Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/0fae7ef9d25f6d0525eca8ec872e4e/dna_s767.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/8c2fef66bf7244d393374cdd6c7171/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/8c2fef66bf7244d393374cdd6c7171/.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 dna_s767.Aligned.sortedByCoord.out.bam --OUTPUT dna_s767.md.bam --METRICS_FILE dna_s767.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:41:40.862 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 07:41:40 GMT 2026] MarkDuplicates --INPUT dna_s767.Aligned.sortedByCoord.out.bam --OUTPUT dna_s767.md.bam --METRICS_FILE dna_s767.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 07:41:40 GMT 2026] Executing as ?@nf-d38c2fef66bf7244d393374cdd6c7171-61fb3-v555r 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 07:41:40 MarkDuplicates Start of doWork freeMemory: 105851816; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:41:40 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:41:40 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:41:47 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:6,462,781
INFO 2026-06-08 07:41:47 MarkDuplicates Tracking 3297 as yet unmatched pairs. 311 records in RAM.
INFO 2026-06-08 07:41:51 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:12,827,204
INFO 2026-06-08 07:41:51 MarkDuplicates Tracking 6803 as yet unmatched pairs. 514 records in RAM.
INFO 2026-06-08 07:41:55 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 4s. Last read position: chr1:16,646,941
INFO 2026-06-08 07:41:55 MarkDuplicates Tracking 11115 as yet unmatched pairs. 2219 records in RAM.
INFO 2026-06-08 07:41:58 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: chr1:21,608,155
INFO 2026-06-08 07:41:58 MarkDuplicates Tracking 12748 as yet unmatched pairs. 1002 records in RAM.
INFO 2026-06-08 07:42:03 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 4s. Last read position: chr1:28,269,158
INFO 2026-06-08 07:42:03 MarkDuplicates Tracking 16055 as yet unmatched pairs. 883 records in RAM.
INFO 2026-06-08 07:42:06 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:37,481,661
INFO 2026-06-08 07:42:06 MarkDuplicates Tracking 20180 as yet unmatched pairs. 1195 records in RAM.
INFO 2026-06-08 07:42:10 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr1:44,786,693
INFO 2026-06-08 07:42:10 MarkDuplicates Tracking 23499 as yet unmatched pairs. 1183 records in RAM.
INFO 2026-06-08 07:42:14 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 4s. Last read position: chr1:53,594,700
INFO 2026-06-08 07:42:14 MarkDuplicates Tracking 27509 as yet unmatched pairs. 1477 records in RAM.
INFO 2026-06-08 07:42:18 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr1:71,402,321
INFO 2026-06-08 07:42:18 MarkDuplicates Tracking 33919 as yet unmatched pairs. 2959 records in RAM.
INFO 2026-06-08 07:42:22 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 4s. Last read position: chr1:93,319,267
INFO 2026-06-08 07:42:22 MarkDuplicates Tracking 38255 as yet unmatched pairs. 1660 records in RAM.
INFO 2026-06-08 07:42:26 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr1:109,610,033
INFO 2026-06-08 07:42:26 MarkDuplicates Tracking 42611 as yet unmatched pairs. 1660 records in RAM.
INFO 2026-06-08 07:42:29 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr1:119,514,075
INFO 2026-06-08 07:42:29 MarkDuplicates Tracking 47371 as yet unmatched pairs. 2484 records in RAM.
INFO 2026-06-08 07:42:32 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:145,751,364
INFO 2026-06-08 07:42:32 MarkDuplicates Tracking 49889 as yet unmatched pairs. 1672 records in RAM.
INFO 2026-06-08 07:42:35 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:150,803,951
INFO 2026-06-08 07:42:35 MarkDuplicates Tracking 52284 as yet unmatched pairs. 1596 records in RAM.
INFO 2026-06-08 07:42:38 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chr1:155,034,449
INFO 2026-06-08 07:42:38 MarkDuplicates Tracking 55119 as yet unmatched pairs. 1734 records in RAM.
INFO 2026-06-08 07:42:41 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: chr1:158,610,846
INFO 2026-06-08 07:42:41 MarkDuplicates Tracking 58525 as yet unmatched pairs. 2215 records in RAM.
INFO 2026-06-08 07:42:45 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 4s. Last read position: chr1:167,860,627
INFO 2026-06-08 07:42:45 MarkDuplicates Tracking 61411 as yet unmatched pairs. 1436 records in RAM.
INFO 2026-06-08 07:42:49 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr1:181,732,381
INFO 2026-06-08 07:42:49 MarkDuplicates Tracking 65751 as yet unmatched pairs. 1334 records in RAM.
INFO 2026-06-08 07:42:52 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr1:202,004,266
INFO 2026-06-08 07:42:52 MarkDuplicates Tracking 70765 as yet unmatched pairs. 1080 records in RAM.
INFO 2026-06-08 07:42:56 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: chr1:205,676,456
INFO 2026-06-08 07:42:56 MarkDuplicates Tracking 75261 as yet unmatched pairs. 2515 records in RAM.
INFO 2026-06-08 07:43:00 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 4s. Last read position: chr1:220,170,726
INFO 2026-06-08 07:43:00 MarkDuplicates Tracking 77782 as yet unmatched pairs. 668 records in RAM.
INFO 2026-06-08 07:43:03 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr1:230,688,389
INFO 2026-06-08 07:43:03 MarkDuplicates Tracking 81600 as yet unmatched pairs. 473 records in RAM.
INFO 2026-06-08 07:43:06 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: chr1:247,329,472
INFO 2026-06-08 07:43:06 MarkDuplicates Tracking 86123 as yet unmatched pairs. 214 records in RAM.
INFO 2026-06-08 07:43:11 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 4s. Last read position: chr2:17,773,065
INFO 2026-06-08 07:43:11 MarkDuplicates Tracking 91061 as yet unmatched pairs. 26750 records in RAM.
INFO 2026-06-08 07:43:15 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 3s. Last read position: chr2:27,236,490
INFO 2026-06-08 07:43:15 MarkDuplicates Tracking 94395 as yet unmatched pairs. 27451 records in RAM.
INFO 2026-06-08 07:43:18 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:43:18 MarkDuplicates Tracking 216192 as yet unmatched pairs. 22255 records in RAM.
INFO 2026-06-08 07:43:21 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 3s. Last read position: chr2:43,675,991
INFO 2026-06-08 07:43:21 MarkDuplicates Tracking 271977 as yet unmatched pairs. 18920 records in RAM.
INFO 2026-06-08 07:43:25 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: chr2:58,217,272
INFO 2026-06-08 07:43:25 MarkDuplicates Tracking 274311 as yet unmatched pairs. 17902 records in RAM.
INFO 2026-06-08 07:43:28 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr2:73,916,628
INFO 2026-06-08 07:43:28 MarkDuplicates Tracking 276564 as yet unmatched pairs. 16718 records in RAM.
INFO 2026-06-08 07:43:32 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: chr2:87,792,013
INFO 2026-06-08 07:43:32 MarkDuplicates Tracking 279186 as yet unmatched pairs. 16342 records in RAM.
INFO 2026-06-08 07:43:36 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: chr2:97,511,342
INFO 2026-06-08 07:43:36 MarkDuplicates Tracking 280137 as yet unmatched pairs. 15005 records in RAM.
