tracking 173377 as yet unmatched pairs. 2708 records in RAM.
INFO	2026-06-08 08:22:56	MarkDuplicates	Read   403,000,000 records.  Elapsed time: 00:14:25s.  Time for last 1,000,000:    1s.  Last read position: chr18:74,598,242
INFO	2026-06-08 08:22:56	MarkDuplicates	Tracking 171701 as yet unmatched pairs. 983 records in RAM.
INFO	2026-06-08 08:22:58	MarkDuplicates	Read   404,000,000 records.  Elapsed time: 00:14:27s.  Time for last 1,000,000:    2s.  Last read position: chr19:632,852
INFO	2026-06-08 08:22:58	MarkDuplicates	Tracking 170365 as yet unmatched pairs. 56063 records in RAM.
INFO	2026-06-08 08:23:01	MarkDuplicates	Read   405,000,000 records.  Elapsed time: 00:14:30s.  Time for last 1,000,000:    2s.  Last read position: chr19:1,081,844
INFO	2026-06-08 08:23:01	MarkDuplicates	Tracking 169257 as yet unmatched pairs. 54938 records in RAM.
INFO	2026-06-08 08:23:03	MarkDuplicates	Read   406,000,000 records.  Elapsed time: 00:14:32s.  Time for last 1,000,000:    1s.  Last read position: chr19:1,440,145
INFO	2026-06-08 08:23:03	MarkDuplicates	Tracking 168473 as yet unmatched pairs. 54131 records in RAM.
INFO	2026-06-08 08:23:05	MarkDuplicates	Read   407,000,000 records.  Elapsed time: 00:14:34s.  Time for last 1,000,000:    1s.  Last read position: chr19:2,071,536
INFO	2026-06-08 08:23:05	MarkDuplicates	Tracking 165112 as yet unmatched pairs. 50766 records in RAM.
INFO	2026-06-08 08:23:07	MarkDuplicates	Read   408,000,000 records.  Elapsed time: 00:14:36s.  Time for last 1,000,000:    1s.  Last read position: chr19:2,634,316
INFO	2026-06-08 08:23:07	MarkDuplicates	Tracking 163407 as yet unmatched pairs. 49046 records in RAM.
INFO	2026-06-08 08:23:08	MarkDuplicates	Read   409,000,000 records.  Elapsed time: 00:14:38s.  Time for last 1,000,000:    1s.  Last read position: chr19:4,090,503
INFO	2026-06-08 08:23:08	MarkDuplicates	Tracking 162575 as yet unmatched pairs. 48201 records in RAM.
INFO	2026-06-08 08:23:10	MarkDuplicates	Read   410,000,000 records.  Elapsed time: 00:14:39s.  Time for last 1,000,000:    1s.  Last read position: chr19:5,220,112
INFO	2026-06-08 08:23:10	MarkDuplicates	Tracking 160300 as yet unmatched pairs. 45924 records in RAM.
INFO	2026-06-08 08:23:12	MarkDuplicates	Read   411,000,000 records.  Elapsed time: 00:14:41s.  Time for last 1,000,000:    1s.  Last read position: chr19:6,468,857
INFO	2026-06-08 08:23:12	MarkDuplicates	Tracking 159252 as yet unmatched pairs. 44852 records in RAM.
INFO	2026-06-08 08:23:14	MarkDuplicates	Read   412,000,000 records.  Elapsed time: 00:14:43s.  Time for last 1,000,000:    2s.  Last read position: chr19:7,694,523
INFO	2026-06-08 08:23:14	MarkDuplicates	Tracking 157973 as yet unmatched pairs. 43562 records in RAM.
INFO	2026-06-08 08:23:16	MarkDuplicates	Read   413,000,000 records.  Elapsed time: 00:14:45s.  Time for last 1,000,000:    1s.  Last read position: chr19:10,113,906
INFO	2026-06-08 08:23:16	MarkDuplicates	Tracking 156258 as yet unmatched pairs. 41840 records in RAM.
INFO	2026-06-08 08:23:18	MarkDuplicates	Read   414,000,000 records.  Elapsed time: 00:14:47s.  Time for last 1,000,000:    2s.  Last read position: chr19:10,561,214
INFO	2026-06-08 08:23:18	MarkDuplicates	Tracking 154547 as yet unmatched pairs. 40118 records in RAM.
INFO	2026-06-08 08:23:20	MarkDuplicates	Read   415,000,000 records.  Elapsed time: 00:14:49s.  Time for last 1,000,000:    2s.  Last read position: chr19:11,442,464
INFO	2026-06-08 08:23:20	MarkDuplicates	Tracking 153472 as yet unmatched pairs. 39036 records in RAM.
INFO	2026-06-08 08:23:22	MarkDuplicates	Read   416,000,000 records.  Elapsed time: 00:14:51s.  Time for last 1,000,000:    1s.  Last read position: chr19:12,876,008
INFO	2026-06-08 08:23:22	MarkDuplicates	Tracking 152283 as yet unmatched pairs. 37826 records in RAM.
INFO	2026-06-08 08:23:24	MarkDuplicates	Read   417,000,000 records.  Elapsed time: 00:14:53s.  Time for last 1,000,000:    1s.  Last read position: chr19:14,136,302
INFO	2026-06-08 08:23:24	MarkDuplicates	Tracking 150723 as yet unmatched pairs. 36253 records in RAM.
INFO	2026-06-08 08:23:26	MarkDuplicates	Read   418,000,000 records.  Elapsed time: 00:14:55s.  Time for last 1,000,000:    1s.  Last read position: chr19:15,255,360
INFO	2026-06-08 08:23:26	MarkDuplicates	Tracking 150112 as yet unmatched pairs. 35637 records in RAM.
INFO	2026-06-08 08:23:27	MarkDuplicates	Read   419,000,000 records.  Elapsed time: 00:14:56s.  Time for last 1,000,000:    1s.  Last read position: chr19:16,425,260
INFO	2026-06-08 08:23:27	MarkDuplicates	Tracking 148095 as yet unmatched pairs. 33610 records in RAM.
INFO	2026-06-08 08:23:29	MarkDuplicates	Read   420,000,000 records.  Elapsed time: 00:14:58s.  Time for last 1,000,000:    1s.  Last read position: chr19:17,726,496
INFO	2026-06-08 08:23:29	MarkDuplicates	Tracking 146428 as yet unmatched pairs. 31938 records in RAM.
INFO	2026-06-08 08:23:31	MarkDuplicates	Read   421,000,000 records.  Elapsed time: 00:15:00s.  Time for last 1,000,000:    1s.  Last read position: chr19:18,432,718
INFO	2026-06-08 08:23:31	MarkDuplicates	Tracking 144516 as yet unmatched pairs. 30026 records in RAM.