INFO 2026-06-08 07:43:38 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr2:108,752,900
INFO 2026-06-08 07:43:38 MarkDuplicates Tracking 281853 as yet unmatched pairs. 14006 records in RAM.
INFO 2026-06-08 07:43:41 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr2:113,186,115
INFO 2026-06-08 07:43:41 MarkDuplicates Tracking 282446 as yet unmatched pairs. 12970 records in RAM.
INFO 2026-06-08 07:43:43 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr2:127,654,341
INFO 2026-06-08 07:43:43 MarkDuplicates Tracking 284257 as yet unmatched pairs. 11632 records in RAM.
INFO 2026-06-08 07:43:46 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: chr2:140,950,343
INFO 2026-06-08 07:43:46 MarkDuplicates Tracking 286077 as yet unmatched pairs. 10463 records in RAM.
INFO 2026-06-08 07:43:49 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr2:165,943,155
INFO 2026-06-08 07:43:49 MarkDuplicates Tracking 289101 as yet unmatched pairs. 9003 records in RAM.
INFO 2026-06-08 07:43:53 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 3s. Last read position: chr2:178,385,483
INFO 2026-06-08 07:43:53 MarkDuplicates Tracking 290916 as yet unmatched pairs. 7683 records in RAM.
INFO 2026-06-08 07:43:56 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: chr2:189,852,317
INFO 2026-06-08 07:43:56 MarkDuplicates Tracking 292544 as yet unmatched pairs. 6477 records in RAM.
INFO 2026-06-08 07:44:00 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: chr2:206,310,128
INFO 2026-06-08 07:44:00 MarkDuplicates Tracking 294951 as yet unmatched pairs. 5154 records in RAM.
INFO 2026-06-08 07:44:03 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr2:219,168,368
INFO 2026-06-08 07:44:03 MarkDuplicates Tracking 296569 as yet unmatched pairs. 3638 records in RAM.
INFO 2026-06-08 07:44:07 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 4s. Last read position: chr2:226,796,583
INFO 2026-06-08 07:44:07 MarkDuplicates Tracking 298955 as yet unmatched pairs. 3448 records in RAM.
INFO 2026-06-08 07:44:11 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 4s. Last read position: chr2:239,050,147
INFO 2026-06-08 07:44:11 MarkDuplicates Tracking 300760 as yet unmatched pairs. 2395 records in RAM.
INFO 2026-06-08 07:44:15 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: chr3:10,026,514
INFO 2026-06-08 07:44:15 MarkDuplicates Tracking 301703 as yet unmatched pairs. 23337 records in RAM.
INFO 2026-06-08 07:44:18 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 3s. Last read position: chr3:12,342,994
INFO 2026-06-08 07:44:18 MarkDuplicates Tracking 302392 as yet unmatched pairs. 21969 records in RAM.
INFO 2026-06-08 07:44:22 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 3s. Last read position: chr3:15,042,784
INFO 2026-06-08 07:44:22 MarkDuplicates Tracking 302209 as yet unmatched pairs. 19867 records in RAM.
INFO 2026-06-08 07:44:25 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr3:38,252,448
INFO 2026-06-08 07:44:25 MarkDuplicates Tracking 304706 as yet unmatched pairs. 18277 records in RAM.
INFO 2026-06-08 07:44:28 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 3s. Last read position: chr3:47,163,689
INFO 2026-06-08 07:44:28 MarkDuplicates Tracking 306191 as yet unmatched pairs. 17317 records in RAM.
INFO 2026-06-08 07:44:31 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 3s. Last read position: chr3:50,366,486
INFO 2026-06-08 07:44:31 MarkDuplicates Tracking 306233 as yet unmatched pairs. 15821 records in RAM.
INFO 2026-06-08 07:44:34 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: chr3:58,395,604
INFO 2026-06-08 07:44:34 MarkDuplicates Tracking 307018 as yet unmatched pairs. 14375 records in RAM.
INFO 2026-06-08 07:44:38 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 3s. Last read position: chr3:77,211,031
INFO 2026-06-08 07:44:38 MarkDuplicates Tracking 308711 as yet unmatched pairs. 12447 records in RAM.
INFO 2026-06-08 07:44:41 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr3:112,931,025
INFO 2026-06-08 07:44:41 MarkDuplicates Tracking 312171 as yet unmatched pairs. 10388 records in RAM.
INFO 2026-06-08 07:44:44 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 3s. Last read position: chr3:126,462,079
INFO 2026-06-08 07:44:44 MarkDuplicates Tracking 313687 as yet unmatched pairs. 8894 records in RAM.
INFO 2026-06-08 07:44:47 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 3s. Last read position: chr3:136,518,199
INFO 2026-06-08 07:44:47 MarkDuplicates Tracking 315457 as yet unmatched pairs. 8222 records in RAM.
INFO 2026-06-08 07:44:50 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 3s. Last read position: chr3:155,987,976
INFO 2026-06-08 07:44:50 MarkDuplicates Tracking 316437 as yet unmatched pairs. 5650 records in RAM.
INFO 2026-06-08 07:44:53 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 3s. Last read position: chr3:180,659,408
INFO 2026-06-08 07:44:53 MarkDuplicates Tracking 318533 as yet unmatched pairs. 3435 records in RAM.
INFO 2026-06-08 07:44:57 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 3s. Last read position: chr3:186,076,912
INFO 2026-06-08 07:44:57 MarkDuplicates Tracking 319865 as yet unmatched pairs. 2614 records in RAM.
INFO 2026-06-08 07:45:01 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 3s. Last read position: chr3:197,016,274
INFO 2026-06-08 07:45:01 MarkDuplicates Tracking 320128 as yet unmatched pairs. 283 records in RAM.
INFO 2026-06-08 07:45:04 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 3s. Last read position: chr4:4,862,796
INFO 2026-06-08 07:45:04 MarkDuplicates Tracking 320676 as yet unmatched pairs. 17126 records in RAM.
INFO 2026-06-08 07:45:07 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: chr4:13,600,687
INFO 2026-06-08 07:45:07 MarkDuplicates Tracking 321224 as yet unmatched pairs. 15801 records in RAM.
INFO 2026-06-08 07:45:10 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 3s. Last read position: chr4:41,257,623
INFO 2026-06-08 07:45:10 MarkDuplicates Tracking 323292 as yet unmatched pairs. 13793 records in RAM.
INFO 2026-06-08 07:45:14 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 3s. Last read position: chr4:56,593,636
INFO 2026-06-08 07:45:14 MarkDuplicates Tracking 324505 as yet unmatched pairs. 12204 records in RAM.
INFO 2026-06-08 07:45:17 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 3s. Last read position: chr4:78,481,781
INFO 2026-06-08 07:45:17 MarkDuplicates Tracking 326126 as yet unmatched pairs. 10214 records in RAM.
INFO 2026-06-08 07:45:21 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 3s. Last read position: chr4:102,578,666
INFO 2026-06-08 07:45:21 MarkDuplicates Tracking 327758 as yet unmatched pairs. 7989 records in RAM.
INFO 2026-06-08 07:45:23 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr4:122,893,168
INFO 2026-06-08 07:45:23 MarkDuplicates Tracking 330080 as yet unmatched pairs. 6721 records in RAM.
INFO 2026-06-08 07:45:26 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr4:152,320,584
INFO 2026-06-08 07:45:26 MarkDuplicates Tracking 332091 as yet unmatched pairs. 4191 records in RAM.
INFO 2026-06-08 07:45:30 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 3s. Last read position: chr4:184,447,713
INFO 2026-06-08 07:45:30 MarkDuplicates Tracking 334433 as yet unmatched pairs. 1832 records in RAM.
INFO 2026-06-08 07:45:34 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 3s. Last read position: chr5:8,085,799
INFO 2026-06-08 07:45:34 MarkDuplicates Tracking 334181 as yet unmatched pairs. 20632 records in RAM.
INFO 2026-06-08 07:45:37 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 3s. Last read position: chr5:38,938,338
INFO 2026-06-08 07:45:37 MarkDuplicates Tracking 337019 as yet unmatched pairs. 19383 records in RAM.
INFO 2026-06-08 07:45:41 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 3s. Last read position: chr5:62,362,472
INFO 2026-06-08 07:45:41 MarkDuplicates Tracking 337738 as yet unmatched pairs. 16182 records in RAM.
INFO 2026-06-08 07:45:43 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr5:77,404,550
INFO 2026-06-08 07:45:43 MarkDuplicates Tracking 338371 as yet unmatched pairs. 14265 records in RAM.
INFO 2026-06-08 07:45:47 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 3s. Last read position: chr5:103,707,736
INFO 2026-06-08 07:45:47 MarkDuplicates Tracking 340028 as yet unmatched pairs. 11829 records in RAM.
INFO 2026-06-08 07:45:50 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 3s. Last read position: chr5:131,592,431
INFO 2026-06-08 07:45:50 MarkDuplicates Tracking 341549 as yet unmatched pairs. 9302 records in RAM.
INFO 2026-06-08 07:45:53 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr5:140,823,030
INFO 2026-06-08 07:45:53 MarkDuplicates Tracking 342156 as yet unmatched pairs. 7841 records in RAM.
INFO 2026-06-08 07:45:56 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr5:149,551,197
INFO 2026-06-08 07:45:56 MarkDuplicates Tracking 343608 as yet unmatched pairs. 7335 records in RAM.
INFO 2026-06-08 07:46:00 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 4s. Last read position: chr5:161,882,542
INFO 2026-06-08 07:46:00 MarkDuplicates Tracking 342119 as yet unmatched pairs. 3438 records in RAM.
INFO 2026-06-08 07:46:03 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 3s. Last read position: chr5:177,459,116
INFO 2026-06-08 07:46:03 MarkDuplicates Tracking 342393 as yet unmatched pairs. 1161 records in RAM.
INFO 2026-06-08 07:46:06 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr6:7,576,965
INFO 2026-06-08 07:46:06 MarkDuplicates Tracking 342626 as yet unmatched pairs. 26987 records in RAM.
INFO 2026-06-08 07:46:09 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 3s. Last read position: chr6:27,824,256
INFO 2026-06-08 07:46:09 MarkDuplicates Tracking 343191 as yet unmatched pairs. 24770 records in RAM.
INFO 2026-06-08 07:46:12 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr6:31,632,284
INFO 2026-06-08 07:46:12 MarkDuplicates Tracking 342792 as yet unmatched pairs. 23065 records in RAM.
INFO 2026-06-08 07:46:15 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr6:33,069,690
INFO 2026-06-08 07:46:15 MarkDuplicates Tracking 342751 as yet unmatched pairs. 22016 records in RAM.
INFO 2026-06-08 07:46:18 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 3s. Last read position: chr6:41,342,901
INFO 2026-06-08 07:46:18 MarkDuplicates Tracking 342257 as yet unmatched pairs. 19864 records in RAM.
INFO 2026-06-08 07:46:22 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 3s. Last read position: chr6:51,659,872
INFO 2026-06-08 07:46:22 MarkDuplicates Tracking 342310 as yet unmatched pairs. 17933 records in RAM.
INFO 2026-06-08 07:46:25 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 3s. Last read position: chr6:80,064,764
INFO 2026-06-08 07:46:25 MarkDuplicates Tracking 343421 as yet unmatched pairs. 15322 records in RAM.
INFO 2026-06-08 07:46:29 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 4s. Last read position: chr6:104,791,506
INFO 2026-06-08 07:46:29 MarkDuplicates Tracking 344055 as yet unmatched pairs. 12533 records in RAM.
INFO 2026-06-08 07:46:33 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 3s. Last read position: chr6:117,329,841
INFO 2026-06-08 07:46:33 MarkDuplicates Tracking 345066 as yet unmatched pairs. 11302 records in RAM.
INFO 2026-06-08 07:46:36 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 3s. Last read position: chr6:130,092,905
INFO 2026-06-08 07:46:36 MarkDuplicates Tracking 343949 as yet unmatched pairs. 7878 records in RAM.
INFO 2026-06-08 07:46:39 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 3s. Last read position: chr6:142,774,364
INFO 2026-06-08 07:46:39 MarkDuplicates Tracking 344856 as yet unmatched pairs. 6474 records in RAM.
INFO 2026-06-08 07:46:42 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 3s. Last read position: chr6:154,832,029
INFO 2026-06-08 07:46:42 MarkDuplicates Tracking 343973 as yet unmatched pairs. 3361 records in RAM.
INFO 2026-06-08 07:46:45 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 3s. Last read position: chr6:163,572,315
INFO 2026-06-08 07:46:45 MarkDuplicates Tracking 344585 as yet unmatched pairs. 2140 records in RAM.
INFO 2026-06-08 07:46:49 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 4s. Last read position: chr7:5,955,973
INFO 2026-06-08 07:46:49 MarkDuplicates Tracking 343450 as yet unmatched pairs. 29758 records in RAM.
INFO 2026-06-08 07:46:52 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 3s. Last read position: chr7:13,950,263
INFO 2026-06-08 07:46:52 MarkDuplicates Tracking 344162 as yet unmatched pairs. 28784 records in RAM.
INFO 2026-06-08 07:46:56 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 3s. Last read position: chr7:30,146,280
INFO 2026-06-08 07:46:56 MarkDuplicates Tracking 342621 as yet unmatched pairs. 24944 records in RAM.
INFO 2026-06-08 07:46:59 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 3s. Last read position: chr7:48,279,639
INFO 2026-06-08 07:46:59 MarkDuplicates Tracking 342505 as yet unmatched pairs. 22498 records in RAM.
INFO 2026-06-08 07:47:02 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 3s. Last read position: chr7:55,208,407
INFO 2026-06-08 07:47:02 MarkDuplicates Tracking 343068 as yet unmatched pairs. 21445 records in RAM.
INFO 2026-06-08 07:47:06 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 3s. Last read position: chr7:73,865,562
INFO 2026-06-08 07:47:06 MarkDuplicates Tracking 341837 as yet unmatched pairs. 17987 records in RAM.
INFO 2026-06-08 07:47:09 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 3s. Last read position: chr7:81,770,081
INFO 2026-06-08 07:47:09 MarkDuplicates Tracking 341580 as yet unmatched pairs. 16408 records in RAM.
INFO 2026-06-08 07:47:12 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 3s. Last read position: chr7:98,908,643
INFO 2026-06-08 07:47:12 MarkDuplicates Tracking 341176 as yet unmatched pairs. 13520 records in RAM.
INFO 2026-06-08 07:47:15 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr7:102,158,531
INFO 2026-06-08 07:47:15 MarkDuplicates Tracking 340691 as yet unmatched pairs. 12041 records in RAM.