INFO	2026-06-08 08:23:33	MarkDuplicates	Read   422,000,000 records.  Elapsed time: 00:15:02s.  Time for last 1,000,000:    1s.  Last read position: chr19:19,147,708
INFO	2026-06-08 08:23:33	MarkDuplicates	Tracking 143332 as yet unmatched pairs. 28834 records in RAM.
INFO	2026-06-08 08:23:35	MarkDuplicates	Read   423,000,000 records.  Elapsed time: 00:15:04s.  Time for last 1,000,000:    1s.  Last read position: chr19:24,127,846
INFO	2026-06-08 08:23:35	MarkDuplicates	Tracking 141500 as yet unmatched pairs. 26979 records in RAM.
INFO	2026-06-08 08:23:37	MarkDuplicates	Read   424,000,000 records.  Elapsed time: 00:15:06s.  Time for last 1,000,000:    2s.  Last read position: chr19:35,278,996
INFO	2026-06-08 08:23:37	MarkDuplicates	Tracking 140928 as yet unmatched pairs. 26389 records in RAM.
INFO	2026-06-08 08:23:39	MarkDuplicates	Read   425,000,000 records.  Elapsed time: 00:15:08s.  Time for last 1,000,000:    2s.  Last read position: chr19:36,111,192
INFO	2026-06-08 08:23:39	MarkDuplicates	Tracking 138304 as yet unmatched pairs. 23763 records in RAM.
INFO	2026-06-08 08:23:41	MarkDuplicates	Read   426,000,000 records.  Elapsed time: 00:15:10s.  Time for last 1,000,000:    1s.  Last read position: chr19:38,701,035
INFO	2026-06-08 08:23:41	MarkDuplicates	Tracking 137174 as yet unmatched pairs. 22621 records in RAM.
INFO	2026-06-08 08:23:43	MarkDuplicates	Read   427,000,000 records.  Elapsed time: 00:15:12s.  Time for last 1,000,000:    1s.  Last read position: chr19:39,433,711
INFO	2026-06-08 08:23:43	MarkDuplicates	Tracking 138818 as yet unmatched pairs. 24255 records in RAM.
INFO	2026-06-08 08:23:45	MarkDuplicates	Read   428,000,000 records.  Elapsed time: 00:15:14s.  Time for last 1,000,000:    1s.  Last read position: chr19:40,590,386
INFO	2026-06-08 08:23:45	MarkDuplicates	Tracking 135225 as yet unmatched pairs. 20661 records in RAM.
INFO	2026-06-08 08:23:47	MarkDuplicates	Read   429,000,000 records.  Elapsed time: 00:15:16s.  Time for last 1,000,000:    1s.  Last read position: chr19:41,897,945
INFO	2026-06-08 08:23:47	MarkDuplicates	Tracking 133989 as yet unmatched pairs. 19418 records in RAM.
INFO	2026-06-08 08:23:49	MarkDuplicates	Read   430,000,000 records.  Elapsed time: 00:15:18s.  Time for last 1,000,000:    1s.  Last read position: chr19:42,272,242
INFO	2026-06-08 08:23:49	MarkDuplicates	Tracking 134357 as yet unmatched pairs. 19784 records in RAM.
INFO	2026-06-08 08:23:51	MarkDuplicates	Read   431,000,000 records.  Elapsed time: 00:15:20s.  Time for last 1,000,000:    2s.  Last read position: chr19:42,360,863
INFO	2026-06-08 08:23:51	MarkDuplicates	Tracking 130694 as yet unmatched pairs. 16102 records in RAM.
INFO	2026-06-08 08:23:53	MarkDuplicates	Read   432,000,000 records.  Elapsed time: 00:15:22s.  Time for last 1,000,000:    1s.  Last read position: chr19:45,302,409
INFO	2026-06-08 08:23:53	MarkDuplicates	Tracking 129175 as yet unmatched pairs. 14561 records in RAM.
INFO	2026-06-08 08:23:55	MarkDuplicates	Read   433,000,000 records.  Elapsed time: 00:15:24s.  Time for last 1,000,000:    1s.  Last read position: chr19:46,383,789
INFO	2026-06-08 08:23:55	MarkDuplicates	Tracking 127380 as yet unmatched pairs. 12753 records in RAM.
INFO	2026-06-08 08:23:57	MarkDuplicates	Read   434,000,000 records.  Elapsed time: 00:15:26s.  Time for last 1,000,000:    1s.  Last read position: chr19:47,495,557
INFO	2026-06-08 08:23:57	MarkDuplicates	Tracking 125857 as yet unmatched pairs. 11212 records in RAM.
INFO	2026-06-08 08:23:58	MarkDuplicates	Read   435,000,000 records.  Elapsed time: 00:15:27s.  Time for last 1,000,000:    1s.  Last read position: chr19:48,919,259
INFO	2026-06-08 08:23:58	MarkDuplicates	Tracking 124195 as yet unmatched pairs. 9543 records in RAM.
INFO	2026-06-08 08:24:00	MarkDuplicates	Read   436,000,000 records.  Elapsed time: 00:15:29s.  Time for last 1,000,000:    1s.  Last read position: chr19:49,596,689
INFO	2026-06-08 08:24:00	MarkDuplicates	Tracking 122887 as yet unmatched pairs. 8230 records in RAM.
INFO	2026-06-08 08:24:02	MarkDuplicates	Read   437,000,000 records.  Elapsed time: 00:15:31s.  Time for last 1,000,000:    1s.  Last read position: chr19:49,889,949
INFO	2026-06-08 08:24:02	MarkDuplicates	Tracking 122113 as yet unmatched pairs. 7444 records in RAM.
INFO	2026-06-08 08:24:04	MarkDuplicates	Read   438,000,000 records.  Elapsed time: 00:15:33s.  Time for last 1,000,000:    1s.  Last read position: chr19:52,065,928
INFO	2026-06-08 08:24:04	MarkDuplicates	Tracking 119837 as yet unmatched pairs. 5155 records in RAM.
INFO	2026-06-08 08:24:05	MarkDuplicates	Read   439,000,000 records.  Elapsed time: 00:15:34s.  Time for last 1,000,000:    1s.  Last read position: chr19:54,458,803
INFO	2026-06-08 08:24:05	MarkDuplicates	Tracking 119322 as yet unmatched pairs. 4636 records in RAM.
INFO	2026-06-08 08:24:07	MarkDuplicates	Read   440,000,000 records.  Elapsed time: 00:15:36s.  Time for last 1,000,000:    2s.  Last read position: chr19:55,642,587
INFO	2026-06-08 08:24:07	MarkDuplicates	Tracking 116832 as yet unmatched pairs. 2139 records in RAM.