INFO 2026-06-08 07:47:17 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr7:107,683,238
INFO 2026-06-08 07:47:17 MarkDuplicates Tracking 340152 as yet unmatched pairs. 10278 records in RAM.
INFO 2026-06-08 07:47:21 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 3s. Last read position: chr7:128,849,417
INFO 2026-06-08 07:47:21 MarkDuplicates Tracking 340020 as yet unmatched pairs. 7293 records in RAM.
INFO 2026-06-08 07:47:24 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 3s. Last read position: chr7:140,734,524
INFO 2026-06-08 07:47:24 MarkDuplicates Tracking 340041 as yet unmatched pairs. 5382 records in RAM.
INFO 2026-06-08 07:47:27 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 3s. Last read position: chr7:149,178,759
INFO 2026-06-08 07:47:27 MarkDuplicates Tracking 338903 as yet unmatched pairs. 2744 records in RAM.
INFO 2026-06-08 07:47:30 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 3s. Last read position: chr7:157,182,135
INFO 2026-06-08 07:47:30 MarkDuplicates Tracking 338199 as yet unmatched pairs. 389 records in RAM.
INFO 2026-06-08 07:47:34 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 3s. Last read position: chr8:8,027,883
INFO 2026-06-08 07:47:34 MarkDuplicates Tracking 339089 as yet unmatched pairs. 28406 records in RAM.
INFO 2026-06-08 07:47:37 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 3s. Last read position: chr8:23,702,517
INFO 2026-06-08 07:47:37 MarkDuplicates Tracking 337392 as yet unmatched pairs. 24691 records in RAM.
INFO 2026-06-08 07:47:41 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 3s. Last read position: chr8:32,640,564
INFO 2026-06-08 07:47:41 MarkDuplicates Tracking 337808 as yet unmatched pairs. 23471 records in RAM.
INFO 2026-06-08 07:47:44 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 3s. Last read position: chr8:32,724,977
INFO 2026-06-08 07:47:44 MarkDuplicates Tracking 336826 as yet unmatched pairs. 21331 records in RAM.
INFO 2026-06-08 07:47:48 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 3s. Last read position: chr8:38,271,617
INFO 2026-06-08 07:47:48 MarkDuplicates Tracking 335852 as yet unmatched pairs. 18923 records in RAM.
INFO 2026-06-08 07:47:51 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 3s. Last read position: chr8:41,930,722
INFO 2026-06-08 07:47:51 MarkDuplicates Tracking 334418 as yet unmatched pairs. 16242 records in RAM.
INFO 2026-06-08 07:47:54 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 3s. Last read position: chr8:60,830,223
INFO 2026-06-08 07:47:54 MarkDuplicates Tracking 333555 as yet unmatched pairs. 13078 records in RAM.
INFO 2026-06-08 07:47:58 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 3s. Last read position: chr8:89,931,150
INFO 2026-06-08 07:47:58 MarkDuplicates Tracking 333610 as yet unmatched pairs. 10049 records in RAM.
INFO 2026-06-08 07:48:01 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 3s. Last read position: chr8:110,219,842
INFO 2026-06-08 07:48:01 MarkDuplicates Tracking 332028 as yet unmatched pairs. 6006 records in RAM.
INFO 2026-06-08 07:48:05 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 3s. Last read position: chr8:138,883,008
INFO 2026-06-08 07:48:05 MarkDuplicates Tracking 331430 as yet unmatched pairs. 2434 records in RAM.
INFO 2026-06-08 07:48:08 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 2s. Last read position: chr8:144,506,734
INFO 2026-06-08 07:48:08 MarkDuplicates Tracking 330449 as yet unmatched pairs. 503 records in RAM.
INFO 2026-06-08 07:48:12 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 4s. Last read position: chr9:8,314,758
INFO 2026-06-08 07:48:12 MarkDuplicates Tracking 330313 as yet unmatched pairs. 28805 records in RAM.
INFO 2026-06-08 07:48:16 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 3s. Last read position: chr9:27,566,736
INFO 2026-06-08 07:48:16 MarkDuplicates Tracking 328574 as yet unmatched pairs. 24918 records in RAM.
INFO 2026-06-08 07:48:19 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 3s. Last read position: chr9:37,441,058
INFO 2026-06-08 07:48:19 MarkDuplicates Tracking 327536 as yet unmatched pairs. 22401 records in RAM.
INFO 2026-06-08 07:48:21 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 2s. Last read position: chr9:61,192,877
INFO 2026-06-08 07:48:21 MarkDuplicates Tracking 327372 as yet unmatched pairs. 21355 records in RAM.
INFO 2026-06-08 07:48:23 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 2s. Last read position: chr9:69,680,478
INFO 2026-06-08 07:48:23 MarkDuplicates Tracking 326466 as yet unmatched pairs. 19602 records in RAM.
INFO 2026-06-08 07:48:26 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 2s. Last read position: chr9:84,740,357
INFO 2026-06-08 07:48:26 MarkDuplicates Tracking 326684 as yet unmatched pairs. 17954 records in RAM.
INFO 2026-06-08 07:48:29 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 3s. Last read position: chr9:84,918,722
INFO 2026-06-08 07:48:29 MarkDuplicates Tracking 325356 as yet unmatched pairs. 15638 records in RAM.
INFO 2026-06-08 07:48:33 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 3s. Last read position: chr9:95,099,511
INFO 2026-06-08 07:48:33 MarkDuplicates Tracking 324715 as yet unmatched pairs. 13521 records in RAM.
INFO 2026-06-08 07:48:37 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 3s. Last read position: chr9:107,487,786
INFO 2026-06-08 07:48:37 MarkDuplicates Tracking 323136 as yet unmatched pairs. 10280 records in RAM.
INFO 2026-06-08 07:48:40 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 3s. Last read position: chr9:125,147,346
INFO 2026-06-08 07:48:40 MarkDuplicates Tracking 322231 as yet unmatched pairs. 7479 records in RAM.
INFO 2026-06-08 07:48:43 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 3s. Last read position: chr9:131,233,289
INFO 2026-06-08 07:48:43 MarkDuplicates Tracking 319792 as yet unmatched pairs. 3943 records in RAM.
INFO 2026-06-08 07:48:46 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr9:136,448,084
INFO 2026-06-08 07:48:46 MarkDuplicates Tracking 318636 as yet unmatched pairs. 1720 records in RAM.
INFO 2026-06-08 07:48:49 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 3s. Last read position: chr10:5,400,841
INFO 2026-06-08 07:48:49 MarkDuplicates Tracking 317493 as yet unmatched pairs. 27263 records in RAM.
INFO 2026-06-08 07:48:53 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 3s. Last read position: chr10:27,155,647
INFO 2026-06-08 07:48:53 MarkDuplicates Tracking 316180 as yet unmatched pairs. 23831 records in RAM.
INFO 2026-06-08 07:48:56 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 3s. Last read position: chr10:43,123,643
INFO 2026-06-08 07:48:56 MarkDuplicates Tracking 315207 as yet unmatched pairs. 21175 records in RAM.
INFO 2026-06-08 07:48:59 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr10:56,361,308
INFO 2026-06-08 07:48:59 MarkDuplicates Tracking 313666 as yet unmatched pairs. 18187 records in RAM.
INFO 2026-06-08 07:49:01 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 2s. Last read position: chr10:72,871,352
INFO 2026-06-08 07:49:01 MarkDuplicates Tracking 312387 as yet unmatched pairs. 15084 records in RAM.
INFO 2026-06-08 07:49:05 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 3s. Last read position: chr10:87,961,026
INFO 2026-06-08 07:49:05 MarkDuplicates Tracking 311996 as yet unmatched pairs. 13064 records in RAM.
INFO 2026-06-08 07:49:07 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 2s. Last read position: chr10:97,441,150
INFO 2026-06-08 07:49:07 MarkDuplicates Tracking 309673 as yet unmatched pairs. 9368 records in RAM.
INFO 2026-06-08 07:49:11 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 3s. Last read position: chr10:105,199,940
INFO 2026-06-08 07:49:11 MarkDuplicates Tracking 308214 as yet unmatched pairs. 6771 records in RAM.
INFO 2026-06-08 07:49:14 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 3s. Last read position: chr10:121,570,685
INFO 2026-06-08 07:49:14 MarkDuplicates Tracking 307758 as yet unmatched pairs. 4464 records in RAM.
INFO 2026-06-08 07:49:17 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 3s. Last read position: chr10:130,179,235
INFO 2026-06-08 07:49:17 MarkDuplicates Tracking 305320 as yet unmatched pairs. 769 records in RAM.
INFO 2026-06-08 07:49:21 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 3s. Last read position: chr11:1,470,350
INFO 2026-06-08 07:49:21 MarkDuplicates Tracking 304101 as yet unmatched pairs. 33108 records in RAM.
INFO 2026-06-08 07:49:25 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 4s. Last read position: chr11:8,880,456
INFO 2026-06-08 07:49:25 MarkDuplicates Tracking 302365 as yet unmatched pairs. 30434 records in RAM.
INFO 2026-06-08 07:49:28 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 3s. Last read position: chr11:27,392,488
INFO 2026-06-08 07:49:28 MarkDuplicates Tracking 300701 as yet unmatched pairs. 27068 records in RAM.
INFO 2026-06-08 07:49:31 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 2s. Last read position: chr11:48,123,834
INFO 2026-06-08 07:49:31 MarkDuplicates Tracking 298704 as yet unmatched pairs. 23360 records in RAM.
INFO 2026-06-08 07:49:33 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 2s. Last read position: chr11:61,813,225
INFO 2026-06-08 07:49:33 MarkDuplicates Tracking 297287 as yet unmatched pairs. 20645 records in RAM.
INFO 2026-06-08 07:49:36 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 2s. Last read position: chr11:65,584,312
INFO 2026-06-08 07:49:36 MarkDuplicates Tracking 295818 as yet unmatched pairs. 18480 records in RAM.
INFO 2026-06-08 07:49:38 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 2s. Last read position: chr11:70,923,239
INFO 2026-06-08 07:49:38 MarkDuplicates Tracking 294039 as yet unmatched pairs. 15857 records in RAM.
INFO 2026-06-08 07:49:41 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 2s. Last read position: chr11:86,244,890
INFO 2026-06-08 07:49:41 MarkDuplicates Tracking 293074 as yet unmatched pairs. 13394 records in RAM.
INFO 2026-06-08 07:49:43 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 2s. Last read position: chr11:102,230,997
INFO 2026-06-08 07:49:43 MarkDuplicates Tracking 291661 as yet unmatched pairs. 10425 records in RAM.
INFO 2026-06-08 07:49:46 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 3s. Last read position: chr11:114,444,464
INFO 2026-06-08 07:49:46 MarkDuplicates Tracking 288665 as yet unmatched pairs. 6116 records in RAM.
INFO 2026-06-08 07:49:50 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 3s. Last read position: chr11:119,307,437
INFO 2026-06-08 07:49:50 MarkDuplicates Tracking 288655 as yet unmatched pairs. 5132 records in RAM.
INFO 2026-06-08 07:49:53 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 3s. Last read position: chr11:134,177,284
INFO 2026-06-08 07:49:53 MarkDuplicates Tracking 285157 as yet unmatched pairs. 267 records in RAM.
INFO 2026-06-08 07:49:57 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 4s. Last read position: chr12:6,601,345
INFO 2026-06-08 07:49:57 MarkDuplicates Tracking 284105 as yet unmatched pairs. 37170 records in RAM.
INFO 2026-06-08 07:50:00 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 3s. Last read position: chr12:11,771,776
INFO 2026-06-08 07:50:00 MarkDuplicates Tracking 282965 as yet unmatched pairs. 35265 records in RAM.
INFO 2026-06-08 07:50:04 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 3s. Last read position: chr12:11,838,034
INFO 2026-06-08 07:50:04 MarkDuplicates Tracking 281335 as yet unmatched pairs. 32941 records in RAM.
INFO 2026-06-08 07:50:07 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 3s. Last read position: chr12:19,439,753
INFO 2026-06-08 07:50:07 MarkDuplicates Tracking 278600 as yet unmatched pairs. 29217 records in RAM.
INFO 2026-06-08 07:50:10 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 3s. Last read position: chr12:42,253,106
INFO 2026-06-08 07:50:10 MarkDuplicates Tracking 276279 as yet unmatched pairs. 25309 records in RAM.
INFO 2026-06-08 07:50:13 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 3s. Last read position: chr12:49,297,680
INFO 2026-06-08 07:50:13 MarkDuplicates Tracking 274478 as yet unmatched pairs. 22699 records in RAM.
INFO 2026-06-08 07:50:17 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 3s. Last read position: chr12:54,246,100
INFO 2026-06-08 07:50:17 MarkDuplicates Tracking 272743 as yet unmatched pairs. 20293 records in RAM.
INFO 2026-06-08 07:50:20 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 3s. Last read position: chr12:57,527,395
INFO 2026-06-08 07:50:20 MarkDuplicates Tracking 270907 as yet unmatched pairs. 17846 records in RAM.
INFO 2026-06-08 07:50:24 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 4s. Last read position: chr12:72,286,551
INFO 2026-06-08 07:50:24 MarkDuplicates Tracking 268671 as yet unmatched pairs. 14260 records in RAM.
INFO 2026-06-08 07:50:27 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 3s. Last read position: chr12:101,764,369
INFO 2026-06-08 07:50:27 MarkDuplicates Tracking 266087 as yet unmatched pairs. 9645 records in RAM.
INFO 2026-06-08 07:50:30 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 3s. Last read position: chr12:112,274,823
INFO 2026-06-08 07:50:30 MarkDuplicates Tracking 263793 as yet unmatched pairs. 6291 records in RAM.
INFO 2026-06-08 07:50:34 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 3s. Last read position: chr12:121,962,028
INFO 2026-06-08 07:50:34 MarkDuplicates Tracking 261594 as yet unmatched pairs. 3157 records in RAM.
INFO 2026-06-08 07:50:37 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 3s. Last read position: chr12:133,006,978
INFO 2026-06-08 07:50:37 MarkDuplicates Tracking 259629 as yet unmatched pairs. 168 records in RAM.
INFO 2026-06-08 07:50:41 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 4s. Last read position: chr13:28,389,812
INFO 2026-06-08 07:50:41 MarkDuplicates Tracking 258093 as yet unmatched pairs. 16892 records in RAM.
INFO 2026-06-08 07:50:44 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 3s. Last read position: chr13:46,045,315
INFO 2026-06-08 07:50:44 MarkDuplicates Tracking 254654 as yet unmatched pairs. 12162 records in RAM.