INFO	2026-06-08 08:24:09	MarkDuplicates	Read   441,000,000 records.  Elapsed time: 00:15:38s.  Time for last 1,000,000:    1s.  Last read position: chr19:58,207,022
INFO	2026-06-08 08:24:09	MarkDuplicates	Tracking 115744 as yet unmatched pairs. 1043 records in RAM.
INFO	2026-06-08 08:24:11	MarkDuplicates	Read   442,000,000 records.  Elapsed time: 00:15:40s.  Time for last 1,000,000:    1s.  Last read position: chr20:2,461,681
INFO	2026-06-08 08:24:11	MarkDuplicates	Tracking 114347 as yet unmatched pairs. 14374 records in RAM.
INFO	2026-06-08 08:24:12	MarkDuplicates	Read   443,000,000 records.  Elapsed time: 00:15:41s.  Time for last 1,000,000:    1s.  Last read position: chr20:5,977,913
INFO	2026-06-08 08:24:12	MarkDuplicates	Tracking 112684 as yet unmatched pairs. 12699 records in RAM.
INFO	2026-06-08 08:24:14	MarkDuplicates	Read   444,000,000 records.  Elapsed time: 00:15:43s.  Time for last 1,000,000:    1s.  Last read position: chr20:25,248,195
INFO	2026-06-08 08:24:14	MarkDuplicates	Tracking 111744 as yet unmatched pairs. 11740 records in RAM.
INFO	2026-06-08 08:24:16	MarkDuplicates	Read   445,000,000 records.  Elapsed time: 00:15:45s.  Time for last 1,000,000:    1s.  Last read position: chr20:34,526,280
INFO	2026-06-08 08:24:16	MarkDuplicates	Tracking 111223 as yet unmatched pairs. 11185 records in RAM.
INFO	2026-06-08 08:24:18	MarkDuplicates	Read   446,000,000 records.  Elapsed time: 00:15:47s.  Time for last 1,000,000:    1s.  Last read position: chr20:36,591,122
INFO	2026-06-08 08:24:18	MarkDuplicates	Tracking 110508 as yet unmatched pairs. 10462 records in RAM.
INFO	2026-06-08 08:24:19	MarkDuplicates	Read   447,000,000 records.  Elapsed time: 00:15:48s.  Time for last 1,000,000:    1s.  Last read position: chr20:41,566,477
INFO	2026-06-08 08:24:19	MarkDuplicates	Tracking 108006 as yet unmatched pairs. 7953 records in RAM.
INFO	2026-06-08 08:24:21	MarkDuplicates	Read   448,000,000 records.  Elapsed time: 00:15:50s.  Time for last 1,000,000:    1s.  Last read position: chr20:46,128,901
INFO	2026-06-08 08:24:21	MarkDuplicates	Tracking 107247 as yet unmatched pairs. 7191 records in RAM.
INFO	2026-06-08 08:24:23	MarkDuplicates	Read   449,000,000 records.  Elapsed time: 00:15:52s.  Time for last 1,000,000:    1s.  Last read position: chr20:49,248,312
INFO	2026-06-08 08:24:23	MarkDuplicates	Tracking 106210 as yet unmatched pairs. 6138 records in RAM.
INFO	2026-06-08 08:24:25	MarkDuplicates	Read   450,000,000 records.  Elapsed time: 00:15:54s.  Time for last 1,000,000:    1s.  Last read position: chr20:57,500,532
INFO	2026-06-08 08:24:25	MarkDuplicates	Tracking 104392 as yet unmatched pairs. 4310 records in RAM.
INFO	2026-06-08 08:24:27	MarkDuplicates	Read   451,000,000 records.  Elapsed time: 00:15:56s.  Time for last 1,000,000:    1s.  Last read position: chr20:62,330,909
INFO	2026-06-08 08:24:27	MarkDuplicates	Tracking 103254 as yet unmatched pairs. 3152 records in RAM.
INFO	2026-06-08 08:24:28	MarkDuplicates	Read   452,000,000 records.  Elapsed time: 00:15:57s.  Time for last 1,000,000:    1s.  Last read position: chr20:63,567,373
INFO	2026-06-08 08:24:28	MarkDuplicates	Tracking 103639 as yet unmatched pairs. 3530 records in RAM.
INFO	2026-06-08 08:24:30	MarkDuplicates	Read   453,000,000 records.  Elapsed time: 00:15:59s.  Time for last 1,000,000:    2s.  Last read position: chr21:5,034,995
INFO	2026-06-08 08:24:30	MarkDuplicates	Tracking 100825 as yet unmatched pairs. 30180 records in RAM.
INFO	2026-06-08 08:24:32	MarkDuplicates	Read   454,000,000 records.  Elapsed time: 00:16:01s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,210,330
INFO	2026-06-08 08:24:32	MarkDuplicates	Tracking 98865 as yet unmatched pairs. 28214 records in RAM.
INFO	2026-06-08 08:24:33	MarkDuplicates	Read   455,000,000 records.  Elapsed time: 00:16:02s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,214,675
INFO	2026-06-08 08:24:33	MarkDuplicates	Tracking 98616 as yet unmatched pairs. 27965 records in RAM.
INFO	2026-06-08 08:24:34	MarkDuplicates	Read   456,000,000 records.  Elapsed time: 00:16:03s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,216,837
INFO	2026-06-08 08:24:34	MarkDuplicates	Tracking 95727 as yet unmatched pairs. 25052 records in RAM.
INFO	2026-06-08 08:24:36	MarkDuplicates	Read   457,000,000 records.  Elapsed time: 00:16:05s.  Time for last 1,000,000:    2s.  Last read position: chr21:8,217,217
INFO	2026-06-08 08:24:36	MarkDuplicates	Tracking 93345 as yet unmatched pairs. 22667 records in RAM.
INFO	2026-06-08 08:24:37	MarkDuplicates	Read   458,000,000 records.  Elapsed time: 00:16:06s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,252,271
INFO	2026-06-08 08:24:37	MarkDuplicates	Tracking 92081 as yet unmatched pairs. 21400 records in RAM.
INFO	2026-06-08 08:24:38	MarkDuplicates	Read   459,000,000 records.  Elapsed time: 00:16:07s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,257,855
INFO	2026-06-08 08:24:38	MarkDuplicates	Tracking 90946 as yet unmatched pairs. 20265 records in RAM.
INFO	2026-06-08 08:24:39	MarkDuplicates	Read   460,000,000 records.  Elapsed time: 00:16:09s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,260,314
INFO	2026-06-08 08:24:39	MarkDuplicates	Tracking 90302 as yet unmatched pairs. 19617 records in RAM.