INFO 2026-06-08 07:50:47 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 3s. Last read position: chr13:77,556,762
INFO 2026-06-08 07:50:47 MarkDuplicates Tracking 251195 as yet unmatched pairs. 6877 records in RAM.
INFO 2026-06-08 07:50:51 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 3s. Last read position: chr13:109,785,767
INFO 2026-06-08 07:50:51 MarkDuplicates Tracking 248414 as yet unmatched pairs. 2154 records in RAM.
INFO 2026-06-08 07:50:54 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 3s. Last read position: chr14:22,952,148
INFO 2026-06-08 07:50:54 MarkDuplicates Tracking 245337 as yet unmatched pairs. 19486 records in RAM.
INFO 2026-06-08 07:50:57 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 3s. Last read position: chr14:37,595,308
INFO 2026-06-08 07:50:57 MarkDuplicates Tracking 243042 as yet unmatched pairs. 16195 records in RAM.
INFO 2026-06-08 07:51:01 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 3s. Last read position: chr14:64,093,256
INFO 2026-06-08 07:51:01 MarkDuplicates Tracking 239307 as yet unmatched pairs. 10941 records in RAM.
INFO 2026-06-08 07:51:04 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 3s. Last read position: chr14:76,635,181
INFO 2026-06-08 07:51:04 MarkDuplicates Tracking 236857 as yet unmatched pairs. 7496 records in RAM.
INFO 2026-06-08 07:51:06 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 2s. Last read position: chr14:96,347,076
INFO 2026-06-08 07:51:06 MarkDuplicates Tracking 233888 as yet unmatched pairs. 3241 records in RAM.
INFO 2026-06-08 07:51:09 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 2s. Last read position: chr15:20,437,303
INFO 2026-06-08 07:51:09 MarkDuplicates Tracking 231283 as yet unmatched pairs. 34763 records in RAM.
INFO 2026-06-08 07:51:11 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 2s. Last read position: chr15:28,529,922
INFO 2026-06-08 07:51:11 MarkDuplicates Tracking 229660 as yet unmatched pairs. 32704 records in RAM.
INFO 2026-06-08 07:51:14 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 2s. Last read position: chr15:35,084,469
INFO 2026-06-08 07:51:14 MarkDuplicates Tracking 227957 as yet unmatched pairs. 30488 records in RAM.
INFO 2026-06-08 07:51:18 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 3s. Last read position: chr15:43,234,706
INFO 2026-06-08 07:51:18 MarkDuplicates Tracking 225223 as yet unmatched pairs. 27134 records in RAM.
INFO 2026-06-08 07:51:21 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 3s. Last read position: chr15:52,112,236
INFO 2026-06-08 07:51:21 MarkDuplicates Tracking 222901 as yet unmatched pairs. 24122 records in RAM.
INFO 2026-06-08 07:51:24 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 3s. Last read position: chr15:68,307,382
INFO 2026-06-08 07:51:24 MarkDuplicates Tracking 219847 as yet unmatched pairs. 20127 records in RAM.
INFO 2026-06-08 07:51:27 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 3s. Last read position: chr15:78,383,116
INFO 2026-06-08 07:51:27 MarkDuplicates Tracking 217363 as yet unmatched pairs. 16955 records in RAM.
INFO 2026-06-08 07:51:31 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 3s. Last read position: chr15:87,942,339
INFO 2026-06-08 07:51:31 MarkDuplicates Tracking 216282 as yet unmatched pairs. 15204 records in RAM.
INFO 2026-06-08 07:51:35 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 4s. Last read position: chr15:88,009,729
INFO 2026-06-08 07:51:35 MarkDuplicates Tracking 214345 as yet unmatched pairs. 12873 records in RAM.
INFO 2026-06-08 07:51:39 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 3s. Last read position: chr15:88,060,752
INFO 2026-06-08 07:51:39 MarkDuplicates Tracking 211919 as yet unmatched pairs. 10004 records in RAM.
INFO 2026-06-08 07:51:43 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 3s. Last read position: chr15:88,115,913
INFO 2026-06-08 07:51:43 MarkDuplicates Tracking 209822 as yet unmatched pairs. 7491 records in RAM.
INFO 2026-06-08 07:51:46 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 3s. Last read position: chr15:90,602,476
INFO 2026-06-08 07:51:46 MarkDuplicates Tracking 206132 as yet unmatched pairs. 3325 records in RAM.
INFO 2026-06-08 07:51:50 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 3s. Last read position: chr16:352,470
INFO 2026-06-08 07:51:50 MarkDuplicates Tracking 204715 as yet unmatched pairs. 32517 records in RAM.
INFO 2026-06-08 07:51:53 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 3s. Last read position: chr16:2,565,457
INFO 2026-06-08 07:51:53 MarkDuplicates Tracking 201198 as yet unmatched pairs. 28699 records in RAM.
INFO 2026-06-08 07:51:57 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 3s. Last read position: chr16:9,755,515
INFO 2026-06-08 07:51:57 MarkDuplicates Tracking 199556 as yet unmatched pairs. 26554 records in RAM.
INFO 2026-06-08 07:52:00 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 3s. Last read position: chr16:16,320,884
INFO 2026-06-08 07:52:00 MarkDuplicates Tracking 196436 as yet unmatched pairs. 23033 records in RAM.
INFO 2026-06-08 07:52:03 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 2s. Last read position: chr16:22,527,591
INFO 2026-06-08 07:52:03 MarkDuplicates Tracking 194627 as yet unmatched pairs. 20868 records in RAM.
INFO 2026-06-08 07:52:06 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 3s. Last read position: chr16:29,911,121
INFO 2026-06-08 07:52:06 MarkDuplicates Tracking 192452 as yet unmatched pairs. 18269 records in RAM.
INFO 2026-06-08 07:52:09 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 3s. Last read position: chr16:33,459,845
INFO 2026-06-08 07:52:09 MarkDuplicates Tracking 190661 as yet unmatched pairs. 16185 records in RAM.
INFO 2026-06-08 07:52:12 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr16:57,668,552
INFO 2026-06-08 07:52:12 MarkDuplicates Tracking 187255 as yet unmatched pairs. 11797 records in RAM.
INFO 2026-06-08 07:52:14 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 2s. Last read position: chr16:69,356,806
INFO 2026-06-08 07:52:14 MarkDuplicates Tracking 184303 as yet unmatched pairs. 8207 records in RAM.
INFO 2026-06-08 07:52:17 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 2s. Last read position: chr16:75,875,068
INFO 2026-06-08 07:52:17 MarkDuplicates Tracking 181865 as yet unmatched pairs. 5293 records in RAM.
INFO 2026-06-08 07:52:21 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 3s. Last read position: chr16:89,285,530
INFO 2026-06-08 07:52:21 MarkDuplicates Tracking 179235 as yet unmatched pairs. 1993 records in RAM.
INFO 2026-06-08 07:52:25 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 4s. Last read position: chr17:3,198,344
INFO 2026-06-08 07:52:25 MarkDuplicates Tracking 176366 as yet unmatched pairs. 40627 records in RAM.
INFO 2026-06-08 07:52:29 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 4s. Last read position: chr17:7,669,476
INFO 2026-06-08 07:52:29 MarkDuplicates Tracking 175055 as yet unmatched pairs. 39026 records in RAM.