INFO	2026-06-08 08:24:41	MarkDuplicates	Read   461,000,000 records.  Elapsed time: 00:16:10s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,396,653
INFO	2026-06-08 08:24:41	MarkDuplicates	Tracking 91180 as yet unmatched pairs. 20495 records in RAM.
INFO	2026-06-08 08:24:42	MarkDuplicates	Read   462,000,000 records.  Elapsed time: 00:16:11s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,399,800
INFO	2026-06-08 08:24:42	MarkDuplicates	Tracking 88898 as yet unmatched pairs. 18211 records in RAM.
INFO	2026-06-08 08:24:43	MarkDuplicates	Read   463,000,000 records.  Elapsed time: 00:16:12s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,400,065
INFO	2026-06-08 08:24:43	MarkDuplicates	Tracking 84551 as yet unmatched pairs. 13863 records in RAM.
INFO	2026-06-08 08:24:45	MarkDuplicates	Read   464,000,000 records.  Elapsed time: 00:16:14s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,435,599
INFO	2026-06-08 08:24:45	MarkDuplicates	Tracking 82981 as yet unmatched pairs. 12285 records in RAM.
INFO	2026-06-08 08:24:46	MarkDuplicates	Read   465,000,000 records.  Elapsed time: 00:16:15s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,440,865
INFO	2026-06-08 08:24:46	MarkDuplicates	Tracking 82564 as yet unmatched pairs. 11868 records in RAM.
INFO	2026-06-08 08:24:47	MarkDuplicates	Read   466,000,000 records.  Elapsed time: 00:16:16s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,443,336
INFO	2026-06-08 08:24:47	MarkDuplicates	Tracking 80545 as yet unmatched pairs. 9849 records in RAM.
INFO	2026-06-08 08:24:49	MarkDuplicates	Read   467,000,000 records.  Elapsed time: 00:16:18s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,444,191
INFO	2026-06-08 08:24:49	MarkDuplicates	Tracking 80451 as yet unmatched pairs. 9755 records in RAM.
INFO	2026-06-08 08:24:51	MarkDuplicates	Read   468,000,000 records.  Elapsed time: 00:16:20s.  Time for last 1,000,000:    2s.  Last read position: chr21:8,444,642
INFO	2026-06-08 08:24:51	MarkDuplicates	Tracking 77893 as yet unmatched pairs. 7197 records in RAM.
INFO	2026-06-08 08:24:53	MarkDuplicates	Read   469,000,000 records.  Elapsed time: 00:16:22s.  Time for last 1,000,000:    1s.  Last read position: chr21:29,326,791
INFO	2026-06-08 08:24:53	MarkDuplicates	Tracking 75793 as yet unmatched pairs. 5088 records in RAM.
INFO	2026-06-08 08:24:55	MarkDuplicates	Read   470,000,000 records.  Elapsed time: 00:16:24s.  Time for last 1,000,000:    1s.  Last read position: chr21:34,708,040
INFO	2026-06-08 08:24:55	MarkDuplicates	Tracking 74359 as yet unmatched pairs. 3651 records in RAM.
INFO	2026-06-08 08:24:57	MarkDuplicates	Read   471,000,000 records.  Elapsed time: 00:16:26s.  Time for last 1,000,000:    1s.  Last read position: chr21:42,852,266
INFO	2026-06-08 08:24:57	MarkDuplicates	Tracking 73330 as yet unmatched pairs. 2622 records in RAM.
INFO	2026-06-08 08:24:58	MarkDuplicates	Read   472,000,000 records.  Elapsed time: 00:16:28s.  Time for last 1,000,000:    1s.  Last read position: chr21:44,304,235
INFO	2026-06-08 08:24:58	MarkDuplicates	Tracking 73094 as yet unmatched pairs. 2384 records in RAM.
INFO	2026-06-08 08:25:00	MarkDuplicates	Read   473,000,000 records.  Elapsed time: 00:16:29s.  Time for last 1,000,000:    1s.  Last read position: chr22:15,563,824
INFO	2026-06-08 08:25:00	MarkDuplicates	Tracking 70711 as yet unmatched pairs. 18398 records in RAM.
INFO	2026-06-08 08:25:02	MarkDuplicates	Read   474,000,000 records.  Elapsed time: 00:16:31s.  Time for last 1,000,000:    1s.  Last read position: chr22:20,712,512
INFO	2026-06-08 08:25:02	MarkDuplicates	Tracking 69392 as yet unmatched pairs. 17069 records in RAM.
INFO	2026-06-08 08:25:04	MarkDuplicates	Read   475,000,000 records.  Elapsed time: 00:16:33s.  Time for last 1,000,000:    1s.  Last read position: chr22:23,285,072
INFO	2026-06-08 08:25:04	MarkDuplicates	Tracking 68303 as yet unmatched pairs. 15973 records in RAM.
INFO	2026-06-08 08:25:05	MarkDuplicates	Read   476,000,000 records.  Elapsed time: 00:16:34s.  Time for last 1,000,000:    1s.  Last read position: chr22:28,772,813
INFO	2026-06-08 08:25:05	MarkDuplicates	Tracking 66970 as yet unmatched pairs. 14636 records in RAM.
INFO	2026-06-08 08:25:07	MarkDuplicates	Read   477,000,000 records.  Elapsed time: 00:16:36s.  Time for last 1,000,000:    1s.  Last read position: chr22:29,299,778
INFO	2026-06-08 08:25:07	MarkDuplicates	Tracking 65829 as yet unmatched pairs. 13491 records in RAM.
INFO	2026-06-08 08:25:09	MarkDuplicates	Read   478,000,000 records.  Elapsed time: 00:16:38s.  Time for last 1,000,000:    1s.  Last read position: chr22:31,738,484
INFO	2026-06-08 08:25:09	MarkDuplicates	Tracking 64562 as yet unmatched pairs. 12217 records in RAM.
INFO	2026-06-08 08:25:10	MarkDuplicates	Read   479,000,000 records.  Elapsed time: 00:16:39s.  Time for last 1,000,000:    1s.  Last read position: chr22:36,511,756
INFO	2026-06-08 08:25:10	MarkDuplicates	Tracking 63664 as yet unmatched pairs. 11314 records in RAM.
INFO	2026-06-08 08:25:12	MarkDuplicates	Read   480,000,000 records.  Elapsed time: 00:16:41s.  Time for last 1,000,000:    1s.  Last read position: chr22:37,755,109
INFO	2026-06-08 08:25:12	MarkDuplicates	Tracking 62062 as yet unmatched pairs. 9703 records in RAM.
INFO	2026-06-08 08:25:14	MarkDuplicates	Read   481,000,000 records.  Elapsed time: 00:16:43s.  Time for last 1,000,000:    1s.  Last read position: chr22:38,982,455
INFO	2026-06-08 08:25:14	MarkDuplicates	Tracking 60538 as yet unmatched pairs. 8178 records in RAM.