INFO 2026-06-08 07:52:31 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 2s. Last read position: chr17:12,956,319
INFO 2026-06-08 07:52:31 MarkDuplicates Tracking 171508 as yet unmatched pairs. 35135 records in RAM.
INFO 2026-06-08 07:52:34 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 2s. Last read position: chr17:19,158,834
INFO 2026-06-08 07:52:34 MarkDuplicates Tracking 169000 as yet unmatched pairs. 32259 records in RAM.
INFO 2026-06-08 07:52:37 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 3s. Last read position: chr17:31,228,862
INFO 2026-06-08 07:52:37 MarkDuplicates Tracking 166539 as yet unmatched pairs. 29311 records in RAM.
INFO 2026-06-08 07:52:39 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 2s. Last read position: chr17:37,542,256
INFO 2026-06-08 07:52:39 MarkDuplicates Tracking 163737 as yet unmatched pairs. 26141 records in RAM.
INFO 2026-06-08 07:52:42 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 2s. Last read position: chr17:40,332,330
INFO 2026-06-08 07:52:42 MarkDuplicates Tracking 163330 as yet unmatched pairs. 25466 records in RAM.
INFO 2026-06-08 07:52:45 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 3s. Last read position: chr17:42,104,700
INFO 2026-06-08 07:52:45 MarkDuplicates Tracking 159411 as yet unmatched pairs. 21290 records in RAM.
INFO 2026-06-08 07:52:48 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 3s. Last read position: chr17:43,530,506
INFO 2026-06-08 07:52:48 MarkDuplicates Tracking 158262 as yet unmatched pairs. 19855 records in RAM.
INFO 2026-06-08 07:52:51 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 3s. Last read position: chr17:47,017,212
INFO 2026-06-08 07:52:51 MarkDuplicates Tracking 155015 as yet unmatched pairs. 16319 records in RAM.
INFO 2026-06-08 07:52:56 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 4s. Last read position: chr17:56,913,472
INFO 2026-06-08 07:52:56 MarkDuplicates Tracking 151912 as yet unmatched pairs. 12763 records in RAM.
INFO 2026-06-08 07:52:59 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 3s. Last read position: chr17:63,713,303
INFO 2026-06-08 07:52:59 MarkDuplicates Tracking 148880 as yet unmatched pairs. 9313 records in RAM.
INFO 2026-06-08 07:53:01 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 2s. Last read position: chr17:72,736,604
INFO 2026-06-08 07:53:01 MarkDuplicates Tracking 145746 as yet unmatched pairs. 5751 records in RAM.
INFO 2026-06-08 07:53:04 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 2s. Last read position: chr17:78,500,244
INFO 2026-06-08 07:53:04 MarkDuplicates Tracking 142998 as yet unmatched pairs. 2677 records in RAM.
INFO 2026-06-08 07:53:06 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 2s. Last read position: chr18:2,544,194
INFO 2026-06-08 07:53:06 MarkDuplicates Tracking 140041 as yet unmatched pairs. 18379 records in RAM.
INFO 2026-06-08 07:53:09 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 2s. Last read position: chr18:31,068,827
INFO 2026-06-08 07:53:09 MarkDuplicates Tracking 135306 as yet unmatched pairs. 12926 records in RAM.
INFO 2026-06-08 07:53:11 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 2s. Last read position: chr18:47,810,105
INFO 2026-06-08 07:53:11 MarkDuplicates Tracking 132614 as yet unmatched pairs. 9700 records in RAM.
INFO 2026-06-08 07:53:13 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 2s. Last read position: chr18:62,143,184
INFO 2026-06-08 07:53:13 MarkDuplicates Tracking 127394 as yet unmatched pairs. 3966 records in RAM.
INFO 2026-06-08 07:53:17 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 3s. Last read position: chr19:1,228,342
INFO 2026-06-08 07:53:17 MarkDuplicates Tracking 123620 as yet unmatched pairs. 35014 records in RAM.
INFO 2026-06-08 07:53:21 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 4s. Last read position: chr19:4,202,920
INFO 2026-06-08 07:53:21 MarkDuplicates Tracking 120368 as yet unmatched pairs. 31583 records in RAM.
INFO 2026-06-08 07:53:25 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 3s. Last read position: chr19:8,334,455
INFO 2026-06-08 07:53:25 MarkDuplicates Tracking 117888 as yet unmatched pairs. 28875 records in RAM.
INFO 2026-06-08 07:53:28 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 3s. Last read position: chr19:10,544,956
INFO 2026-06-08 07:53:28 MarkDuplicates Tracking 115466 as yet unmatched pairs. 26268 records in RAM.
INFO 2026-06-08 07:53:31 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 3s. Last read position: chr19:14,527,823
INFO 2026-06-08 07:53:31 MarkDuplicates Tracking 112980 as yet unmatched pairs. 23591 records in RAM.
INFO 2026-06-08 07:53:35 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 4s. Last read position: chr19:17,839,593
INFO 2026-06-08 07:53:35 MarkDuplicates Tracking 110145 as yet unmatched pairs. 20591 records in RAM.
INFO 2026-06-08 07:53:39 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 3s. Last read position: chr19:35,121,083
INFO 2026-06-08 07:53:39 MarkDuplicates Tracking 106088 as yet unmatched pairs. 16191 records in RAM.
INFO 2026-06-08 07:53:42 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 3s. Last read position: chr19:39,603,889
INFO 2026-06-08 07:53:42 MarkDuplicates Tracking 103258 as yet unmatched pairs. 13157 records in RAM.
INFO 2026-06-08 07:53:45 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 3s. Last read position: chr19:42,748,383
INFO 2026-06-08 07:53:45 MarkDuplicates Tracking 100652 as yet unmatched pairs. 10353 records in RAM.
INFO 2026-06-08 07:53:49 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 3s. Last read position: chr19:47,221,616
INFO 2026-06-08 07:53:49 MarkDuplicates Tracking 98756 as yet unmatched pairs. 8214 records in RAM.
INFO 2026-06-08 07:53:53 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 3s. Last read position: chr19:51,267,153
INFO 2026-06-08 07:53:53 MarkDuplicates Tracking 95182 as yet unmatched pairs. 4461 records in RAM.
INFO 2026-06-08 07:53:56 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 3s. Last read position: chr19:55,723,999
INFO 2026-06-08 07:53:56 MarkDuplicates Tracking 92518 as yet unmatched pairs. 1560 records in RAM.
INFO 2026-06-08 07:53:58 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 2s. Last read position: chr20:6,778,856
INFO 2026-06-08 07:53:58 MarkDuplicates Tracking 89096 as yet unmatched pairs. 19545 records in RAM.
INFO 2026-06-08 07:54:01 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 2s. Last read position: chr20:31,723,771
INFO 2026-06-08 07:54:01 MarkDuplicates Tracking 85215 as yet unmatched pairs. 15330 records in RAM.
INFO 2026-06-08 07:54:04 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 3s. Last read position: chr20:37,404,627
INFO 2026-06-08 07:54:04 MarkDuplicates Tracking 82485 as yet unmatched pairs. 12435 records in RAM.
INFO 2026-06-08 07:54:07 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 2s. Last read position: chr20:46,393,044
INFO 2026-06-08 07:54:07 MarkDuplicates Tracking 77079 as yet unmatched pairs. 6844 records in RAM.
INFO 2026-06-08 07:54:11 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 3s. Last read position: chr20:59,194,569
INFO 2026-06-08 07:54:11 MarkDuplicates Tracking 73110 as yet unmatched pairs. 2629 records in RAM.
INFO 2026-06-08 07:54:15 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 3s. Last read position: chr21:6,118,986
INFO 2026-06-08 07:54:15 MarkDuplicates Tracking 70349 as yet unmatched pairs. 13725 records in RAM.
INFO 2026-06-08 07:54:17 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 2s. Last read position: chr21:23,358,318
INFO 2026-06-08 07:54:17 MarkDuplicates Tracking 66546 as yet unmatched pairs. 9662 records in RAM.
INFO 2026-06-08 07:54:21 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 3s. Last read position: chr21:41,168,241
INFO 2026-06-08 07:54:21 MarkDuplicates Tracking 61835 as yet unmatched pairs. 4717 records in RAM.
INFO 2026-06-08 07:54:25 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 3s. Last read position: chr21:44,227,135
INFO 2026-06-08 07:54:25 MarkDuplicates Tracking 59789 as yet unmatched pairs. 2549 records in RAM.
INFO 2026-06-08 07:54:28 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 3s. Last read position: chr22:18,167,220
INFO 2026-06-08 07:54:28 MarkDuplicates Tracking 55562 as yet unmatched pairs. 19433 records in RAM.
INFO 2026-06-08 07:54:31 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 3s. Last read position: chr22:21,121,862
INFO 2026-06-08 07:54:31 MarkDuplicates Tracking 56666 as yet unmatched pairs. 20492 records in RAM.
INFO 2026-06-08 07:54:34 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr22:23,276,807
INFO 2026-06-08 07:54:34 MarkDuplicates Tracking 52695 as yet unmatched pairs. 16444 records in RAM.
INFO 2026-06-08 07:54:38 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 3s. Last read position: chr22:24,628,043
INFO 2026-06-08 07:54:38 MarkDuplicates Tracking 48740 as yet unmatched pairs. 12402 records in RAM.
INFO 2026-06-08 07:54:41 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 3s. Last read position: chr22:30,376,429
INFO 2026-06-08 07:54:41 MarkDuplicates Tracking 45155 as yet unmatched pairs. 8719 records in RAM.
INFO 2026-06-08 07:54:45 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 4s. Last read position: chr22:39,045,310
INFO 2026-06-08 07:54:45 MarkDuplicates Tracking 41651 as yet unmatched pairs. 5120 records in RAM.
INFO 2026-06-08 07:54:48 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 2s. Last read position: chr22:46,891,327
INFO 2026-06-08 07:54:48 MarkDuplicates Tracking 38185 as yet unmatched pairs. 1554 records in RAM.
INFO 2026-06-08 07:54:51 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 2s. Last read position: chrX:18,241,343
INFO 2026-06-08 07:54:51 MarkDuplicates Tracking 33861 as yet unmatched pairs. 24635 records in RAM.
INFO 2026-06-08 07:54:53 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 2s. Last read position: chrX:48,706,571
INFO 2026-06-08 07:54:53 MarkDuplicates Tracking 29037 as yet unmatched pairs. 19774 records in RAM.
INFO 2026-06-08 07:54:56 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 2s. Last read position: chrX:63,904,118
INFO 2026-06-08 07:54:56 MarkDuplicates Tracking 26076 as yet unmatched pairs. 16795 records in RAM.
INFO 2026-06-08 07:54:58 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 2s. Last read position: chrX:73,889,908
INFO 2026-06-08 07:54:58 MarkDuplicates Tracking 22717 as yet unmatched pairs. 13409 records in RAM.
INFO 2026-06-08 07:55:00 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 2s. Last read position: chrX:111,410,718
INFO 2026-06-08 07:55:00 MarkDuplicates Tracking 17450 as yet unmatched pairs. 8102 records in RAM.
INFO 2026-06-08 07:55:02 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 2s. Last read position: chrX:135,816,129
INFO 2026-06-08 07:55:02 MarkDuplicates Tracking 13287 as yet unmatched pairs. 3911 records in RAM.
INFO 2026-06-08 07:55:04 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 2s. Last read position: chrX:154,860,405
INFO 2026-06-08 07:55:04 MarkDuplicates Tracking 9774 as yet unmatched pairs. 384 records in RAM.
INFO 2026-06-08 07:55:06 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 2s. Last read position: chrY:23,179,252
INFO 2026-06-08 07:55:06 MarkDuplicates Tracking 6721 as yet unmatched pairs. 1074 records in RAM.
INFO 2026-06-08 07:55:08 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: KI270713.1:4,424
INFO 2026-06-08 07:55:08 MarkDuplicates Tracking 3528 as yet unmatched pairs. 1004 records in RAM.
INFO 2026-06-08 07:55:11 MarkDuplicates Read 248973001 records. 0 pairs never matched.
INFO 2026-06-08 07:55:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 34299644288; totalMemory: 62713233408; maxMemory: 63585648640
INFO 2026-06-08 07:55:26 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:55:34 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:56:10 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:56:40 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:56:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300886416; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:56:43 MarkDuplicates Marking 46626532 records as duplicates.
INFO 2026-06-08 07:56:43 MarkDuplicates Found 9892633 optical duplicate clusters.
INFO 2026-06-08 07:56:43 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:57:17 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:33s. Time for last 10,000,000: 33s. Last read position: chr1:93,319,267
INFO 2026-06-08 07:57:50 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 33s. Last read position: chr1:205,676,456
INFO 2026-06-08 07:58:24 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:40s. Time for last 10,000,000: 33s. Last read position: chr2:87,792,013
INFO 2026-06-08 07:58:58 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:02:14s. Time for last 10,000,000: 33s. Last read position: chr2:219,168,368
INFO 2026-06-08 07:59:31 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:47s. Time for last 10,000,000: 33s. Last read position: chr3:77,211,031
INFO 2026-06-08 08:00:05 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:03:21s. Time for last 10,000,000: 33s. Last read position: chr4:41,257,623
INFO 2026-06-08 08:00:40 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:56s. Time for last 10,000,000: 35s. Last read position: chr5:77,404,550
INFO 2026-06-08 08:01:14 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:04:30s. Time for last 10,000,000: 33s. Last read position: chr6:33,069,690
INFO 2026-06-08 08:01:47 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:05:03s. Time for last 10,000,000: 33s. Last read position: chr7:5,955,973
INFO 2026-06-08 08:02:20 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:05:36s. Time for last 10,000,000: 32s. Last read position: chr7:128,849,417
INFO 2026-06-08 08:02:52 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:06:08s. Time for last 10,000,000: 32s. Last read position: chr8:60,830,223
INFO 2026-06-08 08:03:24 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:06:40s. Time for last 10,000,000: 31s. Last read position: chr9:84,740,357
INFO 2026-06-08 08:03:57 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:07:13s. Time for last 10,000,000: 33s. Last read position: chr10:56,361,308
INFO 2026-06-08 08:04:33 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:07:49s. Time for last 10,000,000: 35s. Last read position: chr11:48,123,834
INFO 2026-06-08 08:05:06 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:08:22s. Time for last 10,000,000: 33s. Last read position: chr12:11,771,776
INFO 2026-06-08 08:05:38 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:08:55s. Time for last 10,000,000: 32s. Last read position: chr12:121,962,028
INFO 2026-06-08 08:06:11 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:09:27s. Time for last 10,000,000: 32s. Last read position: chr14:96,347,076