INFO	2026-06-08 08:25:16	MarkDuplicates	Read   482,000,000 records.  Elapsed time: 00:16:45s.  Time for last 1,000,000:    1s.  Last read position: chr22:40,848,311
INFO	2026-06-08 08:25:16	MarkDuplicates	Tracking 59546 as yet unmatched pairs. 7176 records in RAM.
INFO	2026-06-08 08:25:17	MarkDuplicates	Read   483,000,000 records.  Elapsed time: 00:16:46s.  Time for last 1,000,000:    1s.  Last read position: chr22:41,911,228
INFO	2026-06-08 08:25:17	MarkDuplicates	Tracking 58156 as yet unmatched pairs. 5773 records in RAM.
INFO	2026-06-08 08:25:19	MarkDuplicates	Read   484,000,000 records.  Elapsed time: 00:16:48s.  Time for last 1,000,000:    1s.  Last read position: chr22:44,131,520
INFO	2026-06-08 08:25:19	MarkDuplicates	Tracking 57219 as yet unmatched pairs. 4830 records in RAM.
INFO	2026-06-08 08:25:21	MarkDuplicates	Read   485,000,000 records.  Elapsed time: 00:16:50s.  Time for last 1,000,000:    1s.  Last read position: chr22:50,221,214
INFO	2026-06-08 08:25:21	MarkDuplicates	Tracking 56181 as yet unmatched pairs. 3787 records in RAM.
INFO	2026-06-08 08:25:23	MarkDuplicates	Read   486,000,000 records.  Elapsed time: 00:16:52s.  Time for last 1,000,000:    1s.  Last read position: chr22:50,506,393
INFO	2026-06-08 08:25:23	MarkDuplicates	Tracking 55020 as yet unmatched pairs. 2623 records in RAM.
INFO	2026-06-08 08:25:24	MarkDuplicates	Read   487,000,000 records.  Elapsed time: 00:16:54s.  Time for last 1,000,000:    1s.  Last read position: chrX:1,600,427
INFO	2026-06-08 08:25:24	MarkDuplicates	Tracking 51647 as yet unmatched pairs. 15105 records in RAM.
INFO	2026-06-08 08:25:26	MarkDuplicates	Read   488,000,000 records.  Elapsed time: 00:16:55s.  Time for last 1,000,000:    1s.  Last read position: chrX:16,818,573
INFO	2026-06-08 08:25:26	MarkDuplicates	Tracking 50470 as yet unmatched pairs. 13926 records in RAM.
INFO	2026-06-08 08:25:28	MarkDuplicates	Read   489,000,000 records.  Elapsed time: 00:16:57s.  Time for last 1,000,000:    1s.  Last read position: chrX:38,805,269
INFO	2026-06-08 08:25:28	MarkDuplicates	Tracking 49681 as yet unmatched pairs. 13108 records in RAM.
INFO	2026-06-08 08:25:29	MarkDuplicates	Read   490,000,000 records.  Elapsed time: 00:16:59s.  Time for last 1,000,000:    1s.  Last read position: chrX:46,758,720
INFO	2026-06-08 08:25:29	MarkDuplicates	Tracking 48669 as yet unmatched pairs. 12094 records in RAM.
INFO	2026-06-08 08:25:31	MarkDuplicates	Read   491,000,000 records.  Elapsed time: 00:17:00s.  Time for last 1,000,000:    1s.  Last read position: chrX:48,918,627
INFO	2026-06-08 08:25:31	MarkDuplicates	Tracking 47148 as yet unmatched pairs. 10561 records in RAM.
INFO	2026-06-08 08:25:33	MarkDuplicates	Read   492,000,000 records.  Elapsed time: 00:17:02s.  Time for last 1,000,000:    1s.  Last read position: chrX:53,549,070
INFO	2026-06-08 08:25:33	MarkDuplicates	Tracking 46398 as yet unmatched pairs. 9811 records in RAM.
INFO	2026-06-08 08:25:36	MarkDuplicates	Read   493,000,000 records.  Elapsed time: 00:17:05s.  Time for last 1,000,000:    3s.  Last read position: chrX:64,268,787
INFO	2026-06-08 08:25:36	MarkDuplicates	Tracking 44521 as yet unmatched pairs. 7934 records in RAM.
INFO	2026-06-08 08:25:38	MarkDuplicates	Read   494,000,000 records.  Elapsed time: 00:17:07s.  Time for last 1,000,000:    1s.  Last read position: chrX:71,556,770
INFO	2026-06-08 08:25:38	MarkDuplicates	Tracking 44234 as yet unmatched pairs. 7646 records in RAM.
INFO	2026-06-08 08:25:40	MarkDuplicates	Read   495,000,000 records.  Elapsed time: 00:17:09s.  Time for last 1,000,000:    1s.  Last read position: chrX:77,968,995
INFO	2026-06-08 08:25:40	MarkDuplicates	Tracking 42798 as yet unmatched pairs. 6210 records in RAM.
INFO	2026-06-08 08:25:42	MarkDuplicates	Read   496,000,000 records.  Elapsed time: 00:17:11s.  Time for last 1,000,000:    1s.  Last read position: chrX:109,722,662
INFO	2026-06-08 08:25:42	MarkDuplicates	Tracking 41449 as yet unmatched pairs. 4860 records in RAM.
INFO	2026-06-08 08:25:43	MarkDuplicates	Read   497,000,000 records.  Elapsed time: 00:17:12s.  Time for last 1,000,000:    1s.  Last read position: chrX:129,920,484
INFO	2026-06-08 08:25:43	MarkDuplicates	Tracking 40314 as yet unmatched pairs. 3725 records in RAM.
INFO	2026-06-08 08:25:45	MarkDuplicates	Read   498,000,000 records.  Elapsed time: 00:17:14s.  Time for last 1,000,000:    1s.  Last read position: chrX:152,858,793
INFO	2026-06-08 08:25:45	MarkDuplicates	Tracking 39490 as yet unmatched pairs. 2901 records in RAM.
INFO	2026-06-08 08:25:46	MarkDuplicates	Read   499,000,000 records.  Elapsed time: 00:17:16s.  Time for last 1,000,000:    1s.  Last read position: chrX:154,354,996
INFO	2026-06-08 08:25:46	MarkDuplicates	Tracking 38291 as yet unmatched pairs. 1700 records in RAM.
INFO	2026-06-08 08:25:48	MarkDuplicates	Read   500,000,000 records.  Elapsed time: 00:17:17s.  Time for last 1,000,000:    1s.  Last read position: chrX:155,382,995
INFO	2026-06-08 08:25:48	MarkDuplicates	Tracking 36691 as yet unmatched pairs. 100 records in RAM.
INFO	2026-06-08 08:25:50	MarkDuplicates	Read   501,000,000 records.  Elapsed time: 00:17:19s.  Time for last 1,000,000:    1s.  Last read position: chrM:6,798
INFO	2026-06-08 08:25:50	MarkDuplicates	Tracking 36501 as yet unmatched pairs. 875 records in RAM.
INFO	2026-06-08 08:25:51	MarkDuplicates	Read   502,000,000 records.  Elapsed time: 00:17:20s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:111,296
INFO	2026-06-08 08:25:51	MarkDuplicates	Tracking 35207 as yet unmatched pairs. 5902 records in RAM.
INFO	2026-06-08 08:25:52	MarkDuplicates	Read   503,000,000 records.  Elapsed time: 00:17:22s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:114,141
INFO	2026-06-08 08:25:52	MarkDuplicates	Tracking 34347 as yet unmatched pairs. 5042 records in RAM.
INFO	2026-06-08 08:25:54	MarkDuplicates	Read   504,000,000 records.  Elapsed time: 00:17:23s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:116,303
INFO	2026-06-08 08:25:54	MarkDuplicates	Tracking 29667 as yet unmatched pairs. 362 records in RAM.
INFO	2026-06-08 08:25:55	MarkDuplicates	Read   505,000,000 records.  Elapsed time: 00:17:24s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:116,644
INFO	2026-06-08 08:25:55	MarkDuplicates	Tracking 29704 as yet unmatched pairs. 399 records in RAM.
INFO	2026-06-08 08:25:57	MarkDuplicates	Read   506,000,000 records.  Elapsed time: 00:17:26s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:152,802
INFO	2026-06-08 08:25:57	MarkDuplicates	Tracking 29682 as yet unmatched pairs. 377 records in RAM.
INFO	2026-06-08 08:25:59	MarkDuplicates	Read   507,000,000 records.  Elapsed time: 00:17:28s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:157,563
INFO	2026-06-08 08:25:59	MarkDuplicates	Tracking 29660 as yet unmatched pairs. 355 records in RAM.
INFO	2026-06-08 08:26:01	MarkDuplicates	Read   508,000,000 records.  Elapsed time: 00:17:30s.  Time for last 1,000,000:    2s.  Last read position: GL000220.1:159,530
INFO	2026-06-08 08:26:01	MarkDuplicates	Tracking 29406 as yet unmatched pairs. 101 records in RAM.
INFO	2026-06-08 08:26:02	MarkDuplicates	Read   509,000,000 records.  Elapsed time: 00:17:31s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:160,455
INFO	2026-06-08 08:26:02	MarkDuplicates	Tracking 29357 as yet unmatched pairs. 52 records in RAM.
INFO	2026-06-08 08:26:04	MarkDuplicates	Read   510,000,000 records.  Elapsed time: 00:17:33s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:124,558
INFO	2026-06-08 08:26:04	MarkDuplicates	Tracking 29388 as yet unmatched pairs. 29372 records in RAM.
INFO	2026-06-08 08:26:05	MarkDuplicates	Read   511,000,000 records.  Elapsed time: 00:17:34s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:129,615
INFO	2026-06-08 08:26:05	MarkDuplicates	Tracking 28793 as yet unmatched pairs. 28777 records in RAM.
INFO	2026-06-08 08:26:06	MarkDuplicates	Read   512,000,000 records.  Elapsed time: 00:17:35s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:130,998
INFO	2026-06-08 08:26:06	MarkDuplicates	Tracking 28015 as yet unmatched pairs. 27999 records in RAM.
INFO	2026-06-08 08:26:07	MarkDuplicates	Read   513,000,000 records.  Elapsed time: 00:17:36s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:133,166
INFO	2026-06-08 08:26:07	MarkDuplicates	Tracking 21291 as yet unmatched pairs. 21275 records in RAM.
INFO	2026-06-08 08:26:08	MarkDuplicates	Read   514,000,000 records.  Elapsed time: 00:17:38s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:133,591
INFO	2026-06-08 08:26:08	MarkDuplicates	Tracking 24120 as yet unmatched pairs. 24104 records in RAM.
INFO	2026-06-08 08:26:10	MarkDuplicates	Read   515,000,000 records.  Elapsed time: 00:17:39s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:170,762
INFO	2026-06-08 08:26:10	MarkDuplicates	Tracking 17515 as yet unmatched pairs. 17499 records in RAM.
INFO	2026-06-08 08:26:11	MarkDuplicates	Read   516,000,000 records.  Elapsed time: 00:17:40s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:174,678
INFO	2026-06-08 08:26:11	MarkDuplicates	Tracking 47130 as yet unmatched pairs. 47114 records in RAM.
INFO	2026-06-08 08:26:13	MarkDuplicates	Read   517,000,000 records.  Elapsed time: 00:17:42s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:175,856
INFO	2026-06-08 08:26:13	MarkDuplicates	Tracking 307 as yet unmatched pairs. 291 records in RAM.
INFO	2026-06-08 08:26:14	MarkDuplicates	Read   518,000,000 records.  Elapsed time: 00:17:43s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:178,203
INFO	2026-06-08 08:26:14	MarkDuplicates	Tracking 145 as yet unmatched pairs. 129 records in RAM.
INFO	2026-06-08 08:26:15	MarkDuplicates	Read   519,000,000 records.  Elapsed time: 00:17:44s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:178,486
INFO	2026-06-08 08:26:15	MarkDuplicates	Tracking 62 as yet unmatched pairs. 46 records in RAM.
INFO	2026-06-08 08:26:16	MarkDuplicates	Read 519602592 records. 0 pairs never matched.
INFO	2026-06-08 08:27:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 42854085480; totalMemory: 61203283968; maxMemory: 63585648640
INFO	2026-06-08 08:27:26	MarkDuplicates	Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO	2026-06-08 08:27:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2026-06-08 08:28:03	OpticalDuplicateFinder	Large duplicate set. size = 1516
INFO	2026-06-08 08:28:03	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:4,260
INFO	2026-06-08 08:28:10	OpticalDuplicateFinder	Large duplicate set. size = 1021
INFO	2026-06-08 08:28:10	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:18,110
INFO	2026-06-08 08:28:10	OpticalDuplicateFinder	Large duplicate set. size = 1486
INFO	2026-06-08 08:28:10	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:21,330
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1182
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:10,004
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1061
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-31,149
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1069
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:30,901
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1126
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:12,811
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1556
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:22,390
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1196
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-23,455
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1167
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-15,446
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1056
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,900
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1556
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,140
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1285
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-14,685
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1054
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:21,945
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1212
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:15,602
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1267
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:8,313
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1797
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-17,889
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1513
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-28,786
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1394
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-20,268
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1942
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-21,020
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1535
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-23,083
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1309
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-28,980
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1820
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-31,618
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1380
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-17,298
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1003
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:3,823
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	Large duplicate set. size = 1325
INFO	2026-06-08 08:28:16	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:29,461
INFO	2026-06-08 08:28:24	OpticalDuplicateFinder	Large duplicate set. size = 1489
INFO	2026-06-08 08:28:24	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:14,203
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 2344
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:18,094
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-14,354
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1218
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-30,429
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1281
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:10,886
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 2062
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:1,154
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-30,348
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 2900
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:6,137
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:8,362
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 2203
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-26,367
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:20,092
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1281
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:26,281
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1247
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,140
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1710
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-27,330
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1412
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:31,297
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1041
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:14,834
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1053
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-30,356
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1360
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-26,359
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1020
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-29,239
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1144
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:2,197
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1277
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:11,436
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1677
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-27,184
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1126
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:28,207
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1517
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-21,432
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	Large duplicate set. size = 1055
INFO	2026-06-08 08:28:25	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-15,244
INFO	2026-06-08 08:28:37	OpticalDuplicateFinder	Large duplicate set. size = 1175
INFO	2026-06-08 08:28:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:30,003
INFO	2026-06-08 08:28:37	OpticalDuplicateFinder	Large duplicate set. size = 1044
INFO	2026-06-08 08:28:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:32,114
INFO	2026-06-08 08:28:37	OpticalDuplicateFinder	Large duplicate set. size = 1357
INFO	2026-06-08 08:28:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:24,348
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	Large duplicate set. size = 1075
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:19,308
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	Large duplicate set. size = 1211
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:3,637
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	Large duplicate set. size = 2353
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,229
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	compared         2,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:21,775
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	Large duplicate set. size = 1359
INFO	2026-06-08 08:28:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:19,842
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	Large duplicate set. size = 1593
INFO	2026-06-08 08:28:56	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 08:28:56	OpticalDuplicateFinder	Large duplicate set. size = 1008
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:7,084
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	Large duplicate set. size = 1083
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:29,889
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	Large duplicate set. size = 1403
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-26,909
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	Large duplicate set. size = 1891
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:-14,249
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	Large duplicate set. size = 1049
INFO	2026-06-08 08:28:56	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:25,302
INFO	2026-06-08 08:28:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
WARNING	2026-06-08 08:28:56	SortingCollection	There is not enough memory per file for buffering. Reading will be unbuffered.
INFO	2026-06-08 08:29:48	MarkDuplicates	Sorting list of duplicate records.
INFO	2026-06-08 08:29:49	MarkDuplicates	After generateDuplicateIndexes freeMemory: 204599352; totalMemory: 234881024; maxMemory: 63585648640
INFO	2026-06-08 08:29:49	MarkDuplicates	Marking 280360430 records as duplicates.
INFO	2026-06-08 08:29:49	MarkDuplicates	Found 21345988 optical duplicate clusters.
INFO	2026-06-08 08:29:49	MarkDuplicates	Reads are assumed to be ordered by: coordinate
INFO	2026-06-08 08:30:06	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:00:17s.  Time for last 10,000,000:   17s.  Last read position: chr1:28,773,030
INFO	2026-06-08 08:30:23	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:00:34s.  Time for last 10,000,000:   17s.  Last read position: chr1:99,993,586
INFO	2026-06-08 08:30:40	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:00:51s.  Time for last 10,000,000:   16s.  Last read position: chr1:155,660,456
INFO	2026-06-08 08:30:57	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:01:08s.  Time for last 10,000,000:   16s.  Last read position: chr1:212,858,571
INFO	2026-06-08 08:31:14	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:01:25s.  Time for last 10,000,000:   16s.  Last read position: chr2:32,916,406
INFO	2026-06-08 08:31:30	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:01:41s.  Time for last 10,000,000:   16s.  Last read position: chr2:99,404,461
INFO	2026-06-08 08:31:47	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:01:58s.  Time for last 10,000,000:   16s.  Last read position: chr2:207,570,177
INFO	2026-06-08 08:32:04	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:02:15s.  Time for last 10,000,000:   17s.  Last read position: chr3:33,132,587
INFO	2026-06-08 08:32:21	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:02:32s.  Time for last 10,000,000:   17s.  Last read position: chr3:119,390,848
INFO	2026-06-08 08:32:38	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:02:49s.  Time for last 10,000,000:   16s.  Last read position: chr4:957,851
INFO	2026-06-08 08:32:55	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:03:06s.  Time for last 10,000,000:   16s.  Last read position: chr4:139,698,176
INFO	2026-06-08 08:33:12	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:03:23s.  Time for last 10,000,000:   17s.  Last read position: chr5:81,706,664
INFO	2026-06-08 08:33:29	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:03:40s.  Time for last 10,000,000:   16s.  Last read position: chr5:154,803,598
INFO	2026-06-08 08:33:46	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:03:56s.  Time for last 10,000,000:   16s.  Last read position: chr6:27,810,269
INFO	2026-06-08 08:34:02	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:04:13s.  Time for last 10,000,000:   16s.  Last read position: chr6:43,369,206
INFO	2026-06-08 08:34:19	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:04:30s.  Time for last 10,000,000:   16s.  Last read position: chr6:157,190,174
INFO	2026-06-08 08:34:37	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:04:48s.  Time for last 10,000,000:   17s.  Last read position: chr7:56,104,407
INFO	2026-06-08 08:34:54	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:05:05s.  Time for last 10,000,000:   16s.  Last read position: chr7:120,438,208
INFO	2026-06-08 08:35:10	MarkDuplicates	Written   190,000,000 records.  Elapsed time: 00:05:21s.  Time for last 10,000,000:   16s.  Last read position: chr8:30,703,185
INFO	2026-06-08 08:35:27	MarkDuplicates	Written   200,000,000 records.  Elapsed time: 00:05:38s.  Time for last 10,000,000:   16s.  Last read position: chr8:143,581,060
INFO	2026-06-08 08:35:44	MarkDuplicates	Written   210,000,000 records.  Elapsed time: 00:05:55s.  Time for last 10,000,000:   16s.  Last read position: chr9:85,692,768
INFO	2026-06-08 08:36:01	MarkDuplicates	Written   220,000,000 records.  Elapsed time: 00:06:12s.  Time for last 10,000,000:   16s.  Last read position: chr9:135,938,275
INFO	2026-06-08 08:36:18	MarkDuplicates	Written   230,000,000 records.  Elapsed time: 00:06:29s.  Time for last 10,000,000:   16s.  Last read position: chr10:75,030,388
INFO	2026-06-08 08:36:35	MarkDuplicates	Written   240,000,000 records.  Elapsed time: 00:06:45s.  Time for last 10,000,000:   16s.  Last read position: chr11:1,761,371
INFO	2026-06-08 08:36:51	MarkDuplicates	Written   250,000,000 records.  Elapsed time: 00:07:02s.  Time for last 10,000,000:   16s.  Last read position: chr11:64,343,180
INFO	2026-06-08 08:37:09	MarkDuplicates	Written   260,000,000 records.  Elapsed time: 00:07:19s.  Time for last 10,000,000:   17s.  Last read position: chr11:96,147,104
INFO	2026-06-08 08:37:26	MarkDuplicates	Written   270,000,000 records.  Elapsed time: 00:07:37s.  Time for last 10,000,000:   17s.  Last read position: chr12:27,317,972
INFO	2026-06-08 08:37:43	MarkDuplicates	Written   280,000,000 records.  Elapsed time: 00:07:53s.  Time for last 10,000,000:   16s.  Last read position: chr12:68,615,503
INFO	2026-06-08 08:37:59	MarkDuplicates	Written   290,000,000 records.  Elapsed time: 00:08:10s.  Time for last 10,000,000:   16s.  Last read position: chr12:130,875,677
INFO	2026-06-08 08:38:16	MarkDuplicates	Written   300,000,000 records.  Elapsed time: 00:08:27s.  Time for last 10,000,000:   17s.  Last read position: chr14:23,566,571
INFO	2026-06-08 08:38:33	MarkDuplicates	Written   310,000,000 records.  Elapsed time: 00:08:44s.  Time for last 10,000,000:   16s.  Last read position: chr14:71,105,254
INFO	2026-06-08 08:38:50	MarkDuplicates	Written   320,000,000 records.  Elapsed time: 00:09:00s.  Time for last 10,000,000:   16s.  Last read position: chr15:40,036,455
INFO	2026-06-08 08:39:07	MarkDuplicates	Written   330,000,000 records.  Elapsed time: 00:09:17s.  Time for last 10,000,000:   16s.  Last read position: chr15:78,541,921
INFO	2026-06-08 08:39:23	MarkDuplicates	Written   340,000,000 records.  Elapsed time: 00:09:34s.  Time for last 10,000,000:   16s.  Last read position: chr16:12,524,724
INFO	2026-06-08 08:39:40	MarkDuplicates	Written   350,000,000 records.  Elapsed time: 00:09:51s.  Time for last 10,000,000:   16s.  Last read position: chr16:29,454,022
INFO	2026-06-08 08:39:57	MarkDuplicates	Written   360,000,000 records.  Elapsed time: 00:10:08s.  Time for last 10,000,000:   17s.  Last read position: chr16:70,381,699
INFO	2026-06-08 08:40:14	MarkDuplicates	Written   370,000,000 records.  Elapsed time: 00:10:25s.  Time for last 10,000,000:   16s.  Last read position: chr17:7,513,406
INFO	2026-06-08 08:40:31	MarkDuplicates	Written   380,000,000 records.  Elapsed time: 00:10:41s.  Time for last 10,000,000:   16s.  Last read position: chr17:39,658,488
INFO	2026-06-08 08:40:48	MarkDuplicates	Written   390,000,000 records.  Elapsed time: 00:10:59s.  Time for last 10,000,000:   17s.  Last read position: chr17:68,042,911
INFO	2026-06-08 08:41:05	MarkDuplicates	Written   400,000,000 records.  Elapsed time: 00:11:16s.  Time for last 10,000,000:   17s.  Last read position: chr18:36,114,454
INFO	2026-06-08 08:41:22	MarkDuplicates	Written   410,000,000 records.  Elapsed time: 00:11:33s.  Time for last 10,000,000:   16s.  Last read position: chr19:5,220,112
INFO	2026-06-08 08:41:39	MarkDuplicates	Written   420,000,000 records.  Elapsed time: 00:11:50s.  Time for last 10,000,000:   17s.  Last read position: chr19:17,726,496
INFO	2026-06-08 08:41:56	MarkDuplicates	Written   430,000,000 records.  Elapsed time: 00:12:06s.  Time for last 10,000,000:   16s.  Last read position: chr19:42,272,242
INFO	2026-06-08 08:42:13	MarkDuplicates	Written   440,000,000 records.  Elapsed time: 00:12:24s.  Time for last 10,000,000:   17s.  Last read position: chr19:55,642,587
INFO	2026-06-08 08:42:30	MarkDuplicates	Written   450,000,000 records.  Elapsed time: 00:12:41s.  Time for last 10,000,000:   17s.  Last read position: chr20:57,500,532
INFO	2026-06-08 08:42:46	MarkDuplicates	Written   460,000,000 records.  Elapsed time: 00:12:57s.  Time for last 10,000,000:   15s.  Last read position: chr21:8,260,314
INFO	2026-06-08 08:43:01	MarkDuplicates	Written   470,000,000 records.  Elapsed time: 00:13:11s.  Time for last 10,000,000:   14s.  Last read position: chr21:34,708,040
INFO	2026-06-08 08:43:17	MarkDuplicates	Written   480,000,000 records.  Elapsed time: 00:13:28s.  Time for last 10,000,000:   16s.  Last read position: chr22:37,755,109
INFO	2026-06-08 08:43:34	MarkDuplicates	Written   490,000,000 records.  Elapsed time: 00:13:45s.  Time for last 10,000,000:   17s.  Last read position: chrX:46,758,720
INFO	2026-06-08 08:43:52	MarkDuplicates	Written   500,000,000 records.  Elapsed time: 00:14:03s.  Time for last 10,000,000:   17s.  Last read position: chrX:155,382,995
INFO	2026-06-08 08:44:08	MarkDuplicates	Written   510,000,000 records.  Elapsed time: 00:14:18s.  Time for last 10,000,000:   15s.  Last read position: KI270733.1:124,558
INFO	2026-06-08 08:44:24	MarkDuplicates	Written   520,000,000 records.  Elapsed time: 00:14:35s.  Time for last 10,000,000:   16s.  Last read position: */*
INFO	2026-06-08 08:44:34	MarkDuplicates	Writing complete. Closing input iterator.
INFO	2026-06-08 08:44:34	MarkDuplicates	Duplicate Index cleanup.
INFO	2026-06-08 08:44:34	MarkDuplicates	Getting Memory Stats.
INFO	2026-06-08 08:44:34	MarkDuplicates	Before output close freeMemory: 204566056; totalMemory: 234881024; maxMemory: 63585648640
INFO	2026-06-08 08:44:34	MarkDuplicates	Closed outputs. Getting more Memory Stats.
INFO	2026-06-08 08:44:34	MarkDuplicates	After output close freeMemory: 104807144; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:44:34 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 36.09 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory